Starting phenix.real_space_refine on Thu Jun 26 08:38:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6g_33640/06_2025/7y6g_33640_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6g_33640/06_2025/7y6g_33640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6g_33640/06_2025/7y6g_33640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6g_33640/06_2025/7y6g_33640.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6g_33640/06_2025/7y6g_33640_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6g_33640/06_2025/7y6g_33640_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 59 7.16 5 S 96 5.16 5 C 19886 2.51 5 N 5356 2.21 5 O 6030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 233 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31427 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1280 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "P" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.15, per 1000 atoms: 0.55 Number of scatterers: 31427 At special positions: 0 Unit cell: (131.274, 131.274, 131.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 59 26.01 S 96 16.00 O 6030 8.00 N 5356 7.00 C 19886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=31, symmetry=0 Number of additional bonds: simple=31, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.02 Conformation dependent library (CDL) restraints added in 3.5 seconds 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7256 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 83.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 Processing helix chain 'A' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 110 removed outlier: 3.534A pdb=" N MET A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 145 removed outlier: 3.876A pdb=" N ALA A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'B' and resid 4 through 36 Processing helix chain 'B' and resid 37 through 65 removed outlier: 3.614A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 110 Processing helix chain 'B' and resid 113 through 145 removed outlier: 3.888A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'C' and resid 4 through 35 Processing helix chain 'C' and resid 37 through 65 removed outlier: 3.500A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 110 Processing helix chain 'C' and resid 113 through 145 removed outlier: 3.900A pdb=" N ALA C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'D' and resid 4 through 36 Processing helix chain 'D' and resid 37 through 65 removed outlier: 3.568A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 110 Processing helix chain 'D' and resid 113 through 145 removed outlier: 3.910A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'E' and resid 4 through 35 Processing helix chain 'E' and resid 37 through 65 removed outlier: 3.515A pdb=" N LEU E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 110 Processing helix chain 'E' and resid 113 through 145 removed outlier: 3.872A pdb=" N ALA E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'F' and resid 4 through 36 removed outlier: 3.511A pdb=" N GLY F 36 " --> pdb=" O GLN F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 65 removed outlier: 3.520A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 110 removed outlier: 3.572A pdb=" N MET F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 145 removed outlier: 3.869A pdb=" N ALA F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 151 Processing helix chain 'G' and resid 4 through 35 Processing helix chain 'G' and resid 37 through 65 removed outlier: 3.526A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 110 Processing helix chain 'G' and resid 113 through 145 removed outlier: 3.876A pdb=" N ALA G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'H' and resid 4 through 35 Processing helix chain 'H' and resid 37 through 65 removed outlier: 3.508A pdb=" N LEU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 110 Processing helix chain 'H' and resid 113 through 145 removed outlier: 3.906A pdb=" N ALA H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 151 Processing helix chain 'I' and resid 4 through 35 Processing helix chain 'I' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 110 Processing helix chain 'I' and resid 113 through 145 removed outlier: 3.885A pdb=" N ALA I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 151 Processing helix chain 'J' and resid 4 through 36 removed outlier: 3.539A pdb=" N GLY J 36 " --> pdb=" O GLN J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 65 removed outlier: 3.507A pdb=" N ALA J 41 " --> pdb=" O TRP J 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 65 " --> pdb=" O ARG J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 110 Processing helix chain 'J' and resid 113 through 145 removed outlier: 3.872A pdb=" N ALA J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 151 Processing helix chain 'K' and resid 4 through 35 Processing helix chain 'K' and resid 37 through 65 removed outlier: 3.616A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing helix chain 'K' and resid 113 through 145 removed outlier: 3.887A pdb=" N ALA K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'L' and resid 4 through 35 removed outlier: 3.510A pdb=" N LYS L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 65 removed outlier: 3.626A pdb=" N ALA L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 111 Processing helix chain 'L' and resid 113 through 145 removed outlier: 3.791A pdb=" N ALA L 117 " --> pdb=" O ASP L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'M' and resid 4 through 35 removed outlier: 3.503A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 65 Processing helix chain 'M' and resid 82 through 111 removed outlier: 3.506A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 145 removed outlier: 3.708A pdb=" N ALA M 117 " --> pdb=" O ASP M 113 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP M 126 " --> pdb=" O ALA M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 151 Processing helix chain 'N' and resid 4 through 36 Processing helix chain 'N' and resid 37 through 65 Processing helix chain 'N' and resid 82 through 110 Processing helix chain 'N' and resid 113 through 145 removed outlier: 3.874A pdb=" N ALA N 117 " --> pdb=" O ASP N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 151 Processing helix chain 'O' and resid 4 through 35 Processing helix chain 'O' and resid 37 through 65 Processing helix chain 'O' and resid 82 through 111 removed outlier: 3.539A pdb=" N LYS O 111 " --> pdb=" O VAL O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 145 removed outlier: 3.823A pdb=" N ALA O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 151 