Starting phenix.real_space_refine on Fri Mar 6 11:02:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6f_33639/03_2026/7y6f_33639_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6f_33639/03_2026/7y6f_33639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6f_33639/03_2026/7y6f_33639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6f_33639/03_2026/7y6f_33639.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6f_33639/03_2026/7y6f_33639_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6f_33639/03_2026/7y6f_33639_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31427 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1280 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "P" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.79, per 1000 atoms: 0.25 Number of scatterers: 31427 At special positions: 0 Unit cell: (131.274, 131.274, 131.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 59 26.01 S 96 16.00 O 6030 8.00 N 5356 7.00 C 19886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=31, symmetry=0 Number of additional bonds: simple=31, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7256 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 83.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 Processing helix chain 'A' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 110 removed outlier: 3.534A pdb=" N MET A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 145 removed outlier: 3.876A pdb=" N ALA A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'B' and resid 4 through 36 Processing helix chain 'B' and resid 37 through 65 removed outlier: 3.614A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 110 Processing helix chain 'B' and resid 113 through 145 removed outlier: 3.888A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'C' and resid 4 through 35 Processing helix chain 'C' and resid 37 through 65 removed outlier: 3.500A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 110 Processing helix chain 'C' and resid 113 through 145 removed outlier: 3.900A pdb=" N ALA C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'D' and resid 4 through 36 Processing helix chain 'D' and resid 37 through 65 removed outlier: 3.568A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 110 Processing helix chain 'D' and resid 113 through 145 removed outlier: 3.910A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'E' and resid 4 through 35 Processing helix chain 'E' and resid 37 through 65 removed outlier: 3.515A pdb=" N LEU E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 110 Processing helix chain 'E' and resid 113 through 145 removed outlier: 3.872A pdb=" N ALA E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'F' and resid 4 through 36 removed outlier: 3.511A pdb=" N GLY F 36 " --> pdb=" O GLN F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 65 removed outlier: 3.520A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 110 removed outlier: 3.572A pdb=" N MET F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 145 removed outlier: 3.869A pdb=" N ALA F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 151 Processing helix chain 'G' and resid 4 through 35 Processing helix chain 'G' and resid 37 through 65 removed outlier: 3.526A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 110 Processing helix chain 'G' and resid 113 through 145 removed outlier: 3.876A pdb=" N ALA G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'H' and resid 4 through 35 Processing helix chain 'H' and resid 37 through 65 removed outlier: 3.508A pdb=" N LEU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 110 Processing helix chain 'H' and resid 113 through 145 removed outlier: 3.906A pdb=" N ALA H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 151 Processing helix chain 'I' and resid 4 through 35 Processing helix chain 'I' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 110 Processing helix chain 'I' and resid 113 through 145 removed outlier: 3.885A pdb=" N ALA I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 151 Processing helix chain 'J' and resid 4 through 36 removed outlier: 3.539A pdb=" N GLY J 36 " --> pdb=" O GLN J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 65 removed outlier: 3.507A pdb=" N ALA J 41 " --> pdb=" O TRP J 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 65 " --> pdb=" O ARG J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 110 Processing helix chain 'J' and resid 113 through 145 removed outlier: 3.872A pdb=" N ALA J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 151 Processing helix chain 'K' and resid 4 through 35 Processing helix chain 'K' and resid 37 through 65 removed outlier: 3.616A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing helix chain 'K' and resid 113 through 145 removed outlier: 3.887A pdb=" N ALA K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'L' and resid 4 through 35 removed outlier: 3.510A pdb=" N LYS L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 65 removed outlier: 3.626A pdb=" N ALA L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 111 Processing helix chain 'L' and resid 113 through 145 removed outlier: 3.791A pdb=" N ALA L 117 " --> pdb=" O ASP L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'M' and resid 4 through 35 removed outlier: 3.503A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 65 Processing helix chain 'M' and resid 82 through 111 removed outlier: 3.506A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 