Starting phenix.real_space_refine on Fri Mar 6 11:03:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6g_33640/03_2026/7y6g_33640_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6g_33640/03_2026/7y6g_33640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y6g_33640/03_2026/7y6g_33640_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6g_33640/03_2026/7y6g_33640_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y6g_33640/03_2026/7y6g_33640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6g_33640/03_2026/7y6g_33640.map" } resolution = 3.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 59 7.16 5 S 96 5.16 5 C 19886 2.51 5 N 5356 2.21 5 O 6030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 233 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31427 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1280 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "P" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.18, per 1000 atoms: 0.23 Number of scatterers: 31427 At special positions: 0 Unit cell: (131.274, 131.274, 131.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 59 26.01 S 96 16.00 O 6030 8.00 N 5356 7.00 C 19886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=31, symmetry=0 Number of additional bonds: simple=31, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.3 seconds 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7256 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 83.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 Processing helix chain 'A' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 110 removed outlier: 3.534A pdb=" N MET A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 145 removed outlier: 3.876A pdb=" N ALA A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'B' and resid 4 through 36 Processing helix chain 'B' and resid 37 through 65 removed outlier: 3.614A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 110 Processing helix chain 'B' and resid 113 through 145 removed outlier: 3.888A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'C' and resid 4 through 35 Processing helix chain 'C' and resid 37 through 65 removed outlier: 3.500A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 110 Processing helix chain 'C' and resid 113 through 145 removed outlier: 3.900A pdb=" N ALA C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'D' and resid 4 through 36 Processing helix chain 'D' and resid 37 through 65 removed outlier: 3.568A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 110 Processing helix chain 'D' and resid 113 through 145 removed outlier: 3.910A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'E' and resid 4 through 35 Processing helix chain 'E' and resid 37 through 65 removed outlier: 3.515A pdb=" N LEU E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 110 Processing helix chain 'E' and resid 113 through 145 removed outlier: 3.872A pdb=" N ALA E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'F' and resid 4 through 36 removed outlier: 3.511A pdb=" N GLY F 36 " --> pdb=" O GLN F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 65 removed outlier: 3.520A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 110 removed outlier: 3.572A pdb=" N MET F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 145 removed outlier: 3.869A pdb=" N ALA F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 151 Processing helix chain 'G' and resid 4 through 35 Processing helix chain 'G' and resid 37 through 65 removed outlier: 3.526A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 110 Processing helix chain 'G' and resid 113 through 145 removed outlier: 3.876A pdb=" N ALA G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'H' and resid 4 through 35 Processing helix chain 'H' and resid 37 through 65 removed outlier: 3.508A pdb=" N LEU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 110 Processing helix chain 'H' and resid 113 through 145 removed outlier: 3.906A pdb=" N ALA H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 151 Processing helix chain 'I' and resid 4 through 35 Processing helix chain 'I' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 110 Processing helix chain 'I' and resid 113 through 145 removed outlier: 3.885A pdb=" N ALA I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 151 Processing helix chain 'J' and resid 4 through 36 removed outlier: 3.539A pdb=" N GLY J 36 " --> pdb=" O GLN J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 65 removed outlier: 3.507A pdb=" N ALA J 41 " --> pdb=" O TRP J 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 65 " --> pdb=" O ARG J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 110 Processing helix chain 'J' and resid 113 through 145 removed outlier: 3.872A pdb=" N ALA J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 151 Processing helix chain 'K' and resid 4 through 35 Processing helix chain 'K' and resid 37 through 65 removed outlier: 3.616A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing helix chain 'K' and resid 113 through 145 removed outlier: 3.887A pdb=" N ALA K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'L' and resid 4 through 35 removed outlier: 3.510A pdb=" N LYS L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 65 removed outlier: 3.626A pdb=" N ALA L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 111 Processing helix chain 'L' and resid 113 through 145 removed outlier: 3.791A pdb=" N ALA L 117 " --> pdb=" O ASP L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'M' and resid 4 through 35 removed outlier: 3.503A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 65 Processing helix chain 'M' and resid 82 through 111 removed outlier: 3.506A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 145 removed outlier: 3.708A pdb=" N ALA M 117 " --> pdb=" O ASP M 113 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP M 126 " --> pdb=" O ALA M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 151 Processing helix chain 'N' and resid 4 through 36 Processing helix chain 'N' and resid 37 through 65 Processing helix chain 'N' and resid 82 through 110 Processing helix chain 'N' and resid 113 through 145 removed outlier: 3.874A pdb=" N ALA N 117 " --> pdb=" O ASP N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 151 Processing helix chain 'O' and resid 4 through 35 Processing helix chain 'O' and resid 37 through 65 Processing helix chain 'O' and resid 82 through 111 removed outlier: 3.539A pdb=" N LYS O 111 " --> pdb=" O VAL O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 145 removed outlier: 3.823A pdb=" N ALA O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 151 Processing helix chain 'P' and resid 4 through 36 Processing helix chain 'P' and resid 37 through 65 removed outlier: 