Processing helix chain 'P' and resid 4 through 36 Processing helix chain 'P' and resid 37 through 65 removed outlier: 3.611A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU P 65 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 110 Processing helix chain 'P' and resid 113 through 145 removed outlier: 3.899A pdb=" N ALA P 117 " --> pdb=" O ASP P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 151 Processing helix chain 'Q' and resid 4 through 35 Processing helix chain 'Q' and resid 37 through 65 removed outlier: 3.522A pdb=" N ALA Q 41 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 110 Processing helix chain 'Q' and resid 113 through 145 removed outlier: 3.902A pdb=" N ALA Q 117 " --> pdb=" O ASP Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 151 Processing helix chain 'R' and resid 4 through 36 Processing helix chain 'R' and resid 37 through 65 removed outlier: 3.572A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 110 removed outlier: 3.544A pdb=" N MET R 86 " --> pdb=" O SER R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 145 removed outlier: 3.873A pdb=" N ALA R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 151 Processing helix chain 'S' and resid 4 through 36 removed outlier: 3.508A pdb=" N GLY S 36 " --> pdb=" O GLN S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 65 removed outlier: 3.519A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 110 removed outlier: 3.569A pdb=" N MET S 86 " --> pdb=" O SER S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 145 removed outlier: 3.860A pdb=" N ALA S 117 " --> pdb=" O ASP S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 151 Processing helix chain 'T' and resid 4 through 35 Processing helix chain 'T' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU T 65 " --> pdb=" O ARG T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 110 removed outlier: 3.549A pdb=" N MET T 86 " --> pdb=" O SER T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 113 through 145 removed outlier: 3.905A pdb=" N ALA T 117 " --> pdb=" O ASP T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 151 Processing helix chain 'U' and resid 4 through 35 removed outlier: 3.542A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 65 removed outlier: 3.608A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU U 65 " --> pdb=" O ARG U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 110 Processing helix chain 'U' and resid 113 through 145 removed outlier: 3.903A pdb=" N ALA U 117 " --> pdb=" O ASP U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 151 Processing helix chain 'V' and resid 4 through 35 removed outlier: 3.541A pdb=" N ILE V 8 " --> pdb=" O ASP V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 65 Processing helix chain 'V' and resid 82 through 111 Processing helix chain 'V' and resid 113 through 145 removed outlier: 3.711A pdb=" N ALA V 117 " --> pdb=" O ASP V 113 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 145 through 151 Processing helix chain 'W' and resid 4 through 36 removed outlier: 3.601A pdb=" N GLY W 36 " --> pdb=" O GLN W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 65 removed outlier: 3.682A pdb=" N ALA W 41 " --> pdb=" O TRP W 37 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS W 42 " --> pdb=" O THR W 38 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 110 removed outlier: 3.553A pdb=" N MET W 86 " --> pdb=" O SER W 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 145 removed outlier: 3.867A pdb=" N ALA W 117 " --> pdb=" O ASP W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 151 Processing helix chain 'X' and resid 4 through 35 Processing helix chain 'X' and resid 37 through 65 removed outlier: 3.570A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 110 removed outlier: 3.574A pdb=" N MET X 86 " --> pdb=" O SER X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 145 removed outlier: 3.879A pdb=" N ALA X 117 " --> pdb=" O ASP X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 151 2579 hydrogen bonds defined for protein. 7737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.01 Time building geometry restraints manager: 9.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.41: 13351 1.41 - 1.59: 18377 1.59 - 1.78: 6 1.78 - 1.96: 186 1.96 - 2.14: 48 Bond restraints: 31968 Sorted by residual: bond pdb=" C GLN W 14 " pdb=" N LEU W 15 " ideal model delta sigma weight residual 1.335 1.407 -0.072 1.31e-02 5.83e+03 3.01e+01 bond pdb=" C GLU W 13 " pdb=" N GLN W 14 " ideal model delta sigma weight residual 1.335 1.405 -0.070 1.31e-02 5.83e+03 2.89e+01 bond pdb=" CB MET Q 52 " pdb=" CG MET Q 52 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.79e+00 bond pdb=" CGA HEM C 203 " pdb=" O2A HEM C 203 " ideal model delta sigma weight residual 1.258 1.288 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" NB HEM S 203 " pdb="FE HEM S 203 " ideal model delta sigma weight residual 2.080 1.975 0.105 7.00e-02 2.04e+02 2.25e+00 ... (remaining 31963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.37: 43332 6.37 - 12.74: 15 12.74 - 19.12: 2 19.12 - 25.49: 2 25.49 - 31.86: 3 Bond angle restraints: 43354 Sorted by residual: angle pdb=" CB MET C 52 " pdb=" CG MET C 52 " pdb=" SD MET C 52 " ideal model delta sigma weight residual 112.70 83.42 29.28 3.00e+00 1.11e-01 9.52e+01 angle pdb=" CB MET X 52 " pdb=" CG MET X 52 " pdb=" SD MET X 52 " ideal model delta sigma weight residual 112.70 93.08 19.62 3.00e+00 1.11e-01 4.28e+01 angle pdb=" CB MET S 52 " pdb=" CG MET S 52 " pdb=" SD MET S 52 " ideal model delta sigma weight residual 112.70 93.25 19.45 3.00e+00 1.11e-01 4.20e+01 angle pdb=" O GLN W 14 " pdb=" C GLN W 14 " pdb=" N LEU W 15 " ideal model delta sigma weight residual 122.12 115.48 6.64 1.06e+00 8.90e-01 3.92e+01 angle pdb=" CB MET N 52 " pdb=" CG MET N 52 " pdb=" SD MET N 52 " ideal model delta sigma weight residual 112.70 95.16 17.54 3.00e+00 1.11e-01 3.42e+01 ... (remaining 43349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 16867 17.68 - 35.35: 1827 35.35 - 53.03: 296 53.03 - 70.70: 99 70.70 - 88.38: 29 Dihedral angle restraints: 19118 sinusoidal: 7994 harmonic: 11124 Sorted by residual: dihedral pdb=" C2B HEM S 203 " pdb=" C3B HEM S 203 " pdb=" CAB HEM S 203 " pdb=" CBB HEM S 203 " ideal model delta sinusoidal sigma weight residual 0.00 32.74 -32.74 2 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CA GLU Q 51 " pdb=" C GLU Q 51 " pdb=" N MET Q 52 " pdb=" CA MET Q 52 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" C2B HEM K 203 " pdb=" C3B HEM K 203 " pdb=" CAB HEM K 203 " pdb=" CBB HEM K 203 " ideal model delta sinusoidal sigma weight residual 0.00 -30.74 30.74 2 1.00e+01 1.00e-02 