145 removed outlier: 3.708A pdb=" N ALA M 117 " --> pdb=" O ASP M 113 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP M 126 " --> pdb=" O ALA M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 151 Processing helix chain 'N' and resid 4 through 36 Processing helix chain 'N' and resid 37 through 65 Processing helix chain 'N' and resid 82 through 110 Processing helix chain 'N' and resid 113 through 145 removed outlier: 3.874A pdb=" N ALA N 117 " --> pdb=" O ASP N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 151 Processing helix chain 'O' and resid 4 through 35 Processing helix chain 'O' and resid 37 through 65 Processing helix chain 'O' and resid 82 through 111 removed outlier: 3.539A pdb=" N LYS O 111 " --> pdb=" O VAL O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 145 removed outlier: 3.823A pdb=" N ALA O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 151 Processing helix chain 'P' and resid 4 through 36 Processing helix chain 'P' and resid 37 through 65 removed outlier: 3.611A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU P 65 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 110 Processing helix chain 'P' and resid 113 through 145 removed outlier: 3.899A pdb=" N ALA P 117 " --> pdb=" O ASP P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 151 Processing helix chain 'Q' and resid 4 through 35 Processing helix chain 'Q' and resid 37 through 65 removed outlier: 3.522A pdb=" N ALA Q 41 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 110 Processing helix chain 'Q' and resid 113 through 145 removed outlier: 3.902A pdb=" N ALA Q 117 " --> pdb=" O ASP Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 151 Processing helix chain 'R' and resid 4 through 36 Processing helix chain 'R' and resid 37 through 65 removed outlier: 3.572A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 110 removed outlier: 3.544A pdb=" N MET R 86 " --> pdb=" O SER R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 145 removed outlier: 3.873A pdb=" N ALA R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 151 Processing helix chain 'S' and resid 4 through 36 removed outlier: 3.508A pdb=" N GLY S 36 " --> pdb=" O GLN S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 65 removed outlier: 3.519A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 110 removed outlier: 3.569A pdb=" N MET S 86 " --> pdb=" O SER S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 145 removed outlier: 3.860A pdb=" N ALA S 117 " --> pdb=" O ASP S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 151 Processing helix chain 'T' and resid 4 through 35 Processing helix chain 'T' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU T 65 " --> pdb=" O ARG T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 110 removed outlier: 3.549A pdb=" N MET T 86 " --> pdb=" O SER T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 113 through 145 removed outlier: 3.905A pdb=" N ALA T 117 " --> pdb=" O ASP T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 151 Processing helix chain 'U' and resid 4 through 35 removed outlier: 3.542A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 65 removed outlier: 3.608A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU U 65 " --> pdb=" O ARG U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 110 Processing helix chain 'U' and resid 113 through 145 removed outlier: 3.903A pdb=" N ALA U 117 " --> pdb=" O ASP U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 151 Processing helix chain 'V' and resid 4 through 35 removed outlier: 3.541A pdb=" N ILE V 8 " --> pdb=" O ASP V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 65 Processing helix chain 'V' and resid 82 through 111 Processing helix chain 'V' and resid 113 through 145 removed outlier: 3.711A pdb=" N ALA V 117 " --> pdb=" O ASP V 113 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 145 through 151 Processing helix chain 'W' and resid 4 through 36 removed outlier: 3.601A pdb=" N GLY W 36 " --> pdb=" O GLN W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 65 removed outlier: 3.682A pdb=" N ALA W 41 " --> pdb=" O TRP W 37 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS W 42 " --> pdb=" O THR W 38 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 110 removed outlier: 3.553A pdb=" N MET W 86 " --> pdb=" O SER W 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 145 removed outlier: 3.867A pdb=" N ALA W 117 " --> pdb=" O ASP W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 151 Processing helix chain 'X' and resid 4 through 35 Processing helix chain 'X' and resid 37 through 65 removed outlier: 3.570A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 110 removed outlier: 3.574A pdb=" N MET X 86 " --> pdb=" O SER X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 145 removed outlier: 3.879A pdb=" N ALA X 117 " --> pdb=" O ASP X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 151 2579 hydrogen bonds defined for protein. 