3.611A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU P 65 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 110 Processing helix chain 'P' and resid 113 through 145 removed outlier: 3.899A pdb=" N ALA P 117 " --> pdb=" O ASP P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 151 Processing helix chain 'Q' and resid 4 through 35 Processing helix chain 'Q' and resid 37 through 65 removed outlier: 3.522A pdb=" N ALA Q 41 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 110 Processing helix chain 'Q' and resid 113 through 145 removed outlier: 3.902A pdb=" N ALA Q 117 " --> pdb=" O ASP Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 151 Processing helix chain 'R' and resid 4 through 36 Processing helix chain 'R' and resid 37 through 65 removed outlier: 3.572A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 110 removed outlier: 3.544A pdb=" N MET R 86 " --> pdb=" O SER R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 145 removed outlier: 3.873A pdb=" N ALA R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 151 Processing helix chain 'S' and resid 4 through 36 removed outlier: 3.508A pdb=" N GLY S 36 " --> pdb=" O GLN S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 65 removed outlier: 3.519A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 110 removed outlier: 3.569A pdb=" N MET S 86 " --> pdb=" O SER S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 145 removed outlier: 3.860A pdb=" N ALA S 117 " --> pdb=" O ASP S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 151 Processing helix chain 'T' and resid 4 through 35 Processing helix chain 'T' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU T 65 " --> pdb=" O ARG T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 110 removed outlier: 3.549A pdb=" N MET T 86 " --> pdb=" O SER T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 113 through 145 removed outlier: 3.905A pdb=" N ALA T 117 " --> pdb=" O ASP T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 151 Processing helix chain 'U' and resid 4 through 35 removed outlier: 3.542A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 65 removed outlier: 3.608A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU U 65 " --> pdb=" O ARG U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 110 Processing helix chain 'U' and resid 113 through 145 removed outlier: 3.903A pdb=" N ALA U 117 " --> pdb=" O ASP U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 151 Processing helix chain 'V' and resid 4 through 35 removed outlier: 3.541A pdb=" N ILE V 8 " --> pdb=" O ASP V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 65 Processing helix chain 'V' and resid 82 through 111 Processing helix chain 'V' and resid 113 through 145 removed outlier: 3.711A pdb=" N ALA V 117 " --> pdb=" O ASP V 113 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 145 through 151 Processing helix chain 'W' and resid 4 through 36 removed outlier: 3.601A pdb=" N GLY W 36 " --> pdb=" O GLN W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 65 removed outlier: 3.682A pdb=" N ALA W 41 " --> pdb=" O TRP W 37 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS W 42 " --> pdb=" O THR W 38 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 110 removed outlier: 3.553A pdb=" N MET W 86 " --> pdb=" O SER W 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 145 removed outlier: 3.867A pdb=" N ALA W 117 " --> pdb=" O ASP W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 151 Processing helix chain 'X' and resid 4 through 35 Processing helix chain 'X' and resid 37 through 65 removed outlier: 3.570A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 110 removed outlier: 3.574A pdb=" N MET X 86 " --> pdb=" O SER X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 145 removed outlier: 3.879A pdb=" N ALA X 117 " --> pdb=" O ASP X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 151 2579 hydrogen bonds defined for protein. 7737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.41: 13351 1.41 - 1.59: 18377 1.59 - 1.78: 6 1.78 - 1.96: 186 1.96 - 2.14: 48 Bond restraints: 31968 Sorted by residual: bond pdb=" C GLN W 14 " pdb=" N LEU W 15 " ideal model delta sigma weight residual 1.335 1.407 -0.072 1.31e-02 5.83e+03 3.01e+01 bond pdb=" C GLU W 13 " pdb=" N GLN W 14 " ideal model delta sigma weight residual 1.335 1.405 -0.070 1.31e-02 5.83e+03 2.89e+01 bond pdb=" CB MET Q 52 " pdb=" CG MET Q 52 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.79e+00 bond pdb=" CGA HEM C 203 " pdb=" O2A HEM C 203 " ideal model delta sigma weight residual 1.258 1.288 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" NB HEM S 203 " pdb="FE HEM S 203 " ideal model delta sigma weight residual 2.080 1.975 0.105 7.00e-02 2.04e+02 2.25e+00 ... (remaining 31963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.37: 43332 6.37 - 12.74: 15 12.74 - 19.12: 2 19.12 - 25.49: 2 25.49 - 31.86: 3 Bond angle restraints: 43354 Sorted by residual: angle pdb=" CB MET C 52 " pdb=" CG MET C 52 " pdb=" SD MET C 52 " ideal model delta sigma weight residual 112.70 83.42 29.28 3.00e+00 1.11e-01 9.52e+01 angle pdb=" CB MET X 52 " pdb=" CG MET X 52 " pdb=" SD MET X 52 " ideal model delta sigma weight residual 112.70 93.08 19.62 3.00e+00 1.11e-01 4.28e+01 angle pdb=" CB MET S 52 " pdb=" CG MET S 52 " pdb=" SD MET S 52 " ideal model delta sigma weight residual 112.70 93.25 19.45 3.00e+00 1.11e-01 4.20e+01 angle pdb=" O GLN W 14 " pdb=" C GLN W 14 " pdb=" N LEU W 15 " ideal model delta sigma weight residual 122.12 115.48 6.64 1.06e+00 8.90e-01 3.92e+01 angle pdb=" CB MET N 52 " pdb=" CG MET N 52 " pdb=" SD MET N 52 " ideal model delta sigma weight residual 112.70 95.16 17.54 3.00e+00 1.11e-01 3.42e+01 ... (remaining 43349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 16867 17.68 - 35.35: 1827 35.35 - 53.03: 296 53.03 - 70.70: 99 70.70 - 88.38: 29 Dihedral angle restraints: 19118 sinusoidal: 7994 harmonic: 11124 Sorted by residual: dihedral pdb=" C2B HEM S 203 " pdb=" C3B HEM S 203 " pdb=" CAB HEM S 203 " pdb=" CBB HEM S 203 " ideal model delta sinusoidal sigma weight residual 0.00 32.74 -32.74 2 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CA GLU Q 51 " pdb=" C GLU Q 51 " pdb=" N MET Q 52 " pdb=" CA MET Q 52 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" C2B HEM K 203 " pdb=" C3B HEM K 203 " pdb=" CAB HEM K 203 " pdb=" CBB HEM K 203 " ideal model delta sinusoidal sigma weight residual 0.00 -30.74 30.74 2 1.00e+01 1.00e-02 1.25e+01 ... (remaining 19115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3785 0.034 - 0.069: 722 0.069 - 0.103: 269 0.103 - 0.137: 28 0.137 - 0.172: 2 Chirality restraints: 4806 Sorted by residual: chirality pdb=" CA MET Q 52 " pdb=" N MET Q 52 " pdb=" C MET Q 52 " pdb=" CB MET Q 52 