1.25e+01 ... (remaining 19115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3785 0.034 - 0.069: 722 0.069 - 0.103: 269 0.103 - 0.137: 28 0.137 - 0.172: 2 Chirality restraints: 4806 Sorted by residual: chirality pdb=" CA MET Q 52 " pdb=" N MET Q 52 " pdb=" C MET Q 52 " pdb=" CB MET Q 52 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA PHE F 49 " pdb=" N PHE F 49 " pdb=" C PHE F 49 " pdb=" CB PHE F 49 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA MET C 52 " pdb=" N MET C 52 " pdb=" C MET C 52 " pdb=" CB MET C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 4803 not shown) Planarity restraints: 5596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 45 " -0.450 9.50e-02 1.11e+02 2.02e-01 2.63e+01 pdb=" NE ARG R 45 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG R 45 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG R 45 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG R 45 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 49 " 0.016 2.00e-02 2.50e+03 2.93e-02 1.50e+01 pdb=" CG PHE F 49 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE F 49 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE F 49 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE F 49 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE F 49 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 49 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM C 203 " 0.011 2.00e-02 2.50e+03 2.11e-02 1.00e+01 pdb=" C2A HEM C 203 " 0.028 2.00e-02 2.50e+03 pdb=" C3A HEM C 203 " 0.010 2.00e-02 2.50e+03 pdb=" C4A HEM C 203 " 0.004 2.00e-02 2.50e+03 pdb=" CAA HEM C 203 " -0.032 2.00e-02 2.50e+03 pdb=" CHA HEM C 203 " 0.017 2.00e-02 2.50e+03 pdb=" CHB HEM C 203 " 0.003 2.00e-02 2.50e+03 pdb=" CMA HEM C 203 " 0.001 2.00e-02 2.50e+03 pdb=" NA HEM C 203 " -0.041 2.00e-02 2.50e+03 ... (remaining 5593 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 74 2.43 - 3.04: 19740 3.04 - 3.66: 43843 3.66 - 4.28: 68450 4.28 - 4.90: 115959 Nonbonded interactions: 248066 Sorted by model distance: nonbonded pdb=" OE2 GLU H 94 " pdb="FE FE H 202 " model vdw 1.807 2.260 nonbonded pdb=" OE1 GLU G 127 " pdb="FE FE G 202 " model vdw 1.953 2.260 nonbonded pdb=" OE1 GLU T 127 " pdb="FE FE2 T 203 " model vdw 1.972 3.000 nonbonded pdb=" OE1 GLU F 127 " pdb="FE FE2 F 202 " model vdw 1.974 3.000 nonbonded pdb=" OE1 GLU R 127 " pdb="FE FE R 202 " model vdw 2.031 2.260 ... (remaining 248061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 156) selection = (chain 'B' and resid 1 through 156) selection = (chain 'C' and resid 1 through 156) selection = (chain 'D' and resid 1 through 156) selection = (chain 'E' and resid 1 through 156) selection = (chain 'F' and resid 1 through 156) selection = (chain 'G' and resid 1 through 156) selection = (chain 'H' and resid 1 through 156) selection = (chain 'I' and resid 1 through 156) selection = (chain 'J' and resid 1 through 156) selection = (chain 'K' and resid 1 through 156) selection = (chain 'L' and resid 1 through 156) selection = (chain 'M' and resid 1 through 156) selection = (chain 'N' and resid 1 through 156) selection = (chain 'O' and resid 1 through 156) selection = (chain 'P' and resid 1 through 156) selection = (chain 'Q' and resid 1 through 156) selection = (chain 'R' and resid 1 through 156) selection = (chain 'S' and resid 1 through 156) selection = (chain 'T' and resid 1 through 156) selection = (chain 'U' and resid 1 through 156) selection = (chain 'V' and resid 1 through 156) selection = (chain 'W' and resid 1 through 156) selection = (chain 'X' and resid 1 through 156) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 61.530 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.666 31999 Z= 0.211 Angle : 0.618 31.860 43354 Z= 0.323 Chirality : 0.033 0.172 4806 Planarity : 0.004 0.202 5596 Dihedral : 15.053 88.377 11862 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.13), residues: 3724 helix: 3.83 (0.08), residues: 2999 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 37 HIS 0.003 0.001 HIS U 54 PHE 0.062 0.003 PHE F 49 TYR 0.047 0.001 TYR T 71 ARG 0.019 0.000 ARG R 45 Details of bonding type rmsd hydrogen bonds : bond 0.13535 ( 2579) hydrogen bonds : angle 4.25600 ( 7737) covalent geometry : bond 0.00317 (31968) covalent geometry : angle 0.61805 (43354) Misc. bond : bond 0.25639 ( 31) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 3.481 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: 0.4453 time to fit residues: 329.8636 Evaluate side-chains 208 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 184 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 282 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 210 optimal weight: 30.0000 chunk 326 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN J 112 HIS M 137 GLN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 112 HIS S 81 GLN U 156 GLN W 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.035599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.028915 restraints weight = 205584.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.029957 restraints weight = 128219.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.030770 restraints weight = 91417.148| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.301 31999 Z= 0.157 Angle : 0.639 14.540 43354 Z= 0.300 Chirality : 0.032 0.129 4806 Planarity : 0.003 0.078 5596 Dihedral : 6.855 79.272 4204 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.42 % Allowed : 8.27 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.53 (0.13), residues: 3724 helix: 3.98 (0.08), residues: 3062 sheet: None (None), residues: 0 loop : -2.46 (0.20), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 37 HIS 0.004 0.001 HIS V 112 PHE 0.033 0.002 PHE F 49 TYR 0.028 0.001 TYR T 71 ARG 0.006 0.000 ARG P 53 Details of bonding type rmsd hydrogen bonds : bond 0.06757 ( 2579) hydrogen bonds : angle 3.77523 ( 7737) covalent geometry : bond 0.00359 (31968) covalent geometry : angle 0.63894 (43354) Misc. bond : bond 0.08712 ( 31) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 274 time to evaluate : 3.471 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: 0.9345 (m) cc_final: 0.9087 (p) REVERT: E 53 ARG cc_start: 0.9017 (mtt90) cc_final: 0.8777 (mtm-85) REVERT: G 59 THR cc_start: 0.9414 (m) cc_final: 0.9132 (p) REVERT: H 52 MET cc_start: 0.7371 (mtm) cc_final: 0.6871 (mtm) REVERT: I 59 THR cc_start: 0.9364 (m) cc_final: 0.9118 (p) REVERT: J 53 ARG cc_start: 0.9006 (mtt90) cc_final: 0.8685 (mtm-85) REVERT: K 52 MET cc_start: 0.7859 (mtm) cc_final: 0.7533 (mtp) REVERT: L 52 MET cc_start: 0.7596 (mtm) cc_final: 0.7370 (mtm) REVERT: L 108 MET cc_start: 0.9123 (mtm) cc_final: 0.8921 (mtp) REVERT: M 53 ARG cc_start: 0.8966 (mtt90) cc_final: 0.8760 (mtm-85) REVERT: M 86 MET cc_start: 0.9470 (mtt) cc_final: 0.9236 (mtt) REVERT: M 105 ILE cc_start: 0.9602 (tt) cc_final: 0.9359 (mt) REVERT: M 108 MET cc_start: 0.8912 (mtm) cc_final: 0.8704 (mtp) REVERT: O 59 THR cc_start: 0.9377 (m) cc_final: 0.9145 (p) REVERT: V 108 MET cc_start: 0.9171 (mtm) cc_final: 0.8940 (mtp) REVERT: W 52 MET cc_start: 0.6751 (mtm) cc_final: 0.6482 (mtm) outliers start: 14 outliers final: 3 residues processed: 277 average time/residue: 0.3644 time to fit residues: 174.2737 Evaluate side-chains 202 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 199 time to evaluate : 4.