7737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.42 Time building geometry restraints manager: 3.51 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.290 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.666 31999 Z= 0.211 Angle : 0.618 31.860 43354 Z= 0.323 Chirality : 0.033 0.172 4806 Planarity : 0.004 0.202 5596 Dihedral : 15.053 88.377 11862 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.11 (0.13), residues: 3724 helix: 3.83 (0.08), residues: 2999 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG R 45 TYR 0.047 0.001 TYR T 71 PHE 0.062 0.003 PHE F 49 TRP 0.013 0.001 TRP H 37 HIS 0.003 0.001 HIS U 54 Details of bonding type rmsd covalent geometry : bond 0.00317 (31968) covalent geometry : angle 0.61805 (43354) hydrogen bonds : bond 0.13535 ( 2579) hydrogen bonds : angle 4.25600 ( 7737) Misc. bond : bond 0.25639 ( 31) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 712 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 MET cc_start: 0.5264 (mtm) cc_final: 0.5010 (mtm) REVERT: L 129 HIS cc_start: 0.7173 (m-70) cc_final: 0.6953 (m90) REVERT: S 146 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8137 (mm-30) outliers start: 0 outliers final: 0 residues processed: 712 average time/residue: 0.6751 time to fit residues: 559.6542 Evaluate side-chains 655 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.0170 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 9.9990 overall best weight: 1.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 HIS D 156 GLN ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 156 GLN T 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.151870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.146237 restraints weight = 25598.116| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 0.31 r_work: 0.3366 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.488 31999 Z= 0.193 Angle : 0.554 12.270 43354 Z= 0.267 Chirality : 0.033 0.150 4806 Planarity : 0.003 0.085 5596 Dihedral : 6.910 84.635 4204 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.72 % Allowed : 7.24 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.47 (0.13), residues: 3724 helix: 4.03 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.59 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 45 TYR 0.043 0.001 TYR T 71 PHE 0.038 0.002 PHE F 49 TRP 0.010 0.001 TRP H 37 HIS 0.004 0.001 HIS Q 129 Details of bonding type rmsd covalent geometry : bond 0.00341 (31968) covalent geometry : angle 0.55362 (43354) hydrogen bonds : bond 0.10570 ( 2579) hydrogen bonds : angle 3.64267 ( 7737) Misc. bond : bond 0.15276 ( 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 712 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 655 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 66 ASP cc_start: 0.7954 (t70) cc_final: 0.7591 (t0) REVERT: L 129 HIS cc_start: 0.7629 (m-70) cc_final: 0.7421 (m90) REVERT: L 155 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7715 (mt-10) REVERT: Q 66 ASP cc_start: 0.8230 (t0) cc_final: 0.7963 (t0) REVERT: S 66 ASP cc_start: 0.8245 (t0) cc_final: 0.7997 (t0) REVERT: S 146 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8439 (mm-30) REVERT: W 66 ASP cc_start: 0.8264 (t0) cc_final: 0.8005 (t0) outliers start: 57 outliers final: 2 residues processed: 660 average time/residue: 0.7097 time to fit residues: 541.4939 Evaluate side-chains 645 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 643 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain W residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 30.0000 chunk 162 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 156 GLN H 54 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.134923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.127378 restraints weight = 23595.593| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 0.40 r_work: 0.3168 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.489 31999 Z= 0.251 Angle : 0.651 24.150 43354 Z= 0.314 Chirality : 0.036 0.364 4806 Planarity : 0.004 0.073 5596 Dihedral : 7.134 84.612 4204 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.20 % Allowed : 8.03 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.33 (0.13), residues: 3724 helix: 3.82 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.02 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 45 TYR 0.043 0.002 TYR T 71 PHE 0.036 0.003 PHE O 120 TRP 0.005 0.002 TRP C 37 HIS 0.005 0.001 HIS Q 129 Details of bonding type rmsd covalent geometry : bond 0.00463 (31968) covalent geometry : angle 0.65108 (43354) hydrogen bonds : bond 0.13897 ( 2579) hydrogen bonds : angle 3.89024 ( 7737) Misc. bond : bond 0.17398 ( 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 838 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 765 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8460 (mt) REVERT: C 4 ASP cc_start: 0.7577 (m-30) cc_final: 0.7340 (t70) REVERT: C 68 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8410 (mt) REVERT: D 4 ASP cc_start: 0.7583 (m-30) cc_final: 0.7346 (t70) REVERT: E 68 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8447 (mt) REVERT: E 81 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: F 4 ASP cc_start: 0.7521 (m-30) cc_final: 0.7272 (t70) REVERT: G 81 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7784 (mt0) REVERT: H 68 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8456 (mt) REVERT: I 81 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7800 (mt0) REVERT: J 68 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8413 (mt) REVERT: L 66 ASP cc_start: 0.8225 (t70) cc_final: 0.7740 (t0) REVERT: L 81 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: M 66 ASP cc_start: 0.8397 (t70) cc_final: 0.7960 (t0) REVERT: N 4 ASP cc_start: 0.7537 (m-30) cc_final: 0.7325 (t70) REVERT: N 66 ASP cc_start: 0.8413 (t0) cc_final: 0.8077 (t0) REVERT: N 68 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8432 (mt) REVERT: O 68 