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA PHE F 49 " pdb=" N PHE F 49 " pdb=" C PHE F 49 " pdb=" CB PHE F 49 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA MET C 52 " pdb=" N MET C 52 " pdb=" C MET C 52 " pdb=" CB MET C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 4803 not shown) Planarity restraints: 5596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 45 " -0.450 9.50e-02 1.11e+02 2.02e-01 2.63e+01 pdb=" NE ARG R 45 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG R 45 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG R 45 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG R 45 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 49 " 0.016 2.00e-02 2.50e+03 2.93e-02 1.50e+01 pdb=" CG PHE F 49 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE F 49 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE F 49 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE F 49 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE F 49 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 49 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM C 203 " 0.011 2.00e-02 2.50e+03 2.11e-02 1.00e+01 pdb=" C2A HEM C 203 " 0.028 2.00e-02 2.50e+03 pdb=" C3A HEM C 203 " 0.010 2.00e-02 2.50e+03 pdb=" C4A HEM C 203 " 0.004 2.00e-02 2.50e+03 pdb=" CAA HEM C 203 " -0.032 2.00e-02 2.50e+03 pdb=" CHA HEM C 203 " 0.017 2.00e-02 2.50e+03 pdb=" CHB HEM C 203 " 0.003 2.00e-02 2.50e+03 pdb=" CMA HEM C 203 " 0.001 2.00e-02 2.50e+03 pdb=" NA HEM C 203 " -0.041 2.00e-02 2.50e+03 ... (remaining 5593 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 74 2.43 - 3.04: 19740 3.04 - 3.66: 43843 3.66 - 4.28: 68450 4.28 - 4.90: 115959 Nonbonded interactions: 248066 Sorted by model distance: nonbonded pdb=" OE2 GLU H 94 " pdb="FE FE H 202 " model vdw 1.807 2.260 nonbonded pdb=" OE1 GLU G 127 " pdb="FE FE G 202 " model vdw 1.953 2.260 nonbonded pdb=" OE1 GLU T 127 " pdb="FE FE2 T 203 " model vdw 1.972 3.000 nonbonded pdb=" OE1 GLU F 127 " pdb="FE FE2 F 202 " model vdw 1.974 3.000 nonbonded pdb=" OE1 GLU R 127 " pdb="FE FE R 202 " model vdw 2.031 2.260 ... (remaining 248061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 156) selection = (chain 'B' and resid 1 through 156) selection = (chain 'C' and resid 1 through 156) selection = (chain 'D' and resid 1 through 156) selection = (chain 'E' and resid 1 through 156) selection = (chain 'F' and resid 1 through 156) selection = (chain 'G' and resid 1 through 156) selection = (chain 'H' and resid 1 through 156) selection = (chain 'I' and resid 1 through 156) selection = (chain 'J' and resid 1 through 156) selection = (chain 'K' and resid 1 through 156) selection = (chain 'L' and resid 1 through 156) selection = (chain 'M' and resid 1 through 156) selection = (chain 'N' and resid 1 through 156) selection = (chain 'O' and resid 1 through 156) selection = (chain 'P' and resid 1 through 156) selection = (chain 'Q' and resid 1 through 156) selection = (chain 'R' and resid 1 through 156) selection = (chain 'S' and resid 1 through 156) selection = (chain 'T' and resid 1 through 156) selection = (chain 'U' and resid 1 through 156) selection = (chain 'V' and resid 1 through 156) selection = (chain 'W' and resid 1 through 156) selection = (chain 'X' and resid 1 through 156) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.500 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.666 31999 Z= 0.211 Angle : 0.618 31.860 43354 Z= 0.323 Chirality : 0.033 0.172 4806 Planarity : 0.004 0.202 5596 Dihedral : 15.053 88.377 11862 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.83 (0.08), residues: 2999 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG R 45 TYR 0.047 0.001 TYR T 71 PHE 0.062 0.003 PHE F 49 TRP 0.013 0.001 TRP H 37 HIS 0.003 0.001 HIS U 54 Details of bonding type rmsd covalent geometry : bond 0.00317 (31968) covalent geometry : angle 0.61805 (43354) hydrogen bonds : bond 0.13535 ( 2579) hydrogen bonds : angle 4.25600 ( 7737) Misc. bond : bond 0.25639 ( 31) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.2073 time to fit residues: 154.9197 Evaluate side-chains 208 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.0570 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 overall best weight: 7.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 112 HIS M 137 GLN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 112 HIS U 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.034149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.027430 restraints weight = 208770.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.028472 restraints weight = 130241.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.029281 restraints weight = 92476.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.029875 restraints weight = 69617.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.030331 restraints weight = 55237.266| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.310 31999 Z= 0.194 Angle : 0.661 15.120 43354 Z= 0.317 Chirality : 0.033 0.127 4806 Planarity : 0.003 0.075 5596 Dihedral : 6.846 80.010 4204 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.03 % Allowed : 7.94 % Favored : 91.04 % 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: 4.34 (0.13), residues: 3724 helix: 3.85 (0.08), residues: 3062 sheet: None (None), residues: 0 loop : -2.53 (0.20), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 45 TYR 0.030 0.001 TYR T 71 PHE 0.034 0.002 PHE F 49 TRP 0.010 0.001 TRP H 37 HIS 0.005 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00434 (31968) covalent geometry : angle 0.66143 (43354) hydrogen bonds : bond 0.07474 ( 2579) hydrogen bonds : angle 3.99604 ( 7737) Misc. bond : bond 0.08648 ( 31) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9402 (m) cc_final: 0.9158 (p) REVERT: E 53 ARG cc_start: 0.8972 (mtt90) cc_final: 0.8720 (mtm-85) REVERT: H 52 MET cc_start: 0.7307 (mtm) cc_final: 0.6887 (mtm) REVERT: J 53 ARG cc_start: 0.8974 (mtt90) cc_final: 0.8758 (mtm-85) REVERT: K 52 MET cc_start: 0.7720 (mtm) cc_final: 0.7377 (mtp) REVERT: L 52 MET cc_start: 0.7476 (mtm) cc_final: 0.7270 (mtm) REVERT: M 86 MET cc_start: 0.9470 (mtt) cc_final: 0.9233 (mtt) REVERT: O 59 THR cc_start: 0.9434 (m) cc_final: 0.9204 (p) REVERT: V 1 MET cc_start: 0.7741 (tpt) cc_final: 0.7510 (tpp) outliers start: 34 outliers final: 17 residues processed: 260 average time/residue: 0.1633 time to fit residues: 73.8627 Evaluate side-chains 199 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain X residue 98 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 50.0000 chunk 162 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 266 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 242 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 164 optimal weight: 0.5980 overall best weight: 6.