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 302 optimal weight: 7.9990 chunk 335 optimal weight: 40.0000 chunk 73 optimal weight: 8.9990 chunk 273 optimal weight: 5.9990 chunk 308 optimal weight: 8.9990 chunk 314 optimal weight: 6.9990 chunk 350 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 310 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN B 130 HIS H 130 HIS I 130 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS T 81 GLN T 130 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.034173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.027380 restraints weight = 213150.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.028418 restraints weight = 134380.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.029209 restraints weight = 95885.628| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.295 31999 Z= 0.185 Angle : 0.634 15.325 43354 Z= 0.297 Chirality : 0.033 0.121 4806 Planarity : 0.003 0.054 5596 Dihedral : 6.960 87.689 4204 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.78 % Allowed : 9.66 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.43 (0.13), residues: 3724 helix: 3.87 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -2.36 (0.20), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 37 HIS 0.003 0.001 HIS L 54 PHE 0.021 0.002 PHE S 26 TYR 0.038 0.001 TYR T 71 ARG 0.004 0.001 ARG P 53 Details of bonding type rmsd hydrogen bonds : bond 0.06930 ( 2579) hydrogen bonds : angle 3.88622 ( 7737) covalent geometry : bond 0.00414 (31968) covalent geometry : angle 0.63363 (43354) Misc. bond : bond 0.07763 ( 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 229 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 3.795 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: 0.9373 (m) cc_final: 0.9116 (p) REVERT: A 86 MET cc_start: 0.9406 (mtt) cc_final: 0.8875 (mpp) REVERT: C 59 THR cc_start: 0.9297 (m) cc_final: 0.9050 (p) REVERT: D 86 MET cc_start: 0.9436 (mtt) cc_final: 0.9228 (mtt) REVERT: E 53 ARG cc_start: 0.8996 (mtt90) cc_final: 0.8588 (mtm-85) REVERT: F 59 THR cc_start: 0.9409 (m) cc_final: 0.9160 (p) REVERT: F 86 MET cc_start: 0.9410 (mtt) cc_final: 0.8876 (mpp) REVERT: G 59 THR cc_start: 0.9385 (m) cc_final: 0.9129 (p) REVERT: H 52 MET cc_start: 0.7636 (mtm) cc_final: 0.7139 (mtm) REVERT: I 59 THR cc_start: 0.9379 (m) cc_final: 0.9129 (p) REVERT: J 53 ARG cc_start: 0.8963 (mtt90) cc_final: 0.8626 (mtm-85) REVERT: K 52 MET cc_start: 0.7956 (mtm) cc_final: 0.7637 (mtp) REVERT: M 53 ARG cc_start: 0.8905 (mtt90) cc_final: 0.8689 (mtm-85) REVERT: O 59 THR cc_start: 0.9389 (m) cc_final: 0.9142 (p) REVERT: R 86 MET cc_start: 0.9400 (mtt) cc_final: 0.8869 (mpp) REVERT: S 86 MET cc_start: 0.9410 (mtt) cc_final: 0.8879 (mpp) REVERT: T 86 MET cc_start: 0.9402 (mtt) cc_final: 0.8854 (mpp) REVERT: W 86 MET cc_start: 0.9414 (mtt) cc_final: 0.8870 (mpp) REVERT: X 86 MET cc_start: 0.9411 (mtt) cc_final: 0.8882 (mpp) outliers start: 26 outliers final: 18 residues processed: 204 average time/residue: 0.3935 time to fit residues: 140.0432 Evaluate side-chains 196 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 3.633 ------------------------------------------------------------------------------- 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 T residue 98 ILE Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain W residue 98 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 71 optimal weight: 20.0000 chunk 324 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 201 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 341 optimal weight: 9.9990 chunk 176 optimal weight: 30.0000 chunk 355 optimal weight: 8.9990 chunk 333 optimal weight: 0.3980 chunk 47 optimal weight: 9.9990 chunk 290 optimal weight: 7.9990 overall best weight: 7.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.033650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.026955 restraints weight = 217762.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.027987 restraints weight = 139126.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.028771 restraints weight = 99109.595| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.302 31999 Z= 0.184 Angle : 0.621 15.672 43354 Z= 0.294 Chirality : 0.033 0.126 4806 Planarity : 0.002 0.044 5596 Dihedral : 7.008 88.602 4204 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.09 % Allowed : 9.81 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.40 (0.13), residues: 3724 helix: 3.83 (0.08), residues: 3067 sheet: None (None), residues: 0 loop : -2.20 (0.20), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 37 HIS 0.003 0.001 HIS J 34 PHE 0.021 0.002 PHE S 26 TYR 0.032 0.001 TYR T 71 ARG 0.003 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.06786 ( 2579) hydrogen bonds : angle 3.90262 ( 7737) covalent geometry : bond 0.00407 (31968) covalent geometry : angle 0.62068 (43354) Misc. bond : bond 0.09335 ( 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 222 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 3.724 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: A 59 THR cc_start: 0.9362 (m) cc_final: 0.9090 (p) REVERT: B 108 MET cc_start: 0.8845 (ptm) cc_final: 0.8518 (ppp) REVERT: C 59 THR cc_start: 0.9293 (m) cc_final: 0.9038 (p) REVERT: C 108 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8817 (ppp) REVERT: D 86 MET cc_start: 0.9396 (mtt) cc_final: 0.9188 (mtt) REVERT: E 53 ARG cc_start: 0.8957 (mtt90) cc_final: 0.8530 (mtm-85) REVERT: F 59 THR cc_start: 0.9429 (m) cc_final: 0.9158 (p) REVERT: G 59 THR cc_start: 0.9358 (m) cc_final: 0.9086 (p) REVERT: H 52 MET cc_start: 0.7585 (mtm) cc_final: 0.7191 (mtm) REVERT: I 59 THR cc_start: 0.9393 (m) cc_final: 0.9121 (p) REVERT: J 53 ARG cc_start: 0.8924 (mtt90) cc_final: 0.8602 (mtm-85) REVERT: K 59 THR cc_start: 0.9423 (m) cc_final: 0.9173 (p) REVERT: M 53 ARG cc_start: 0.8880 (mtt90) cc_final: 0.8520 (mtm-85) REVERT: N 108 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8812 (ppp) REVERT: O 59 THR cc_start: 0.9385 (m) cc_final: 0.9126 (p) REVERT: O 108 