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8508 (mt) REVERT: P 68 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8449 (mt) REVERT: Q 66 ASP cc_start: 0.8459 (t0) cc_final: 0.8062 (t0) REVERT: Q 68 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8442 (mt) REVERT: Q 81 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7919 (mt0) REVERT: R 68 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8419 (mt) REVERT: R 81 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7524 (mt0) REVERT: S 4 ASP cc_start: 0.7568 (m-30) cc_final: 0.7353 (t70) REVERT: S 66 ASP cc_start: 0.8427 (t0) cc_final: 0.8046 (t0) REVERT: S 68 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8457 (mt) REVERT: U 81 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7852 (mt0) REVERT: V 66 ASP cc_start: 0.7972 (t0) cc_final: 0.7657 (t0) REVERT: W 4 ASP cc_start: 0.7532 (m-30) cc_final: 0.7308 (t70) REVERT: W 66 ASP cc_start: 0.8500 (t0) cc_final: 0.8119 (t0) REVERT: W 68 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8470 (mt) REVERT: X 4 ASP cc_start: 0.7574 (m-30) cc_final: 0.7352 (t70) REVERT: X 66 ASP cc_start: 0.8432 (t0) cc_final: 0.7974 (t0) outliers start: 73 outliers final: 5 residues processed: 775 average time/residue: 0.7398 time to fit residues: 659.8655 Evaluate side-chains 779 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 755 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 68 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 272 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 325 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 264 optimal weight: 9.9990 chunk 278 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 336 optimal weight: 0.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3374 r_free = 0.3374 target = 0.133513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.125973 restraints weight = 23629.894| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 0.40 r_work: 0.3152 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.423 31999 Z= 0.253 Angle : 0.646 23.202 43354 Z= 0.315 Chirality : 0.037 0.427 4806 Planarity : 0.004 0.069 5596 Dihedral : 7.330 89.435 4204 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.63 % Allowed : 10.80 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.19 (0.13), residues: 3724 helix: 3.73 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.13 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 45 TYR 0.043 0.002 TYR T 71 PHE 0.020 0.002 PHE K 120 TRP 0.005 0.002 TRP C 37 HIS 0.007 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00466 (31968) covalent geometry : angle 0.64568 (43354) hydrogen bonds : bond 0.14090 ( 2579) hydrogen bonds : angle 3.89088 ( 7737) Misc. bond : bond 0.16495 ( 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 859 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 772 time to evaluate : 1.172 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: B 81 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: C 4 ASP cc_start: 0.7556 (m-30) cc_final: 0.7348 (t70) REVERT: D 4 ASP cc_start: 0.7606 (m-30) cc_final: 0.7375 (t70) REVERT: D 81 GLN cc_start: 0.8491 (mt0) cc_final: 0.8216 (mt0) REVERT: E 81 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: F 4 ASP cc_start: 0.7526 (m-30) cc_final: 0.7316 (t70) REVERT: F 52 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.7027 (mtt) REVERT: G 81 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7782 (mt0) REVERT: G 128 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: I 81 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: J 81 GLN cc_start: 0.8491 (mt0) cc_final: 0.8226 (mt0) REVERT: K 81 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7851 (mt0) REVERT: L 66 ASP cc_start: 0.8263 (t70) cc_final: 0.7746 (t0) REVERT: L 68 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8512 (mt) REVERT: L 81 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7900 (mt0) REVERT: M 35 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8513 (mtmm) REVERT: M 66 ASP cc_start: 0.8432 (t70) cc_final: 0.7947 (t0) REVERT: N 66 ASP cc_start: 0.8460 (t0) cc_final: 0.8046 (t0) REVERT: N 68 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8474 (mt) REVERT: N 81 GLN cc_start: 0.8470 (mt0) cc_final: 0.8196 (mt0) REVERT: O 35 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8401 (mtmm) REVERT: O 66 ASP cc_start: 0.8154 (t70) cc_final: 0.7688 (t0) REVERT: O 68 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8492 (mt) REVERT: P 81 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: Q 66 ASP cc_start: 0.8504 (t0) cc_final: 0.8070 (t0) REVERT: Q 68 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8443 (mt) REVERT: Q 81 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: R 81 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7603 (mt0) REVERT: S 66 ASP cc_start: 0.8473 (t0) cc_final: 0.8041 (t0) REVERT: S 68 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8454 (mt) REVERT: S 81 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: T 68 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8430 (mt) REVERT: U 81 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7869 (mt0) REVERT: V 66 ASP cc_start: 0.8073 (t0) cc_final: 0.7696 (t0) REVERT: V 68 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8504 (mt) REVERT: W 4 ASP cc_start: 0.7551 (m-30) cc_final: 0.7316 (t70) REVERT: W 68 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8475 (mt) REVERT: X 4 ASP cc_start: 0.7604 (m-30) cc_final: 