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS H 130 HIS I 130 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 130 HIS Q 130 HIS T 130 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.034279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.027466 restraints weight = 212326.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.028512 restraints weight = 135500.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.029306 restraints weight = 96340.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.029968 restraints weight = 73670.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.030463 restraints weight = 58253.695| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.336 31999 Z= 0.174 Angle : 0.628 14.635 43354 Z= 0.293 Chirality : 0.033 0.120 4806 Planarity : 0.002 0.051 5596 Dihedral : 6.982 88.952 4204 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.78 % Allowed : 10.14 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.44 (0.13), residues: 3724 helix: 3.92 (0.08), residues: 3057 sheet: None (None), residues: 0 loop : -2.44 (0.19), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 53 TYR 0.039 0.001 TYR T 71 PHE 0.021 0.002 PHE F 49 TRP 0.007 0.001 TRP R 37 HIS 0.003 0.001 HIS L 54 Details of bonding type rmsd covalent geometry : bond 0.00389 (31968) covalent geometry : angle 0.62842 (43354) hydrogen bonds : bond 0.06740 ( 2579) hydrogen bonds : angle 3.85581 ( 7737) Misc. bond : bond 0.09703 ( 31) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9381 (m) cc_final: 0.9118 (p) REVERT: A 86 MET cc_start: 0.9394 (mtt) cc_final: 0.8855 (mpp) REVERT: C 59 THR cc_start: 0.9300 (m) cc_final: 0.9047 (p) REVERT: D 86 MET cc_start: 0.9417 (mtt) cc_final: 0.9196 (mtt) REVERT: E 53 ARG cc_start: 0.8991 (mtt90) cc_final: 0.8589 (mtm-85) REVERT: F 59 THR cc_start: 0.9398 (m) cc_final: 0.9139 (p) REVERT: F 86 MET cc_start: 0.9388 (mtt) cc_final: 0.8857 (mpp) REVERT: G 59 THR cc_start: 0.9402 (m) cc_final: 0.9136 (p) REVERT: H 52 MET cc_start: 0.7482 (mtm) cc_final: 0.6980 (mtm) REVERT: I 59 THR cc_start: 0.9387 (m) cc_final: 0.9128 (p) REVERT: J 53 ARG cc_start: 0.8981 (mtt90) cc_final: 0.8664 (mtm-85) REVERT: K 52 MET cc_start: 0.7839 (mtm) cc_final: 0.7577 (mtp) REVERT: M 53 ARG cc_start: 0.8998 (mtm-85) cc_final: 0.8537 (mtm-85) REVERT: N 86 MET cc_start: 0.9415 (mtt) cc_final: 0.9204 (mtt) REVERT: O 59 THR cc_start: 0.9390 (m) cc_final: 0.9134 (p) REVERT: R 86 MET cc_start: 0.9388 (mtt) cc_final: 0.8854 (mpp) REVERT: S 86 MET cc_start: 0.9392 (mtt) cc_final: 0.8860 (mpp) REVERT: T 86 MET cc_start: 0.9392 (mtt) cc_final: 0.8841 (mpp) REVERT: V 86 MET cc_start: 0.9414 (mtt) cc_final: 0.9212 (mtt) REVERT: V 108 MET cc_start: 0.8828 (mtp) cc_final: 0.8459 (ptm) REVERT: W 86 MET cc_start: 0.9388 (mtt) cc_final: 0.8839 (mpp) REVERT: X 86 MET cc_start: 0.9397 (mtt) cc_final: 0.8871 (mpp) outliers start: 26 outliers final: 17 residues processed: 206 average time/residue: 0.1623 time to fit residues: 58.3916 Evaluate side-chains 192 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain X residue 98 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 272 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 325 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 336 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS H 130 HIS I 130 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 130 HIS T 130 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.034416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.027694 restraints weight = 216017.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.028729 restraints weight = 138259.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.029552 restraints weight = 98853.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030182 restraints weight = 74934.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.030665 restraints weight = 59722.793| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.284 31999 Z= 0.157 Angle : 0.595 13.075 43354 Z= 0.280 Chirality : 0.032 0.122 4806 Planarity : 0.002 0.046 5596 Dihedral : 6.998 88.882 4204 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.81 % Allowed : 10.17 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.47 (0.13), residues: 3724 helix: 3.88 (0.08), residues: 3067 sheet: None (None), residues: 0 loop : -2.20 (0.20), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 53 TYR 0.025 0.001 TYR T 71 PHE 0.019 0.001 PHE S 26 TRP 0.005 0.001 TRP D 37 HIS 0.003 0.001 HIS L 54 Details of bonding type rmsd covalent geometry : bond 0.00352 (31968) covalent geometry : angle 0.59478 (43354) hydrogen bonds : bond 0.06295 ( 2579) hydrogen bonds : angle 3.76267 ( 7737) Misc. bond : bond 0.08878 ( 31) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9341 (m) cc_final: 0.9055 (p) REVERT: B 59 THR cc_start: 0.9420 (m) cc_final: 0.9143 (p) REVERT: B 108 MET cc_start: 0.8688 (ptm) cc_final: 0.8432 (ppp) REVERT: C 59 THR cc_start: 0.9289 (m) cc_final: 0.9025 (p) REVERT: C 108 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8798 (ppp) REVERT: D 86 MET cc_start: 0.9394 (mtt) cc_final: 0.9181 (mtt) REVERT: E 53 ARG cc_start: 0.8969 (mtt90) cc_final: 0.8551 (mtm-85) REVERT: F 59 THR cc_start: 0.9402 (m) cc_final: 0.9118 (p) REVERT: F 108 MET cc_start: 0.8888 (ptm) cc_final: 0.8535 (ppp) REVERT: G 59 THR cc_start: 0.9367 (m) cc_final: 0.9081 (p) REVERT: H 52 MET cc_start: 0.7474 (mtm) cc_final: 0.7086 (mtm) REVERT: H 108 MET cc_start: 0.8767 (ptm) cc_final: 0.8493 (ppp) REVERT: I 59 THR cc_start: 0.9371 (m) cc_final: 0.9088 (p) REVERT: J 53 ARG cc_start: 0.8930 (mtt90) cc_final: 0.8604 (mtm-85) REVERT: K 52 MET cc_start: 0.7983 (mtm) cc_final: 0.7629 (mtp) REVERT: K 59 THR cc_start: 0.9415 (m) cc_final: 0.9147 (p) REVERT: M 86 MET cc_start: 0.9435 (mtt) cc_final: 0.8856 (mpp) REVERT: N 86 MET cc_start: 0.9398 (mtt) cc_final: 0.9197 (mtt) REVERT: O 59 THR cc_start: 0.9368 (m) cc_final: 0.9097 (p) REVERT: O 108 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.9058 (ppp) REVERT: R 59 THR cc_start: 0.9407 (m) cc_final: 0.9137 (p) REVERT: R 108 MET cc_start: 0.8661 (ptm) cc_final: 0.8380 (ppp) REVERT: W 108 MET cc_start: 0.8809 (ptm) cc_final: 0.8449 (ppp) REVERT: X 108 MET cc_start: 0.8779 (ptm) cc_final: 0.8508 (ppp) outliers start: 27 outliers final: 12 residues processed: 200 average time/residue: 0.1652 time to fit residues: 57.1665 Evaluate side-chains 189 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain X residue 98 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 84 optimal weight: 6.9990 chunk 343 optimal weight: 10.0000 chunk 251 optimal weight: 8.9990 chunk 243 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 357 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 130 HIS M 156 GLN N 130 HIS P 130 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.033468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.026785 restraints weight = 219728.