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.9069 (ppp) REVERT: R 59 THR cc_start: 0.9412 (m) cc_final: 0.9157 (p) REVERT: R 108 MET cc_start: 0.8811 (ptm) cc_final: 0.8336 (ppp) REVERT: W 108 MET cc_start: 0.8763 (ptm) cc_final: 0.8469 (ppp) REVERT: X 108 MET cc_start: 0.8830 (ptm) cc_final: 0.8529 (ppp) outliers start: 36 outliers final: 22 residues processed: 191 average time/residue: 0.3709 time to fit residues: 122.5161 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 : 3.642 ------------------------------------------------------------------------------- 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 N residue 98 ILE Chi-restraints excluded: chain N residue 108 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 283 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 224 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS M 156 GLN N 130 HIS P 130 HIS X 130 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.033642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.026965 restraints weight = 219835.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.027997 restraints weight = 139844.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.028790 restraints weight = 99654.106| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.679 31999 Z= 0.171 Angle : 0.603 15.588 43354 Z= 0.280 Chirality : 0.032 0.120 4806 Planarity : 0.002 0.039 5596 Dihedral : 6.999 89.853 4204 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.09 % Allowed : 10.17 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.45 (0.13), residues: 3724 helix: 3.83 (0.08), residues: 3067 sheet: None (None), residues: 0 loop : -2.01 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 37 HIS 0.003 0.001 HIS P 34 PHE 0.019 0.001 PHE N 26 TYR 0.033 0.001 TYR T 71 ARG 0.003 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.06496 ( 2579) hydrogen bonds : angle 3.76785 ( 7737) covalent geometry : bond 0.00377 (31968) covalent geometry : angle 0.60280 (43354) Misc. bond : bond 0.13827 ( 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 221 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 3.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8683 (ptm) cc_final: 0.8394 (ppp) REVERT: B 108 MET cc_start: 0.8748 (ptm) cc_final: 0.8469 (ppp) REVERT: D 108 MET cc_start: 0.8715 (ptm) cc_final: 0.8398 (ppp) REVERT: E 53 ARG cc_start: 0.8954 (mtt90) cc_final: 0.8525 (mtm-85) REVERT: E 59 THR cc_start: 0.9411 (m) cc_final: 0.9153 (p) REVERT: E 108 MET cc_start: 0.8890 (ptm) cc_final: 0.8543 (ppp) REVERT: F 59 THR cc_start: 0.9400 (m) cc_final: 0.9117 (p) REVERT: G 59 THR cc_start: 0.9333 (m) cc_final: 0.9056 (p) REVERT: G 108 MET cc_start: 0.8723 (ptm) cc_final: 0.8400 (ppp) REVERT: H 52 MET cc_start: 0.7507 (mtm) cc_final: 0.7191 (ttm) REVERT: I 59 THR cc_start: 0.9387 (m) cc_final: 0.9101 (p) REVERT: I 108 MET cc_start: 0.8673 (ptm) cc_final: 0.8397 (ppp) REVERT: J 53 ARG cc_start: 0.8918 (mtt90) cc_final: 0.8578 (mtm-85) REVERT: K 59 THR cc_start: 0.9407 (m) cc_final: 0.9147 (p) REVERT: K 108 MET cc_start: 0.8666 (ptm) cc_final: 0.8402 (ppp) REVERT: M 53 ARG cc_start: 0.8874 (mtt90) cc_final: 0.8520 (mtm-85) REVERT: O 59 THR cc_start: 0.9371 (m) cc_final: 0.9104 (p) REVERT: O 108 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9008 (ppp) REVERT: P 108 MET cc_start: 0.8645 (ptm) cc_final: 0.8345 (ppp) REVERT: Q 108 MET cc_start: 0.8742 (ptm) cc_final: 0.8416 (ppp) REVERT: R 59 THR cc_start: 0.9394 (m) cc_final: 0.9125 (p) REVERT: R 108 MET cc_start: 0.8780 (ptm) cc_final: 0.8328 (ppp) REVERT: S 59 THR cc_start: 0.9415 (m) cc_final: 0.9158 (p) REVERT: S 108 MET cc_start: 0.8893 (ptm) cc_final: 0.8549 (ppp) REVERT: T 108 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8991 (ptm) REVERT: U 108 MET cc_start: 0.8783 (ptm) cc_final: 0.8428 (ppp) REVERT: V 81 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8389 (pp30) REVERT: V 86 MET cc_start: 0.9393 (mtt) cc_final: 0.8799 (mpp) REVERT: W 59 THR cc_start: 0.9470 (m) cc_final: 0.9205 (p) REVERT: W 108 MET cc_start: 0.8684 (ptm) cc_final: 0.8465 (ppp) REVERT: X 108 MET cc_start: 0.8812 (ptm) cc_final: 0.8587 (ppp) outliers start: 36 outliers final: 21 residues processed: 197 average time/residue: 0.3861 time to fit residues: 129.2459 Evaluate side-chains 197 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 3.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain I 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 T residue 108 MET 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 207 optimal weight: 5.9990 chunk 180 optimal weight: 30.0000 chunk 277 optimal weight: 9.9990 chunk 345 optimal weight: 0.9990 chunk 278 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 354 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 339 optimal weight: 5.9990 chunk 254 optimal weight: 6.9990 chunk 292 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 C 130 HIS N 130 HIS P 130 HIS X 130 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.034178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.027490 restraints weight = 219176.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.028515 restraints weight = 139632.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.029302 restraints weight = 99727.166| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.757 31999 Z= 0.150 Angle : 0.605 16.004 43354 Z= 0.278 Chirality : 0.033 0.143 4806 Planarity : 0.002 0.030 5596 Dihedral : 6.901 85.750 4204 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.97 % Allowed : 10.89 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.52 (0.13), residues: 3724 helix: 3.85 (0.08), residues: 3065 sheet: None (None), residues: 0 loop : -1.79 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 37 HIS 0.002 0.001 HIS P 34 PHE 0.018 0.001 PHE S 26 TYR 0.029 0.001 TYR T 71 ARG 0.003 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.06002 ( 2579) hydrogen bonds : angle 3.66665 ( 7737) covalent geometry : bond 0.00328 (31968) covalent geometry : angle 0.60459 (43354) Misc. bond : bond 0.15311 ( 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 217 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 5.584 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: 0.9204 (mtm) cc_final: 0.8778 (mpp) REVERT: A 108 MET cc_start: 0.8612 (ptm) cc_final: 0.8410 (ppp) REVERT: B 108 MET cc_start: 0.8654 (ptm) cc_final: 0.8291 (ppp) REVERT: D 86 MET cc_start: 0.9404 (mtt) cc_final: 0.8795 (mpp) REVERT: D 108 MET cc_start: 0.8617 (ptm) cc_final: 0.8393 (ppp) REVERT: E 53 ARG cc_start: 0.8955 (mtt90) cc_final: 0.8539 (mtm-85) REVERT: E 108 MET cc_start: 0.8786 (ptm) cc_final: 0.8502 (ppp) REVERT: F 59 THR cc_start: 0.9371 (m) cc_final: 