0.7388 (t70) REVERT: X 35 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8470 (mtmm) REVERT: X 155 GLU cc_start: 0.7892 (tt0) cc_final: 0.7672 (tt0) outliers start: 87 outliers final: 14 residues processed: 787 average time/residue: 0.7096 time to fit residues: 645.5333 Evaluate side-chains 795 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 757 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 13 GLU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 35 LYS Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 81 GLN Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain X residue 35 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 84 optimal weight: 7.9990 chunk 343 optimal weight: 0.9980 chunk 251 optimal weight: 0.9990 chunk 243 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 357 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.134051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.126529 restraints weight = 23622.597| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 0.40 r_work: 0.3160 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.426 31999 Z= 0.248 Angle : 0.640 25.956 43354 Z= 0.308 Chirality : 0.037 0.455 4806 Planarity : 0.004 0.064 5596 Dihedral : 7.385 86.540 4204 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.17 % Allowed : 11.41 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.24 (0.13), residues: 3724 helix: 3.77 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.13 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG S 45 TYR 0.033 0.002 TYR T 71 PHE 0.014 0.002 PHE L 120 TRP 0.004 0.002 TRP P 37 HIS 0.007 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00457 (31968) covalent geometry : angle 0.64043 (43354) hydrogen bonds : bond 0.13820 ( 2579) hydrogen bonds : angle 3.85668 ( 7737) Misc. bond : bond 0.16483 ( 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 857 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 752 time to evaluate : 1.073 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: B 81 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: C 4 ASP cc_start: 0.7551 (m-30) cc_final: 0.7347 (t70) REVERT: C 81 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: D 4 ASP cc_start: 0.7577 (m-30) cc_final: 0.7374 (t70) REVERT: D 81 GLN cc_start: 0.8497 (mt0) cc_final: 0.8216 (mt0) REVERT: E 81 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: F 4 ASP cc_start: 0.7545 (m-30) cc_final: 0.7344 (t70) REVERT: G 81 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: I 81 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: J 81 GLN cc_start: 0.8459 (mt0) cc_final: 0.8199 (mt0) REVERT: K 81 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: L 66 ASP cc_start: 0.8357 (t70) cc_final: 0.7867 (t0) REVERT: L 81 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: M 66 ASP cc_start: 0.8444 (t70) cc_final: 0.7988 (t0) REVERT: N 66 ASP cc_start: 0.8446 (t0) cc_final: 0.8049 (t0) REVERT: N 68 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8455 (mt) REVERT: N 81 GLN cc_start: 0.8464 (mt0) cc_final: 0.8189 (mt0) REVERT: O 35 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8439 (mtmm) REVERT: O 66 ASP cc_start: 0.8110 (t70) cc_final: 0.7637 (t0) REVERT: O 68 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8499 (mt) REVERT: P 81 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: Q 66 ASP cc_start: 0.8494 (t0) cc_final: 0.8090 (t0) REVERT: Q 81 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7883 (mt0) REVERT: R 81 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7586 (mt0) REVERT: S 66 ASP cc_start: 0.8441 (t0) cc_final: 0.8055 (t0) REVERT: S 81 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: T 68 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8475 (mt) REVERT: U 81 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7827 (mt0) REVERT: V 66 ASP cc_start: 0.8071 (t0) cc_final: 0.7709 (t0) REVERT: V 68 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8499 (mt) REVERT: X 4 ASP cc_start: 0.7602 (m-30) cc_final: 0.7396 (t70) REVERT: X 35 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8505 (mtmm) REVERT: X 68 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8440 (mt) outliers start: 105 outliers final: 22 residues processed: 776 average time/residue: 0.7246 time to fit residues: 649.0339 Evaluate side-chains 787 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 746 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 13 GLU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain S residue 13 GLU Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain S residue 81 GLN Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 35 LYS Chi-restraints excluded: chain X residue 68 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 134 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 142 optimal weight: 0.9980 chunk 308 optimal weight: 4.9990 chunk 344 optimal weight: 0.0970 chunk 317 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 238 optimal weight: 0.7980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.151615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.144583 restraints weight = 24310.126| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 0.40 r_work: 0.3388 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.473 31999 Z= 0.176 Angle : 0.562 28.789 43354 Z= 0.258 Chirality : 0.033 0.346 4806 Planarity : 0.003 0.038 5596 Dihedral : 7.397 89.857 4204 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.81 % Allowed : 13.46 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.67 (0.13), residues: 3724 helix: 4.18 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.58 (0.19), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 53 TYR 0.016 0.001 TYR T 71 PHE 0.023 0.001 PHE F 49 TRP 0.005 0.001 TRP H 37 HIS 0.003 0.001 HIS Q 129 Details of bonding type rmsd covalent geometry : bond 0.00317 (31968) covalent geometry : angle 0.56177 (43354) hydrogen bonds : bond 0.09529 ( 2579) hydrogen bonds : angle 3.44397 ( 7737) Misc. bond : bond 0.15503 ( 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 723 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 663 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7167 (t0) REVERT: D 1 MET cc_start: 0.4889 (mtm) cc_final: 0.4682 (mtt) REVERT: D 81 GLN cc_start: 0.8285 (mt0) cc_final: 0.8049 (mt0) REVERT: E 4 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.7133 (t0) REVERT: E 81 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: G 81 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: H 4 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7200 (t0) REVERT: I 4 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7170 (t0) REVERT: J 1 MET cc_start: 0.4415 (OUTLIER) cc_final: 0.3726 (mmm) REVERT: J 81 GLN cc_start: 0.8256 (mt0) cc_final: 0.8025 (mt0) REVERT: K 81 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: L 81 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7639 (mt0) REVERT: N 81 GLN cc_start: 0.8264 (mt0) cc_final: 0.8030 (mt0) REVERT: P 4 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7211 (t0) REVERT: P 81 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: R 4 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7161 (t0) REVERT: T 4 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.7075 (t70) REVERT: T 66 ASP cc_start: 0.8315 (t0) cc_final: 0.7996 (t0) REVERT: W 66 ASP cc_start: 0.8040 (t70) cc_final: 0.7684 (t0) outliers start: 60 outliers final: 10 residues processed: 684 average time/residue: 0.6979 time to fit residues: 553.7871 Evaluate side-chains 650 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 627 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 4 ASP Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain P residue 4 ASP Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 155 GLU Chi-restraints excluded: chain T residue 4 ASP Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 60 ASP Chi-restraints excluded: chain V residue 60 ASP Chi-restraints excluded: chain W residue 4 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 323 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.137561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.130069 restraints weight = 23844.312| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 0.40 r_work: 0.3210 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.541 31999 Z= 0.228 Angle : 0.624 28.934 43354 Z= 0.290 Chirality : 0.034 0.191 4806 Planarity : 0.004 0.143 5596 Dihedral : 7.596 89.448 4204 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.50 % Allowed : 14.27 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.51 (0.13), residues: 3724 helix: 3.96 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.05 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 45 TYR 0.024 0.002 TYR T 71 PHE 0.029 0.002 PHE F 49 TRP 0.004 0.001 TRP P 37 HIS 0.005 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00420 (31968) covalent geometry : angle 0.62389 (43354) hydrogen bonds : bond 0.12689 ( 2579) hydrogen bonds : angle 3.72381 ( 7737) Misc. bond : bond 0.17409 ( 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 796 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 713 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8415 (mt) REVERT: B 81 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: C 81 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7886 (mt0) REVERT: D 81 GLN cc_start: 0.8434 (mt0) cc_final: 0.8146 (mt0) REVERT: E 81 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7690 (mt0) REVERT: F 68 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8447 (mt) REVERT: G 81 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: I 4 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7367 (t0) REVERT: J 1 MET cc_start: 0.4555 (OUTLIER) cc_final: 0.4183 (mtt) REVERT: J 81 GLN cc_start: 0.8381 (mt0) cc_final: 0.8092 (mt0) REVERT: K 68 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8430 (mt) REVERT: K 81 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7786 (mt0) REVERT: L 66 ASP cc_start: 0.8218 (t70) cc_final: 0.7782 (t0) REVERT: N 81 GLN cc_start: 0.8392 (mt0) cc_final: 0.8096 (mt0) REVERT: P 81 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7691 (mt0) REVERT: S 4 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7421 (t0) outliers start: 83 outliers final: 6 residues processed: 734 average time/residue: 0.7107 time to fit residues: 603.8111 Evaluate side-chains 731 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 713 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain W residue 44 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 307 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 chunk 302 optimal weight: 8.9990 chunk 318 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.130312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.122704 restraints weight = 23508.106| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 0.40 r_work: 0.3107 