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.027817 restraints weight = 140339.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.028604 restraints weight = 100049.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.029238 restraints weight = 76376.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.029720 restraints weight = 60771.390| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.688 31999 Z= 0.179 Angle : 0.607 18.197 43354 Z= 0.283 Chirality : 0.033 0.119 4806 Planarity : 0.002 0.038 5596 Dihedral : 7.035 89.690 4204 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.27 % Allowed : 10.20 % Favored : 88.53 % 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: 4.35 (0.13), residues: 3724 helix: 3.75 (0.08), residues: 3067 sheet: None (None), residues: 0 loop : -1.99 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 45 TYR 0.030 0.001 TYR T 71 PHE 0.020 0.001 PHE S 26 TRP 0.004 0.001 TRP R 37 HIS 0.003 0.001 HIS P 34 Details of bonding type rmsd covalent geometry : bond 0.00391 (31968) covalent geometry : angle 0.60737 (43354) hydrogen bonds : bond 0.06567 ( 2579) hydrogen bonds : angle 3.81289 ( 7737) Misc. bond : bond 0.14945 ( 31) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8705 (ptm) cc_final: 0.8405 (ppp) REVERT: B 108 MET cc_start: 0.8695 (ptm) cc_final: 0.8354 (ppp) REVERT: C 59 THR cc_start: 0.9292 (m) cc_final: 0.9025 (p) REVERT: C 108 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8825 (ppp) REVERT: D 86 MET cc_start: 0.9408 (mtt) cc_final: 0.9191 (mtt) REVERT: D 108 MET cc_start: 0.8749 (ptm) cc_final: 0.8420 (ppp) REVERT: E 53 ARG cc_start: 0.8933 (mtt90) cc_final: 0.8502 (mtm-85) REVERT: E 59 THR cc_start: 0.9443 (m) cc_final: 0.9188 (p) REVERT: E 108 MET cc_start: 0.8906 (ptm) cc_final: 0.8551 (ppp) REVERT: F 59 THR cc_start: 0.9422 (m) cc_final: 0.9138 (p) REVERT: F 108 MET cc_start: 0.8842 (ptm) cc_final: 0.8565 (ppp) REVERT: G 59 THR cc_start: 0.9376 (m) cc_final: 0.9090 (p) REVERT: G 108 MET cc_start: 0.8737 (ptm) cc_final: 0.8405 (ppp) REVERT: H 52 MET cc_start: 0.7659 (mtm) cc_final: 0.7275 (ttm) REVERT: H 108 MET cc_start: 0.8792 (ptm) cc_final: 0.8559 (ppp) REVERT: I 59 THR cc_start: 0.9404 (m) cc_final: 0.9119 (p) REVERT: I 108 MET cc_start: 0.8849 (ptm) cc_final: 0.8335 (ppp) REVERT: J 53 ARG cc_start: 0.8906 (mtt90) cc_final: 0.8583 (mtm-85) REVERT: J 108 MET cc_start: 0.8877 (ptm) cc_final: 0.8375 (ppp) REVERT: K 52 MET cc_start: 0.8007 (mtm) cc_final: 0.7804 (mtm) REVERT: K 59 THR cc_start: 0.9428 (m) cc_final: 0.9164 (p) REVERT: K 108 MET cc_start: 0.8796 (ptm) cc_final: 0.8468 (ppp) REVERT: L 108 MET cc_start: 0.8947 (ptm) cc_final: 0.8346 (ppp) REVERT: M 108 MET cc_start: 0.8935 (ptm) cc_final: 0.8501 (ppp) REVERT: N 86 MET cc_start: 0.9417 (mtt) cc_final: 0.9210 (mtt) REVERT: O 59 THR cc_start: 0.9388 (m) cc_final: 0.9116 (p) REVERT: O 108 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.8969 (ppp) REVERT: P 108 MET cc_start: 0.8668 (ptm) cc_final: 0.8372 (ppp) REVERT: Q 108 MET cc_start: 0.8769 (ptm) cc_final: 0.8431 (ppp) REVERT: R 59 THR cc_start: 0.9423 (m) cc_final: 0.9160 (p) REVERT: R 108 MET cc_start: 0.8665 (ptm) cc_final: 0.8444 (ppp) REVERT: S 59 THR cc_start: 0.9442 (m) cc_final: 0.9187 (p) REVERT: T 59 THR cc_start: 0.9459 (m) cc_final: 0.9181 (p) REVERT: T 108 MET cc_start: 0.8826 (ptm) cc_final: 0.8328 (ppp) REVERT: U 108 MET cc_start: 0.8801 (ptm) cc_final: 0.8441 (ppp) REVERT: W 108 MET cc_start: 0.8779 (ptm) cc_final: 0.8485 (ppp) REVERT: X 108 MET cc_start: 0.8826 (ptm) cc_final: 0.8585 (ppp) outliers start: 42 outliers final: 23 residues processed: 202 average time/residue: 0.1839 time to fit residues: 62.0651 Evaluate side-chains 195 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain X residue 98 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 134 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 290 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 142 optimal weight: 30.0000 chunk 308 optimal weight: 6.9990 chunk 344 optimal weight: 7.9990 chunk 317 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS B 130 HIS C 130 HIS F 130 HIS G 130 HIS H 130 HIS O 130 HIS T 130 HIS W 130 HIS X 130 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.033285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.026640 restraints weight = 216846.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.027644 restraints weight = 139139.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.028398 restraints weight = 99671.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.029005 restraints weight = 76560.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.029470 restraints weight = 61531.307| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.718 31999 Z= 0.183 Angle : 0.631 14.985 43354 Z= 0.295 Chirality : 0.033 0.147 4806 Planarity : 0.002 0.032 5596 Dihedral : 6.933 85.732 4204 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.15 % Allowed : 11.23 % Favored : 87.63 % 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: 4.34 (0.13), residues: 3724 helix: 3.72 (0.08), residues: 3067 sheet: None (None), residues: 0 loop : -1.85 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 73 TYR 0.027 0.001 TYR T 71 PHE 0.020 0.001 PHE S 26 TRP 0.005 0.001 TRP O 37 HIS 0.003 0.001 HIS Q 34 Details of bonding type rmsd covalent geometry : bond 0.00397 (31968) covalent geometry : angle 0.63138 (43354) hydrogen bonds : bond 0.06608 ( 2579) hydrogen bonds : angle 3.83549 ( 7737) Misc. bond : bond 0.16244 ( 31) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9224 (mtm) cc_final: 0.8799 (mpp) REVERT: A 108 MET cc_start: 0.8693 (ptm) cc_final: 0.8472 (ppp) REVERT: B 108 MET cc_start: 0.8667 (ptm) cc_final: 0.8334 (ppp) REVERT: C 108 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8834 (ppp) REVERT: D 86 MET cc_start: 0.9410 (mtt) cc_final: 0.9200 (mtt) REVERT: D 108 MET cc_start: 0.8706 (ptm) cc_final: 0.8371 (ppp) REVERT: E 53 ARG cc_start: 0.8950 (mtt90) cc_final: 0.8545 (mtm-85) REVERT: E 59 THR cc_start: 0.9432 (m) cc_final: 0.9171 (p) REVERT: E 108 MET cc_start: 0.8882 (ptm) cc_final: 0.8526 (ppp) REVERT: F 59 THR cc_start: 0.9432 (m) cc_final: 0.9150 (p) REVERT: F 86 MET cc_start: 0.9229 (mtm) cc_final: 0.8787 (mpp) REVERT: F 108 MET cc_start: 0.8856 (ptm) cc_final: 0.8422 (ppp) REVERT: G 108 MET cc_start: 0.8705 (ptm) cc_final: 0.8393 (ppp) REVERT: H 52 MET cc_start: 0.7803 (mtm) cc_final: 0.7386 (mtm) REVERT: H 108 MET cc_start: 0.8774 (ptm) cc_final: 0.8407 (ppp) REVERT: I 59 THR cc_start: 0.9399 (m) cc_final: 0.9114 (p) REVERT: I 108 MET