0.9082 (p) REVERT: F 86 MET cc_start: 0.9176 (mtm) cc_final: 0.8754 (mpp) REVERT: G 108 MET cc_start: 0.8640 (ptm) cc_final: 0.8377 (ppp) REVERT: H 52 MET cc_start: 0.7568 (mtm) cc_final: 0.7290 (mtm) REVERT: I 108 MET cc_start: 0.8582 (ptm) cc_final: 0.8378 (ppp) REVERT: J 53 ARG cc_start: 0.8872 (mtt90) cc_final: 0.8562 (mtm-85) REVERT: J 86 MET cc_start: 0.9397 (mtt) cc_final: 0.8814 (mpp) REVERT: J 108 MET cc_start: 0.8743 (ptm) cc_final: 0.8416 (ppp) REVERT: K 59 THR cc_start: 0.9371 (m) cc_final: 0.9099 (p) REVERT: L 108 MET cc_start: 0.8952 (ptm) cc_final: 0.8358 (ppp) REVERT: M 53 ARG cc_start: 0.8850 (mtt90) cc_final: 0.8522 (mtm-85) REVERT: M 108 MET cc_start: 0.8773 (ptm) cc_final: 0.8520 (ppp) REVERT: N 86 MET cc_start: 0.9394 (mtt) cc_final: 0.8829 (mpp) REVERT: O 59 THR cc_start: 0.9334 (m) cc_final: 0.9057 (p) REVERT: O 108 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8977 (ppp) REVERT: P 108 MET cc_start: 0.8561 (ptm) cc_final: 0.8350 (ppp) REVERT: Q 108 MET cc_start: 0.8657 (ptm) cc_final: 0.8413 (ppp) REVERT: R 59 THR cc_start: 0.9369 (m) cc_final: 0.9087 (p) REVERT: R 86 MET cc_start: 0.9161 (mtm) cc_final: 0.8744 (mpp) REVERT: R 108 MET cc_start: 0.8723 (ptm) cc_final: 0.8303 (ppp) REVERT: S 59 THR cc_start: 0.9392 (m) cc_final: 0.9116 (p) REVERT: S 86 MET cc_start: 0.9174 (mtm) cc_final: 0.8760 (mpp) REVERT: S 108 MET cc_start: 0.8826 (ptm) cc_final: 0.8540 (ppp) REVERT: T 86 MET cc_start: 0.9191 (mtm) cc_final: 0.8760 (mpp) REVERT: T 108 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8968 (ptm) REVERT: U 108 MET cc_start: 0.8704 (ptm) cc_final: 0.8380 (ppp) REVERT: V 108 MET cc_start: 0.9216 (ptp) cc_final: 0.8986 (ptm) REVERT: W 59 THR cc_start: 0.9454 (m) cc_final: 0.9192 (p) REVERT: W 86 MET cc_start: 0.9213 (mtm) cc_final: 0.8762 (mpp) REVERT: X 86 MET cc_start: 0.9178 (mtm) cc_final: 0.8747 (mpp) outliers start: 32 outliers final: 14 residues processed: 205 average time/residue: 0.5744 time to fit residues: 199.9300 Evaluate side-chains 189 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 3.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain T residue 108 MET Chi-restraints excluded: chain V residue 79 VAL 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 336 optimal weight: 5.9990 chunk 284 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 321 optimal weight: 8.9990 chunk 351 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 155 optimal weight: 30.0000 chunk 143 optimal weight: 20.0000 chunk 221 optimal weight: 6.9990 chunk 300 optimal weight: 30.0000 chunk 241 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS F 130 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.033762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.027069 restraints weight = 216553.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.028088 restraints weight = 138916.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.028853 restraints weight = 99660.748| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.835 31999 Z= 0.165 Angle : 0.604 14.481 43354 Z= 0.279 Chirality : 0.033 0.118 4806 Planarity : 0.002 0.034 5596 Dihedral : 6.845 82.992 4204 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.75 % Allowed : 11.35 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.46 (0.13), residues: 3724 helix: 3.79 (0.08), residues: 3065 sheet: None (None), residues: 0 loop : -1.68 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 37 HIS 0.003 0.001 HIS B 34 PHE 0.018 0.001 PHE S 26 TYR 0.028 0.001 TYR T 71 ARG 0.004 0.000 ARG E 73 Details of bonding type rmsd hydrogen bonds : bond 0.06240 ( 2579) hydrogen bonds : angle 3.70344 ( 7737) covalent geometry : bond 0.00361 (31968) covalent geometry : angle 0.60360 (43354) Misc. bond : bond 0.16258 ( 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 200 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 3.448 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: 0.9227 (mtm) cc_final: 0.8801 (mpp) REVERT: B 108 MET cc_start: 0.8689 (ptm) cc_final: 0.8311 (ppp) REVERT: D 108 MET cc_start: 0.8648 (ptm) cc_final: 0.8400 (ppp) REVERT: E 53 ARG cc_start: 0.8925 (mtt90) cc_final: 0.8530 (mtm-85) REVERT: E 108 MET cc_start: 0.8822 (ptm) cc_final: 0.8542 (ppp) REVERT: F 59 THR cc_start: 0.9378 (m) cc_final: 0.9089 (p) REVERT: F 86 MET cc_start: 0.9227 (mtm) cc_final: 0.8788 (mpp) REVERT: G 108 MET cc_start: 0.8658 (ptm) cc_final: 0.8387 (ppp) REVERT: H 52 MET cc_start: 0.7674 (mtm) cc_final: 0.7293 (mtm) REVERT: I 108 MET cc_start: 0.8602 (ptm) cc_final: 0.8276 (ppp) REVERT: J 53 ARG cc_start: 0.8886 (mtt90) cc_final: 0.8564 (mtm-85) REVERT: J 108 MET cc_start: 0.8709 (ptm) cc_final: 0.8424 (ppp) REVERT: K 59 THR cc_start: 0.9392 (m) cc_final: 0.9123 (p) REVERT: L 108 MET cc_start: 0.8945 (ptm) cc_final: 0.8359 (ppp) REVERT: M 53 ARG cc_start: 0.8894 (mtt90) cc_final: 0.8557 (mtm-85) REVERT: M 108 MET cc_start: 0.8752 (ptm) cc_final: 0.8521 (ppp) REVERT: O 59 THR cc_start: 0.9349 (m) cc_final: 0.9075 (p) REVERT: O 108 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9161 (ptm) REVERT: P 108 MET cc_start: 0.8604 (ptm) cc_final: 0.8369 (ppp) REVERT: Q 108 MET cc_start: 0.8675 (ptm) cc_final: 0.8429 (ppp) REVERT: R 86 MET cc_start: 0.9213 (mtm) cc_final: 0.8782 (mpp) REVERT: R 108 MET cc_start: 0.8756 (ptm) cc_final: 0.8352 (ppp) REVERT: S 59 THR cc_start: 0.9409 (m) cc_final: 0.9140 (p) REVERT: S 86 MET cc_start: 0.9218 (mtm) cc_final: 0.8799 (mpp) REVERT: S 108 MET cc_start: 0.8843 (ptm) cc_final: 0.8552 (ppp) REVERT: T 86 MET cc_start: 0.9219 (mtm) cc_final: 0.8787 (mpp) REVERT: T 108 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8971 (ptm) REVERT: U 108 MET cc_start: 0.8716 (ptm) cc_final: 0.8415 (ppp) REVERT: V 86 MET cc_start: 0.9348 (mtt) cc_final: 0.8716 (mpp) REVERT: V 108 MET cc_start: 0.9228 (ptp) cc_final: 0.9009 (ptm) REVERT: W 59 THR cc_start: 0.9447 (m) cc_final: 0.9184 (p) REVERT: W 86 MET cc_start: 0.9251 (mtm) cc_final: 0.8795 (mpp) REVERT: X 86 MET cc_start: 0.9232 (mtm) cc_final: 0.8794 (mpp) outliers start: 25 outliers final: 19 residues processed: 184 average time/residue: 0.4065 time to fit residues: 127.7055 Evaluate side-chains 190 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 108 MET Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain X residue 98 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 46 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 327 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 chunk 65 optimal weight: 40.0000 chunk 198 optimal weight: 6.9990 chunk 280 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS D 130 HIS E 130 HIS N 130 HIS O 81 GLN P 130 HIS R 130 HIS U 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 = 0.2827 r_free = 0.2827 target = 0.033178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.026394 restraints weight = 209206.