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.547 31999 Z= 0.276 Angle : 0.727 35.406 43354 Z= 0.340 Chirality : 0.038 0.280 4806 Planarity : 0.004 0.092 5596 Dihedral : 7.717 89.971 4204 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.90 % Allowed : 14.30 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.13 (0.13), residues: 3724 helix: 3.69 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.13 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 73 TYR 0.032 0.002 TYR T 71 PHE 0.021 0.002 PHE F 49 TRP 0.008 0.002 TRP P 37 HIS 0.009 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00538 (31968) covalent geometry : angle 0.72667 (43354) hydrogen bonds : bond 0.15030 ( 2579) hydrogen bonds : angle 3.93697 ( 7737) Misc. bond : bond 0.17451 ( 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 825 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 762 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: C 4 ASP cc_start: 0.7619 (m-30) cc_final: 0.7372 (t70) REVERT: C 81 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: D 4 ASP cc_start: 0.7672 (m-30) cc_final: 0.7419 (t70) REVERT: D 81 GLN cc_start: 0.8490 (mt0) cc_final: 0.8212 (mt0) REVERT: E 66 ASP cc_start: 0.8544 (t0) cc_final: 0.8319 (t70) REVERT: E 81 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: F 4 ASP cc_start: 0.7643 (m-30) cc_final: 0.7400 (t70) REVERT: G 81 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: I 4 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7506 (t0) REVERT: J 66 ASP cc_start: 0.8634 (t0) cc_final: 0.8391 (t70) REVERT: J 81 GLN cc_start: 0.8460 (mt0) cc_final: 0.8189 (mt0) REVERT: K 81 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: L 66 ASP cc_start: 0.8352 (t70) cc_final: 0.7830 (t0) REVERT: M 66 ASP cc_start: 0.8476 (t70) cc_final: 0.7961 (t0) REVERT: N 81 GLN cc_start: 0.8460 (mt0) cc_final: 0.8178 (mt0) REVERT: O 66 ASP cc_start: 0.8345 (t70) cc_final: 0.7846 (t0) REVERT: P 81 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: Q 66 ASP cc_start: 0.8510 (t70) cc_final: 0.8046 (t0) REVERT: R 155 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7643 (tt0) REVERT: S 4 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7619 (t0) REVERT: S 66 ASP cc_start: 0.8452 (t70) cc_final: 0.8006 (t0) REVERT: T 66 ASP cc_start: 0.8624 (t0) cc_final: 0.8379 (t70) REVERT: V 66 ASP cc_start: 0.8243 (t0) cc_final: 0.7790 (t0) REVERT: W 4 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7390 (t70) REVERT: X 4 ASP cc_start: 0.7687 (m-30) cc_final: 0.7436 (t70) REVERT: X 35 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8581 (mtmm) outliers start: 63 outliers final: 15 residues processed: 786 average time/residue: 0.7280 time to fit residues: 659.7410 Evaluate side-chains 771 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 746 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain W residue 4 ASP Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 35 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 41 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 346 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 354 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 334 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.133961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.126356 restraints weight = 23417.072| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 0.40 r_work: 0.3157 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.571 31999 Z= 0.250 Angle : 0.728 38.038 43354 Z= 0.328 Chirality : 0.037 0.332 4806 Planarity : 0.004 0.077 5596 Dihedral : 7.565 89.210 4204 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.07 % Favored : 98.90 % Rotamer: Outliers : 1.90 % Allowed : 15.06 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.19 (0.13), residues: 3724 helix: 3.74 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.14 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 73 TYR 0.026 0.002 TYR T 71 PHE 0.031 0.002 PHE F 49 TRP 0.005 0.002 TRP Q 37 HIS 0.007 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00476 (31968) covalent geometry : angle 0.72796 (43354) hydrogen bonds : bond 0.13760 ( 2579) hydrogen bonds : angle 3.86996 ( 7737) Misc. bond : bond 0.17440 ( 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 807 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 744 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7860 (mt0) REVERT: C 4 ASP cc_start: 0.7546 (m-30) cc_final: 0.7307 (t70) REVERT: C 81 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: D 4 ASP cc_start: 0.7586 (m-30) cc_final: 0.7352 (t70) REVERT: D 81 GLN cc_start: 0.8436 (mt0) cc_final: 0.8163 (mt0) REVERT: E 81 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7708 (mt0) REVERT: G 81 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7712 (mt0) REVERT: I 4 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7449 (t0) REVERT: J 81 GLN cc_start: 0.8381 (mt0) cc_final: 0.8107 (mt0) REVERT: K 81 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7808 (mt0) REVERT: L 66 ASP cc_start: 0.8351 (t70) cc_final: 0.7868 (t0) REVERT: L 68 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8522 (mt) REVERT: M 66 ASP cc_start: 0.8425 (t70) cc_final: 0.7964 (t0) REVERT: N 66 ASP cc_start: 0.8383 (t70) cc_final: 0.7934 (t0) REVERT: N 68 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8443 (mt) REVERT: N 81 GLN cc_start: 0.8400 (mt0) cc_final: 0.8112 (mt0) REVERT: O 66 ASP cc_start: 0.8211 (t70) cc_final: 