cc_start: 0.8821 (ptm) cc_final: 0.8347 (ppp) REVERT: J 53 ARG cc_start: 0.8885 (mtt90) cc_final: 0.8571 (mtm-85) REVERT: J 86 MET cc_start: 0.9403 (mtt) cc_final: 0.8801 (mpp) REVERT: J 108 MET cc_start: 0.8846 (ptm) cc_final: 0.8363 (ppp) REVERT: K 52 MET cc_start: 0.8074 (mtm) cc_final: 0.7854 (mtm) REVERT: K 59 THR cc_start: 0.9437 (m) cc_final: 0.9166 (p) REVERT: K 108 MET cc_start: 0.8779 (ptm) cc_final: 0.8460 (ppp) REVERT: L 108 MET cc_start: 0.8996 (ptm) cc_final: 0.8390 (ppp) REVERT: M 108 MET cc_start: 0.8920 (ptm) cc_final: 0.8574 (ppp) REVERT: O 59 THR cc_start: 0.9379 (m) cc_final: 0.9105 (p) REVERT: O 108 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.9181 (ptm) REVERT: P 108 MET cc_start: 0.8648 (ptm) cc_final: 0.8398 (ppp) REVERT: Q 108 MET cc_start: 0.8747 (ptm) cc_final: 0.8411 (ppp) REVERT: R 59 THR cc_start: 0.9420 (m) cc_final: 0.9148 (p) REVERT: R 86 MET cc_start: 0.9215 (mtm) cc_final: 0.8775 (mpp) REVERT: R 108 MET cc_start: 0.8655 (ptm) cc_final: 0.8294 (ppp) REVERT: S 59 THR cc_start: 0.9434 (m) cc_final: 0.9165 (p) REVERT: S 86 MET cc_start: 0.9219 (mtm) cc_final: 0.8799 (mpp) REVERT: T 59 THR cc_start: 0.9427 (m) cc_final: 0.9149 (p) REVERT: T 86 MET cc_start: 0.9229 (mtm) cc_final: 0.8789 (mpp) REVERT: T 108 MET cc_start: 0.8797 (ptm) cc_final: 0.8334 (ppp) REVERT: U 108 MET cc_start: 0.8790 (ptm) cc_final: 0.8448 (ppp) REVERT: W 59 THR cc_start: 0.9476 (m) cc_final: 0.9228 (p) REVERT: W 86 MET cc_start: 0.9258 (mtm) cc_final: 0.8805 (mpp) REVERT: W 108 MET cc_start: 0.8781 (ptm) cc_final: 0.8475 (ppp) REVERT: X 86 MET cc_start: 0.9242 (mtm) cc_final: 0.8806 (mpp) REVERT: X 108 MET cc_start: 0.8827 (ptm) cc_final: 0.8601 (ppp) outliers start: 38 outliers final: 27 residues processed: 191 average time/residue: 0.1720 time to fit residues: 56.0745 Evaluate side-chains 202 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain X residue 98 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 155 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 323 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 chunk 105 optimal weight: 0.0050 chunk 86 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 202 optimal weight: 30.0000 chunk 38 optimal weight: 0.1980 chunk 132 optimal weight: 9.9990 overall best weight: 4.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS C 130 HIS F 130 HIS G 130 HIS O 130 HIS P 130 HIS W 130 HIS X 130 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.034650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.028001 restraints weight = 217137.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.029035 restraints weight = 138803.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.029801 restraints weight = 99121.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.030430 restraints weight = 75698.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.030863 restraints weight = 60333.116| |-----------------------------------------------------------------------------| r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.704 31999 Z= 0.131 Angle : 0.575 13.718 43354 Z= 0.263 Chirality : 0.032 0.116 4806 Planarity : 0.002 0.030 5596 Dihedral : 6.890 83.859 4204 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.39 % Allowed : 11.50 % Favored : 88.11 % 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: 4.63 (0.13), residues: 3724 helix: 3.91 (0.08), residues: 3067 sheet: None (None), residues: 0 loop : -1.65 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 73 TYR 0.024 0.001 TYR T 71 PHE 0.016 0.001 PHE S 26 TRP 0.007 0.001 TRP O 37 HIS 0.002 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00287 (31968) covalent geometry : angle 0.57475 (43354) hydrogen bonds : bond 0.05631 ( 2579) hydrogen bonds : angle 3.52777 ( 7737) Misc. bond : bond 0.15937 ( 31) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9136 (mtm) cc_final: 0.8746 (mpp) REVERT: B 108 MET cc_start: 0.8539 (ptm) cc_final: 0.8232 (ppp) REVERT: C 108 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8779 (ppp) REVERT: D 108 MET cc_start: 0.8601 (ptm) cc_final: 0.8382 (ppp) REVERT: E 53 ARG cc_start: 0.8969 (mtt90) cc_final: 0.8563 (mtm-85) REVERT: E 108 MET cc_start: 0.8768 (ptm) cc_final: 0.8501 (ppp) REVERT: F 59 THR cc_start: 0.9347 (m) cc_final: 0.9044 (p) REVERT: F 86 MET cc_start: 0.9147 (mtm) cc_final: 0.8778 (mpp) REVERT: F 108 MET cc_start: 0.8719 (ptm) cc_final: 0.8517 (ppp) REVERT: G 108 MET cc_start: 0.8569 (ptm) cc_final: 0.8363 (ppp) REVERT: H 52 MET cc_start: 0.7809 (mtm) cc_final: 0.7440 (mtm) REVERT: H 108 MET cc_start: 0.8650 (ptm) cc_final: 0.8323 (ppp) REVERT: I 108 MET cc_start: 0.8734 (ptm) cc_final: 0.8281 (ppp) REVERT: J 53 ARG cc_start: 0.8900 (mtt90) cc_final: 0.8575 (mtm-85) REVERT: J 108 MET cc_start: 0.8753 (ptm) cc_final: 0.8301 (ppp) REVERT: K 108 MET cc_start: 0.8642 (ptm) cc_final: 0.8427 (ppp) REVERT: L 108 MET cc_start: 0.8950 (ptm) cc_final: 0.8364 (ppp) REVERT: M 108 MET cc_start: 0.8831 (ptm) cc_final: 0.8532 (ppp) REVERT: N 86 MET cc_start: 0.9410 (mtt) cc_final: 0.8814 (mpp) REVERT: O 59 THR cc_start: 0.9294 (m) cc_final: 0.9002 (p) REVERT: O 108 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.8965 (ppp) REVERT: Q 108 MET cc_start: 0.8644 (ptm) cc_final: 0.8421 (ppp) REVERT: R 59 THR cc_start: 0.9357 (m) cc_final: 0.9068 (p) REVERT: R 86 MET cc_start: 0.9121 (mtm) cc_final: 0.8765 (mpp) REVERT: S 59 THR cc_start: 0.9396 (m) cc_final: 0.9111 (p) REVERT: S 86 MET cc_start: 0.9133 (mtm) cc_final: 0.8778 (mpp) REVERT: T 59 THR cc_start: 0.9370 (m) cc_final: 0.9064 (p) REVERT: T 86 MET cc_start: 0.9136 (mtm) cc_final: 0.8766 (mpp) REVERT: T 108 MET cc_start: 0.8701 (ptm) cc_final: 0.8270 (ppp) REVERT: U 108 MET cc_start: 0.8656 (ptm) cc_final: 0.8415 (ppp) REVERT: V 86 MET cc_start: 0.9338 (mtt) cc_final: 0.8725 (mpp) REVERT: V 108 MET cc_start: 0.9201 (ptp) cc_final: 0.8986 (ptm) REVERT: W 59 THR cc_start: 0.9410 (m) cc_final: 0.9150 (p) REVERT: W 86 MET cc_start: 0.9165 (mtm) cc_final: 0.8750 (mpp) REVERT: W 108 MET cc_start: 0.8635 (ptm) cc_final: 0.8419 (ppp) REVERT: X 86 MET cc_start: 0.9140 (mtm) cc_final: 0.8746 (mpp) outliers start: 13 outliers final: 8 residues processed: 187 average time/residue: 0.1586 time to fit residues: 51.7045 Evaluate side-chains 180 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain V residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 307 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 chunk 149 optimal weight: 0.3980 chunk 245 optimal weight: 9.9990 chunk 330 optimal weight: 30.0000 chunk 94 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 302 optimal weight: 8.9990 chunk 318 optimal weight: 6.9990 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 130 HIS V 2 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.034622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.027955 restraints weight = 217417.