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.027374 restraints weight = 135341.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.028123 restraints weight = 97486.714| |-----------------------------------------------------------------------------| r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.862 31999 Z= 0.182 Angle : 0.622 14.753 43354 Z= 0.291 Chirality : 0.033 0.126 4806 Planarity : 0.002 0.033 5596 Dihedral : 6.873 81.558 4204 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.88 % Allowed : 11.26 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.40 (0.13), residues: 3724 helix: 3.74 (0.08), residues: 3065 sheet: None (None), residues: 0 loop : -1.69 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 37 HIS 0.003 0.001 HIS T 34 PHE 0.019 0.001 PHE S 26 TYR 0.029 0.001 TYR T 71 ARG 0.004 0.000 ARG J 73 Details of bonding type rmsd hydrogen bonds : bond 0.06570 ( 2579) hydrogen bonds : angle 3.78615 ( 7737) covalent geometry : bond 0.00400 (31968) covalent geometry : angle 0.62160 (43354) Misc. bond : bond 0.16918 ( 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 200 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 3.710 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: 0.9268 (mtm) cc_final: 0.8883 (mpp) REVERT: B 108 MET cc_start: 0.8703 (ptm) cc_final: 0.8317 (ppp) REVERT: D 108 MET cc_start: 0.8680 (ptm) cc_final: 0.8425 (ppp) REVERT: E 53 ARG cc_start: 0.8930 (mtt90) cc_final: 0.8555 (mtm-85) REVERT: E 108 MET cc_start: 0.8852 (ptm) cc_final: 0.8395 (ppp) REVERT: F 59 THR cc_start: 0.9400 (m) cc_final: 0.9118 (p) REVERT: F 86 MET cc_start: 0.9264 (mtm) cc_final: 0.8864 (mpp) REVERT: G 108 MET cc_start: 0.8677 (ptm) cc_final: 0.8266 (ppp) REVERT: H 52 MET cc_start: 0.7706 (mtm) cc_final: 0.7323 (mtm) REVERT: I 108 MET cc_start: 0.8644 (ptm) cc_final: 0.8301 (ppp) REVERT: J 53 ARG cc_start: 0.8883 (mtt90) cc_final: 0.8570 (mtm-85) REVERT: J 86 MET cc_start: 0.9411 (mtt) cc_final: 0.8798 (mpp) REVERT: J 108 MET cc_start: 0.8752 (ptm) cc_final: 0.8433 (ppp) REVERT: K 59 THR cc_start: 0.9408 (m) cc_final: 0.9144 (p) REVERT: L 108 MET cc_start: 0.8977 (ptm) cc_final: 0.8392 (ppp) REVERT: M 53 ARG cc_start: 0.8889 (mtt90) cc_final: 0.8550 (mtm-85) REVERT: M 108 MET cc_start: 0.8785 (ptm) cc_final: 0.8430 (ppp) REVERT: O 59 THR cc_start: 0.9373 (m) cc_final: 0.9103 (p) REVERT: O 108 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.9140 (ptm) REVERT: P 108 MET cc_start: 0.8634 (ptm) cc_final: 0.8244 (ppp) REVERT: Q 108 MET cc_start: 0.8722 (ptm) cc_final: 0.8448 (ppp) REVERT: R 86 MET cc_start: 0.9243 (mtm) cc_final: 0.8857 (mpp) REVERT: R 108 MET cc_start: 0.8750 (ptm) cc_final: 0.8346 (ppp) REVERT: S 59 THR cc_start: 0.9423 (m) cc_final: 0.9157 (p) REVERT: S 86 MET cc_start: 0.9259 (mtm) cc_final: 0.8882 (mpp) REVERT: S 108 MET cc_start: 0.8864 (ptm) cc_final: 0.8377 (ppp) REVERT: T 86 MET cc_start: 0.9260 (mtm) cc_final: 0.8867 (mpp) REVERT: T 108 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8970 (ptm) REVERT: U 108 MET cc_start: 0.8750 (ptm) cc_final: 0.8300 (ppp) REVERT: V 86 MET cc_start: 0.9372 (mtt) cc_final: 0.8775 (mpp) REVERT: V 108 MET cc_start: 0.9229 (ptp) cc_final: 0.9024 (ptm) REVERT: W 59 THR cc_start: 0.9465 (m) cc_final: 0.9210 (p) REVERT: W 86 MET cc_start: 0.9278 (mtm) cc_final: 0.8842 (mpp) REVERT: X 86 MET cc_start: 0.9266 (mtm) cc_final: 0.8874 (mpp) outliers start: 29 outliers final: 25 residues processed: 177 average time/residue: 0.3898 time to fit residues: 119.4314 Evaluate side-chains 194 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain 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 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 T residue 108 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 88 optimal weight: 9.9990 chunk 172 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 303 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 R 130 HIS U 130 HIS W 130 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.033309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.026531 restraints weight = 209442.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.027513 restraints weight = 135596.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.028268 restraints weight = 97562.697| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.847 31999 Z= 0.176 Angle : 0.625 14.742 43354 Z= 0.290 Chirality : 0.033 0.127 4806 Planarity : 0.002 0.032 5596 Dihedral : 6.864 81.890 4204 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.81 % Allowed : 11.53 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.41 (0.13), residues: 3724 helix: 3.75 (0.08), residues: 3070 sheet: None (None), residues: 0 loop : -1.72 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 37 HIS 0.003 0.001 HIS P 34 PHE 0.019 0.001 PHE S 26 TYR 0.028 0.001 TYR T 71 ARG 0.004 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.06446 ( 2579) hydrogen bonds : angle 3.74791 ( 7737) covalent geometry : bond 0.00385 (31968) covalent geometry : angle 0.62543 (43354) Misc. bond : bond 0.17631 ( 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 196 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 3.629 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: 0.9266 (mtm) cc_final: 0.8878 (mpp) REVERT: B 108 MET cc_start: 0.8675 (ptm) cc_final: 0.8323 (ppp) REVERT: D 86 MET cc_start: 0.9404 (mtt) cc_final: 0.8803 (mpp) REVERT: D 108 MET cc_start: 0.8661 (ptm) cc_final: 0.8266 (ppp) REVERT: E 53 ARG cc_start: 0.8933 (mtt90) cc_final: 0.8529 (mtm-85) REVERT: E 108 MET cc_start: 0.8835 (ptm) cc_final: 0.8400 (ppp) REVERT: F 59 THR cc_start: 0.9394 (m) cc_final: 0.9109 (p) REVERT: F 86 MET cc_start: 0.9265 (mtm) cc_final: 0.8864 (mpp) REVERT: G 108 MET cc_start: 0.8667 (ptm) cc_final: 0.8266 (ppp) REVERT: H 52 MET cc_start: 0.7694 (mtm) cc_final: 0.7312 (mtm) REVERT: I 108 MET cc_start: 0.8630 (ptm) cc_final: 0.8282 (ppp) REVERT: J 53 ARG cc_start: 0.8888 (mtt90) cc_final: 0.8576 (mtm-85) REVERT: J 108 MET cc_start: 0.8737 (ptm) cc_final: 0.8430 (ppp) REVERT: K 59 THR cc_start: 0.9400 (m) cc_final: 0.9133 (p) REVERT: L 108 MET cc_start: 0.8978 (ptm) cc_final: 0.8403 (ppp) REVERT: M 53 ARG cc_start: 0.8887 (mtt90) cc_final: 0.8410 (mtm-85) REVERT: M 108 MET cc_start: 0.8775 (ptm) cc_final: 0.8430 (ppp) REVERT: O 59 THR cc_start: 0.9360 (m) cc_final: 0.9090 (p) REVERT: O 108 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.9146 (ptm) REVERT: P 108 MET cc_start: 0.8603 (ptm) cc_final: 0.8211 (ppp) REVERT: Q 108 MET cc_start: 0.8679 (ptm) cc_final: 