0.7720 (t0) REVERT: O 68 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8489 (mt) REVERT: P 81 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7713 (mt0) REVERT: Q 66 ASP cc_start: 0.8436 (t70) cc_final: 0.7971 (t0) REVERT: R 155 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7683 (tt0) REVERT: S 4 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7555 (t0) REVERT: S 66 ASP cc_start: 0.8399 (t70) cc_final: 0.7951 (t0) REVERT: S 81 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: V 66 ASP cc_start: 0.8193 (t70) cc_final: 0.7781 (t0) REVERT: V 68 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8476 (mt) REVERT: W 4 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7299 (t70) REVERT: X 35 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8515 (mtmm) outliers start: 63 outliers final: 13 residues processed: 765 average time/residue: 0.7263 time to fit residues: 641.4494 Evaluate side-chains 764 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 736 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain S residue 81 GLN Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain W residue 4 ASP Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 35 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 56 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 326 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.145034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.137737 restraints weight = 23869.180| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 0.40 r_work: 0.3302 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.668 31999 Z= 0.199 Angle : 0.680 37.930 43354 Z= 0.294 Chirality : 0.033 0.316 4806 Planarity : 0.003 0.063 5596 Dihedral : 7.388 88.663 4204 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.91 % Allowed : 16.14 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.61 (0.13), residues: 3724 helix: 4.03 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.02 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 53 TYR 0.016 0.001 TYR T 71 PHE 0.023 0.001 PHE F 49 TRP 0.004 0.001 TRP H 37 HIS 0.004 0.001 HIS X 54 Details of bonding type rmsd covalent geometry : bond 0.00375 (31968) covalent geometry : angle 0.68024 (43354) hydrogen bonds : bond 0.10788 ( 2579) hydrogen bonds : angle 3.64815 ( 7737) Misc. bond : bond 0.17789 ( 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 691 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 661 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7805 (mt0) REVERT: D 81 GLN cc_start: 0.8384 (mt0) cc_final: 0.8114 (mt0) REVERT: G 81 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: I 4 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7295 (t0) REVERT: J 81 GLN cc_start: 0.8307 (mt0) cc_final: 0.8041 (mt0) REVERT: K 81 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7719 (mt0) REVERT: L 66 ASP cc_start: 0.8066 (t70) cc_final: 0.7693 (t0) REVERT: N 66 ASP cc_start: 0.8150 (t70) cc_final: 0.7799 (t0) REVERT: N 81 GLN cc_start: 0.8303 (mt0) cc_final: 0.8040 (mt0) REVERT: P 4 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7317 (t0) REVERT: P 81 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7658 (mt0) REVERT: Q 66 ASP cc_start: 0.8209 (t70) cc_final: 0.7842 (t0) REVERT: R 4 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7260 (t0) REVERT: R 155 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7628 (tt0) REVERT: S 4 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7340 (t0) REVERT: S 66 ASP cc_start: 0.8158 (t70) cc_final: 0.7800 (t0) REVERT: W 66 ASP cc_start: 0.8158 (t70) cc_final: 0.7750 (t0) outliers start: 30 outliers final: 13 residues processed: 681 average time/residue: 0.6983 time to fit residues: 552.2850 Evaluate side-chains 677 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 656 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain P residue 4 ASP Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain T residue 82 SER Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain W residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 247 optimal weight: 0.0370 chunk 151 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 338 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 225 optimal weight: 20.0000 overall best weight: 1.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.146213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.138946 restraints weight = 24090.102| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 0.40 r_work: 0.3318 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.667 31999 Z= 0.200 Angle : 0.692 41.596 43354 Z= 0.290 Chirality : 0.034 0.426 4806 Planarity : 0.003 0.055 5596 Dihedral : 7.407 89.567 4204 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 0.97 % Favored : 99.01 % Rotamer: Outliers : 0.94 % Allowed : 17.32 % Favored : 81.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.69 (0.13), residues: 3724 helix: 4.09 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.00 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 100 TYR 0.015 0.001 TYR T 71 PHE 0.030 0.001 PHE F 49 TRP 0.004 0.001 TRP O 37 HIS 0.003 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00381 (31968) covalent geometry : angle 0.69206 (43354) hydrogen bonds : bond 0.10580 ( 2579) hydrogen bonds : angle 3.61767 ( 7737) Misc. bond : bond 0.18746 ( 31) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11779.19 seconds wall clock time: 200 minutes 30.93 seconds (12030.93 seconds total)