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.028974 restraints weight = 139082.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.029740 restraints weight = 99477.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.030369 restraints weight = 76056.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.030841 restraints weight = 60688.382| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.709 31999 Z= 0.136 Angle : 0.586 13.840 43354 Z= 0.266 Chirality : 0.032 0.122 4806 Planarity : 0.002 0.026 5596 Dihedral : 6.854 83.137 4204 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.33 % Allowed : 11.89 % Favored : 87.78 % 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: 4.60 (0.13), residues: 3724 helix: 3.87 (0.08), residues: 3067 sheet: None (None), residues: 0 loop : -1.54 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 45 TYR 0.024 0.001 TYR T 71 PHE 0.017 0.001 PHE S 26 TRP 0.005 0.001 TRP O 37 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00300 (31968) covalent geometry : angle 0.58569 (43354) hydrogen bonds : bond 0.05586 ( 2579) hydrogen bonds : angle 3.53246 ( 7737) Misc. bond : bond 0.14721 ( 31) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9150 (mtm) cc_final: 0.8816 (mpp) REVERT: B 108 MET cc_start: 0.8533 (ptm) cc_final: 0.8207 (ppp) REVERT: C 108 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8756 (ppp) REVERT: D 86 MET cc_start: 0.9394 (mtt) cc_final: 0.8804 (mpp) REVERT: D 108 MET cc_start: 0.8556 (ptm) cc_final: 0.8330 (ppp) REVERT: E 53 ARG cc_start: 0.8930 (mtt90) cc_final: 0.8539 (mtm-85) REVERT: E 108 MET cc_start: 0.8750 (ptm) cc_final: 0.8484 (ppp) REVERT: F 86 MET cc_start: 0.9159 (mtm) cc_final: 0.8784 (mpp) REVERT: F 108 MET cc_start: 0.8711 (ptm) cc_final: 0.8344 (ppp) REVERT: H 52 MET cc_start: 0.7878 (mtm) cc_final: 0.7448 (mtm) REVERT: H 108 MET cc_start: 0.8647 (ptm) cc_final: 0.8305 (ppp) REVERT: I 108 MET cc_start: 0.8727 (ptm) cc_final: 0.8282 (ppp) REVERT: J 53 ARG cc_start: 0.8892 (mtt90) cc_final: 0.8557 (mtm-85) REVERT: J 86 MET cc_start: 0.9376 (mtt) cc_final: 0.8768 (mpp) REVERT: J 108 MET cc_start: 0.8750 (ptm) cc_final: 0.8312 (ppp) REVERT: L 108 MET cc_start: 0.8975 (ptm) cc_final: 0.8410 (ppp) REVERT: M 108 MET cc_start: 0.8806 (ptm) cc_final: 0.8524 (ppp) REVERT: N 86 MET cc_start: 0.9407 (mtt) cc_final: 0.8803 (mpp) REVERT: O 108 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9126 (ptm) REVERT: Q 108 MET cc_start: 0.8610 (ptm) cc_final: 0.8368 (ppp) REVERT: R 86 MET cc_start: 0.9139 (mtm) cc_final: 0.8806 (mpp) REVERT: S 59 THR cc_start: 0.9399 (m) cc_final: 0.9109 (p) REVERT: S 86 MET cc_start: 0.9141 (mtm) cc_final: 0.8818 (mpp) REVERT: T 86 MET cc_start: 0.9153 (mtm) cc_final: 0.8806 (mpp) REVERT: T 108 MET cc_start: 0.8694 (ptm) cc_final: 0.8275 (ppp) REVERT: U 108 MET cc_start: 0.8636 (ptm) cc_final: 0.8393 (ppp) REVERT: V 86 MET cc_start: 0.9322 (mtt) cc_final: 0.8713 (mpp) REVERT: V 108 MET cc_start: 0.9212 (ptp) cc_final: 0.8989 (ptm) REVERT: W 59 THR cc_start: 0.9406 (m) cc_final: 0.9144 (p) REVERT: W 86 MET cc_start: 0.9187 (mtm) cc_final: 0.8794 (mpp) REVERT: W 108 MET cc_start: 0.8616 (ptm) cc_final: 0.8410 (ppp) REVERT: X 86 MET cc_start: 0.9150 (mtm) cc_final: 0.8796 (mpp) outliers start: 11 outliers final: 9 residues processed: 183 average time/residue: 0.1596 time to fit residues: 51.2880 Evaluate side-chains 179 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain V residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 41 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 346 optimal weight: 10.0000 chunk 232 optimal weight: 20.0000 chunk 172 optimal weight: 30.0000 chunk 354 optimal weight: 10.0000 chunk 120 optimal weight: 30.0000 chunk 334 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 overall best weight: 11.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS C 130 HIS D 130 HIS E 130 HIS F 130 HIS G 130 HIS K 130 HIS L 130 HIS M 81 GLN P 130 HIS R 130 HIS S 130 HIS U 130 HIS W 130 HIS X 130 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.031752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.025004 restraints weight = 208552.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.025937 restraints weight = 136762.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.026645 restraints weight = 99604.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.027215 restraints weight = 77351.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.027681 restraints weight = 62792.942| |-----------------------------------------------------------------------------| r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.803 31999 Z= 0.264 Angle : 0.718 15.269 43354 Z= 0.342 Chirality : 0.036 0.129 4806 Planarity : 0.003 0.041 5596 Dihedral : 6.947 82.210 4204 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.69 % Allowed : 11.86 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.00 (0.13), residues: 3724 helix: 3.44 (0.08), residues: 3078 sheet: None (None), residues: 0 loop : -1.81 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 100 TYR 0.031 0.001 TYR T 71 PHE 0.022 0.001 PHE S 26 TRP 0.004 0.001 TRP C 37 HIS 0.004 0.001 HIS N 34 Details of bonding type rmsd covalent geometry : bond 0.00569 (31968) covalent geometry : angle 0.71784 (43354) hydrogen bonds : bond 0.07854 ( 2579) hydrogen bonds : angle 4.19415 ( 7737) Misc. bond : bond 0.18239 ( 31) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9357 (mtm) cc_final: 0.8913 (mpp) REVERT: B 108 MET cc_start: 0.8806 (ptm) cc_final: 0.8400 (ppp) REVERT: D 86 MET cc_start: 0.9457 (mtt) cc_final: 0.8824 (mpp) REVERT: D 108 MET cc_start: 0.8815 (ptm) cc_final: 0.8325 (ppp) REVERT: E 53 ARG cc_start: 0.8924 (mtt90) cc_final: 0.8515 (mtm-85) REVERT: E 108 MET cc_start: 0.8957 (ptm) cc_final: 0.8432 (ppp) REVERT: F 86 MET cc_start: 0.9365 (mtm) cc_final: 0.8915 (mpp) REVERT: F 108 MET cc_start: 0.8939 (ptm) cc_final: 0.8495 (ppp) REVERT: H 52 MET cc_start: 0.7851 (mtm) cc_final: 0.7409 (mtm) REVERT: H 108 MET cc_start: 0.8916 (ptm) cc_final: 0.8489 (ppp) REVERT: I 108 MET cc_start: 0.8895 (ptm) cc_final: 0.8457 (ppp) REVERT: J 53 ARG cc_start: 0.8857 (mtt90) cc_final: 0.8555 (mtm-85) REVERT: J 86 MET cc_start: 0.9432 (mtt) cc_final: 0.8794 (mpp) REVERT: J 108 MET cc_start: 0.8913 (ptm) cc_final: 0.8468 (ppp) REVERT: K 59 THR cc_start: 0.9508 (m) cc_final: 0.9259 (p) REVERT: K 108 MET cc_start: 0.8541 (ppp) cc_final: 0.8221 (ppp) REVERT: L 108 MET cc_start: 0.9093 (ptm) cc_final: 0.8534 (ppp) REVERT: M 108 MET cc_start: 0.8946 (ptm) cc_final: 0.8445 (ppp) REVERT: N 86 MET cc_start: 0.9484 (mtt) cc_final: 0.8831 (mpp) REVERT: O 59 THR cc_start: 