0.8291 (ppp) REVERT: R 86 MET cc_start: 0.9245 (mtm) cc_final: 0.8858 (mpp) REVERT: R 108 MET cc_start: 0.8733 (ptm) cc_final: 0.8343 (ppp) REVERT: S 59 THR cc_start: 0.9418 (m) cc_final: 0.9150 (p) REVERT: S 86 MET cc_start: 0.9259 (mtm) cc_final: 0.8881 (mpp) REVERT: S 108 MET cc_start: 0.8831 (ptm) cc_final: 0.8363 (ppp) REVERT: T 86 MET cc_start: 0.9260 (mtm) cc_final: 0.8880 (mpp) REVERT: T 108 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8875 (ppp) REVERT: U 108 MET cc_start: 0.8722 (ptm) cc_final: 0.8319 (ppp) REVERT: V 86 MET cc_start: 0.9356 (mtt) cc_final: 0.8739 (mpp) REVERT: W 59 THR cc_start: 0.9457 (m) cc_final: 0.9200 (p) REVERT: W 86 MET cc_start: 0.9276 (mtm) cc_final: 0.8870 (mpp) REVERT: X 86 MET cc_start: 0.9263 (mtm) cc_final: 0.8873 (mpp) outliers start: 27 outliers final: 25 residues processed: 174 average time/residue: 0.3730 time to fit residues: 112.9818 Evaluate side-chains 191 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain 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 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 T residue 108 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 33 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 307 optimal weight: 5.9990 chunk 354 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 342 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS C 130 HIS E 130 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.033734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.026999 restraints weight = 208896.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.027996 restraints weight = 134753.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.028754 restraints weight = 96757.975| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.835 31999 Z= 0.157 Angle : 0.612 14.667 43354 Z= 0.282 Chirality : 0.032 0.126 4806 Planarity : 0.002 0.030 5596 Dihedral : 6.858 82.863 4204 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.81 % Allowed : 11.47 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.48 (0.13), residues: 3724 helix: 3.79 (0.08), residues: 3070 sheet: None (None), residues: 0 loop : -1.70 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 37 HIS 0.002 0.001 HIS P 34 PHE 0.018 0.001 PHE S 26 TYR 0.026 0.001 TYR T 71 ARG 0.003 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.06090 ( 2579) hydrogen bonds : angle 3.65501 ( 7737) covalent geometry : bond 0.00345 (31968) covalent geometry : angle 0.61196 (43354) Misc. bond : bond 0.16791 ( 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 200 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 3.676 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: 0.9243 (mtm) cc_final: 0.8871 (mpp) REVERT: B 108 MET cc_start: 0.8620 (ptm) cc_final: 0.8297 (ppp) REVERT: D 108 MET cc_start: 0.8620 (ptm) cc_final: 0.8392 (ppp) REVERT: E 53 ARG cc_start: 0.8934 (mtt90) cc_final: 0.8519 (mtm-85) REVERT: E 108 MET cc_start: 0.8799 (ptm) cc_final: 0.8373 (ppp) REVERT: F 86 MET cc_start: 0.9244 (mtm) cc_final: 0.8855 (mpp) REVERT: G 108 MET cc_start: 0.8619 (ptm) cc_final: 0.8259 (ppp) REVERT: H 52 MET cc_start: 0.7681 (mtm) cc_final: 0.7312 (mtm) REVERT: I 108 MET cc_start: 0.8587 (ptm) cc_final: 0.8251 (ppp) REVERT: J 53 ARG cc_start: 0.8882 (mtt90) cc_final: 0.8565 (mtm-85) REVERT: J 108 MET cc_start: 0.8691 (ptm) cc_final: 0.8434 (ppp) REVERT: L 108 MET cc_start: 0.8955 (ptm) cc_final: 0.8385 (ppp) REVERT: M 53 ARG cc_start: 0.8888 (mtt90) cc_final: 0.8415 (mtm-85) REVERT: M 108 MET cc_start: 0.8715 (ptm) cc_final: 0.8382 (ppp) REVERT: N 86 MET cc_start: 0.9323 (mtm) cc_final: 0.8810 (mpp) REVERT: O 59 THR cc_start: 0.9328 (m) cc_final: 0.9050 (p) REVERT: O 108 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.9120 (ptm) REVERT: P 108 MET cc_start: 0.8571 (ptm) cc_final: 0.8192 (ppp) REVERT: Q 108 MET cc_start: 0.8637 (ptm) cc_final: 0.8411 (ppp) REVERT: R 86 MET cc_start: 0.9219 (mtm) cc_final: 0.8847 (mpp) REVERT: R 108 MET cc_start: 0.8712 (ptm) cc_final: 0.8330 (ppp) REVERT: S 59 THR cc_start: 0.9412 (m) cc_final: 0.9132 (p) REVERT: S 86 MET cc_start: 0.9240 (mtm) cc_final: 0.8877 (mpp) REVERT: S 108 MET cc_start: 0.8785 (ptm) cc_final: 0.8375 (ppp) REVERT: T 86 MET cc_start: 0.9240 (mtm) cc_final: 0.8862 (mpp) REVERT: T 108 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8858 (ppp) REVERT: U 108 MET cc_start: 0.8671 (ptm) cc_final: 0.8267 (ppp) REVERT: V 86 MET cc_start: 0.9339 (mtt) cc_final: 0.8727 (mpp) REVERT: V 108 MET cc_start: 0.8985 (ptm) cc_final: 0.8466 (ppp) REVERT: W 59 THR cc_start: 0.9433 (m) cc_final: 0.9170 (p) REVERT: W 86 MET cc_start: 0.9258 (mtm) cc_final: 0.8863 (mpp) REVERT: X 86 MET cc_start: 0.9238 (mtm) cc_final: 0.8873 (mpp) outliers start: 27 outliers final: 24 residues processed: 178 average time/residue: 0.3689 time to fit residues: 113.9670 Evaluate side-chains 190 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain T residue 108 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 195 optimal weight: 0.0970 chunk 256 optimal weight: 5.9990 chunk 65 optimal weight: 40.0000 chunk 247 optimal weight: 7.9990 chunk 324 optimal weight: 9.9990 chunk 273 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 chunk 209 optimal weight: 9.9990 overall best weight: 3.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS D 130 HIS P 130 HIS R 130 HIS U 130 HIS X 130 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.034743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.027997 restraints weight = 208060.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.029005 restraints weight = 134129.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.029763 restraints weight = 96257.852| |-----------------------------------------------------------------------------| r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.805 31999 Z= 0.131 Angle : 0.600 14.142 43354 Z= 0.271 Chirality : 0.032 0.118 4806 Planarity : 0.002 0.024 5596 Dihedral : 6.844 84.565 4204 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.30 % Allowed : 12.10 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.63 (0.13), residues: 3724 helix: 3.90 (0.08), residues: 3070 sheet: None (None), residues: 0 loop : -1.63 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 37 HIS 0.003 0.001 HIS F 54 PHE 0.017 0.001 PHE F 49 TYR 0.024 0.001 TYR T 71 ARG 0.004 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.05353 ( 2579) hydrogen bonds : angle 3.48364 ( 7737) covalent geometry : bond 0.00289 (31968) covalent geometry : angle 0.60004 (43354) Misc. bond : bond 0.18383 ( 31) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6935.03 seconds wall clock time: 124 minutes 16.66 seconds (7456.66 seconds total)