0.9437 (m) cc_final: 0.9177 (p) REVERT: O 108 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.8989 (ppp) REVERT: Q 108 MET cc_start: 0.8826 (ptm) cc_final: 0.8338 (ppp) REVERT: R 59 THR cc_start: 0.9485 (m) cc_final: 0.9237 (p) REVERT: R 86 MET cc_start: 0.9347 (mtm) cc_final: 0.8910 (mpp) REVERT: S 59 THR cc_start: 0.9508 (m) cc_final: 0.9257 (p) REVERT: S 86 MET cc_start: 0.9354 (mtm) cc_final: 0.8928 (mpp) REVERT: T 86 MET cc_start: 0.9352 (mtm) cc_final: 0.8898 (mpp) REVERT: T 108 MET cc_start: 0.8852 (ptm) cc_final: 0.8423 (ppp) REVERT: U 108 MET cc_start: 0.8857 (ptm) cc_final: 0.8357 (ppp) REVERT: V 86 MET cc_start: 0.9413 (mtt) cc_final: 0.8782 (mpp) REVERT: V 108 MET cc_start: 0.9314 (ptp) cc_final: 0.9088 (ptm) REVERT: W 59 THR cc_start: 0.9520 (m) cc_final: 0.9286 (p) REVERT: W 86 MET cc_start: 0.9384 (mtm) cc_final: 0.8926 (mpp) REVERT: W 108 MET cc_start: 0.8831 (ptm) cc_final: 0.8372 (ppp) REVERT: X 86 MET cc_start: 0.9368 (mtm) cc_final: 0.8929 (mpp) outliers start: 23 outliers final: 20 residues processed: 176 average time/residue: 0.1632 time to fit residues: 50.4869 Evaluate side-chains 186 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain X residue 154 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 56 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 326 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 243 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 202 optimal weight: 0.3980 chunk 45 optimal weight: 20.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS C 130 HIS D 130 HIS E 130 HIS F 130 HIS G 130 HIS K 130 HIS L 130 HIS P 130 HIS R 130 HIS S 130 HIS U 130 HIS W 130 HIS X 130 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.034589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.027951 restraints weight = 209491.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.028930 restraints weight = 132836.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.029657 restraints weight = 95964.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.030262 restraints weight = 73994.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.030724 restraints weight = 59436.517| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.739 31999 Z= 0.132 Angle : 0.608 14.684 43354 Z= 0.274 Chirality : 0.032 0.115 4806 Planarity : 0.002 0.023 5596 Dihedral : 6.918 85.818 4204 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.33 % Allowed : 12.28 % Favored : 87.39 % 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: 4.64 (0.13), residues: 3724 helix: 3.91 (0.08), residues: 3065 sheet: None (None), residues: 0 loop : -1.66 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 53 TYR 0.021 0.001 TYR T 71 PHE 0.017 0.001 PHE U 26 TRP 0.006 0.001 TRP O 37 HIS 0.002 0.001 HIS M 112 Details of bonding type rmsd covalent geometry : bond 0.00288 (31968) covalent geometry : angle 0.60797 (43354) hydrogen bonds : bond 0.05432 ( 2579) hydrogen bonds : angle 3.51273 ( 7737) Misc. bond : bond 0.16553 ( 31) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9140 (mtm) cc_final: 0.8856 (mpp) REVERT: B 108 MET cc_start: 0.8499 (ptm) cc_final: 0.8180 (ppp) REVERT: C 108 MET cc_start: 0.8829 (ptm) cc_final: 0.8355 (ppp) REVERT: D 86 MET cc_start: 0.9375 (mtt) cc_final: 0.8775 (mpp) REVERT: E 53 ARG cc_start: 0.8971 (mtt90) cc_final: 0.8579 (mtm-85) REVERT: E 108 MET cc_start: 0.8713 (ptm) cc_final: 0.8484 (ppp) REVERT: F 86 MET cc_start: 0.9156 (mtm) cc_final: 0.8855 (mpp) REVERT: F 108 MET cc_start: 0.8679 (ptm) cc_final: 0.8362 (ppp) REVERT: H 52 MET cc_start: 0.7969 (mtm) cc_final: 0.7564 (mtm) REVERT: H 108 MET cc_start: 0.8608 (ptm) cc_final: 0.8288 (ppp) REVERT: I 108 MET cc_start: 0.8716 (ptm) cc_final: 0.8347 (ppp) REVERT: J 53 ARG cc_start: 0.8897 (mtt90) cc_final: 0.8571 (mtm-85) REVERT: J 108 MET cc_start: 0.8720 (ptm) cc_final: 0.8346 (ppp) REVERT: L 108 MET cc_start: 0.8910 (ptm) cc_final: 0.8361 (ppp) REVERT: M 108 MET cc_start: 0.8750 (ptm) cc_final: 0.8532 (ppp) REVERT: O 59 THR cc_start: 0.9282 (m) cc_final: 0.8992 (p) REVERT: O 86 MET cc_start: 0.9178 (mtm) cc_final: 0.8678 (mpp) REVERT: O 108 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8959 (ppp) REVERT: Q 108 MET cc_start: 0.8587 (ptm) cc_final: 0.8381 (ppp) REVERT: R 86 MET cc_start: 0.9129 (mtm) cc_final: 0.8836 (mpp) REVERT: S 59 THR cc_start: 0.9378 (m) cc_final: 0.9086 (p) REVERT: S 86 MET cc_start: 0.9129 (mtm) cc_final: 0.8856 (mpp) REVERT: T 86 MET cc_start: 0.9148 (mtm) cc_final: 0.8843 (mpp) REVERT: T 108 MET cc_start: 0.8681 (ptm) cc_final: 0.8319 (ppp) REVERT: U 108 MET cc_start: 0.8588 (ptm) cc_final: 0.8372 (ppp) REVERT: V 86 MET cc_start: 0.9298 (mtt) cc_final: 0.8674 (mpp) REVERT: V 108 MET cc_start: 0.9195 (ptp) cc_final: 0.8993 (ptm) REVERT: W 59 THR cc_start: 0.9390 (m) cc_final: 0.9122 (p) REVERT: X 86 MET cc_start: 0.9152 (mtm) cc_final: 0.8861 (mpp) outliers start: 11 outliers final: 10 residues processed: 183 average time/residue: 0.1620 time to fit residues: 52.4264 Evaluate side-chains 171 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain V residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 247 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 193 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 338 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 225 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.034090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.027386 restraints weight = 208946.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.028355 restraints weight = 133017.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.029093 restraints weight = 96186.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.029712 restraints weight = 74359.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.030172 restraints weight = 59704.047| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.773 31999 Z= 0.151 Angle : 0.620 14.253 43354 Z= 0.281 Chirality : 0.032 0.118 4806 Planarity : 0.002 0.028 5596 Dihedral : 6.896 85.361 4204 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.48 % Allowed : 12.13 % Favored : 87.39 % 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: 4.53 (0.13), residues: 3724 helix: 3.82 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -1.66 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 45 TYR 0.024 0.001 TYR T 71 PHE 0.018 0.001 PHE S 26 TRP 0.004 0.001 TRP O 37 HIS 0.002 0.001 HIS L 54 Details of bonding type rmsd covalent geometry : bond 0.00333 (31968) covalent geometry : angle 0.62045 (43354) hydrogen bonds : bond 0.05801 ( 2579) hydrogen bonds : angle 3.59947 ( 7737) Misc. bond : bond 0.16921 ( 31) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3266.86 seconds wall clock time: 58 minutes 13.99 seconds (3493.99 seconds total)