Starting phenix.real_space_refine on Wed May 28 06:23:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6f_33639/05_2025/7y6f_33639_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6f_33639/05_2025/7y6f_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_33639/05_2025/7y6f_33639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6f_33639/05_2025/7y6f_33639.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6f_33639/05_2025/7y6f_33639_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6f_33639/05_2025/7y6f_33639_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31427 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1280 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "P" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.06, per 1000 atoms: 0.54 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: 7.89 Conformation dependent library (CDL) restraints added in 3.4 seconds 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7256 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 83.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 Processing helix chain 'A' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 110 removed outlier: 3.534A pdb=" N MET A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 145 removed outlier: 3.876A pdb=" N ALA A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'B' and resid 4 through 36 Processing helix chain 'B' and resid 37 through 65 removed outlier: 3.614A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 110 Processing helix chain 'B' and resid 113 through 145 removed outlier: 3.888A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'C' and resid 4 through 35 Processing helix chain 'C' and resid 37 through 65 removed outlier: 3.500A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 110 Processing helix chain 'C' and resid 113 through 145 removed outlier: 3.900A pdb=" N ALA C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'D' and resid 4 through 36 Processing helix chain 'D' and resid 37 through 65 removed outlier: 3.568A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 110 Processing helix chain 'D' and resid 113 through 145 removed outlier: 3.910A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'E' and resid 4 through 35 Processing helix chain 'E' and resid 37 through 65 removed outlier: 3.515A pdb=" N LEU E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 110 Processing helix chain 'E' and resid 113 through 145 removed outlier: 3.872A pdb=" N ALA E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'F' and resid 4 through 36 removed outlier: 3.511A pdb=" N GLY F 36 " --> pdb=" O GLN F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 65 removed outlier: 3.520A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 110 removed outlier: 3.572A pdb=" N MET F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 145 removed outlier: 3.869A pdb=" N ALA F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 151 Processing helix chain 'G' and resid 4 through 35 Processing helix chain 'G' and resid 37 through 65 removed outlier: 3.526A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 110 Processing helix chain 'G' and resid 113 through 145 removed outlier: 3.876A pdb=" N ALA G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'H' and resid 4 through 35 Processing helix chain 'H' and resid 37 through 65 removed outlier: 3.508A pdb=" N LEU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 110 Processing helix chain 'H' and resid 113 through 145 removed outlier: 3.906A pdb=" N ALA H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 151 Processing helix chain 'I' and resid 4 through 35 Processing helix chain 'I' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 110 Processing helix chain 'I' and resid 113 through 145 removed outlier: 3.885A pdb=" N ALA I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 151 Processing helix chain 'J' and resid 4 through 36 removed outlier: 3.539A pdb=" N GLY J 36 " --> pdb=" O GLN J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 65 removed outlier: 3.507A pdb=" N ALA J 41 " --> pdb=" O TRP J 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 65 " --> pdb=" O ARG J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 110 Processing helix chain 'J' and resid 113 through 145 removed outlier: 3.872A pdb=" N ALA J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 151 Processing helix chain 'K' and resid 4 through 35 Processing helix chain 'K' and resid 37 through 65 removed outlier: 3.616A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing helix chain 'K' and resid 113 through 145 removed outlier: 3.887A pdb=" N ALA K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'L' and resid 4 through 35 removed outlier: 3.510A pdb=" N LYS L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 65 removed outlier: 3.626A pdb=" N ALA L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 111 Processing helix chain 'L' and resid 113 through 145 removed outlier: 3.791A pdb=" N ALA L 117 " --> pdb=" O ASP L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'M' and resid 4 through 35 removed outlier: 3.503A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 65 Processing helix chain 'M' and resid 82 through 111 removed outlier: 3.506A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 145 removed outlier: 3.708A pdb=" N ALA M 117 " --> pdb=" O ASP M 113 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP M 126 " --> pdb=" O ALA M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 151 Processing helix chain 'N' and resid 4 through 36 Processing helix chain 'N' and resid 37 through 65 Processing helix chain 'N' and resid 82 through 110 Processing helix chain 'N' and resid 113 through 145 removed outlier: 3.874A pdb=" N ALA N 117 " --> pdb=" O ASP N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 151 Processing helix chain 'O' and resid 4 through 35 Processing helix chain 'O' and resid 37 through 65 Processing helix chain 'O' and resid 82 through 111 removed outlier: 3.539A pdb=" N LYS O 111 " --> pdb=" O VAL O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 145 removed outlier: 3.823A pdb=" N ALA O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 151 Processing helix chain 'P' and resid 4 through 36 Processing helix chain 'P' and resid 37 through 65 removed outlier: 3.611A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU P 65 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 110 Processing helix chain 'P' and resid 113 through 145 removed outlier: 3.899A pdb=" N ALA P 117 " --> pdb=" O ASP P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 151 Processing helix chain 'Q' and resid 4 through 35 Processing helix chain 'Q' and resid 37 through 65 removed outlier: 3.522A pdb=" N ALA Q 41 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 110 Processing helix chain 'Q' and resid 113 through 145 removed outlier: 3.902A pdb=" N ALA Q 117 " --> pdb=" O ASP Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 151 Processing helix chain 'R' and resid 4 through 36 Processing helix chain 'R' and resid 37 through 65 removed outlier: 3.572A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 110 removed outlier: 3.544A pdb=" N MET R 86 " --> pdb=" O SER R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 145 removed outlier: 3.873A pdb=" N ALA R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 151 Processing helix chain 'S' and resid 4 through 36 removed outlier: 3.508A pdb=" N GLY S 36 " --> pdb=" O GLN S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 65 removed outlier: 3.519A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 110 removed outlier: 3.569A pdb=" N MET S 86 " --> pdb=" O SER S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 145 removed outlier: 3.860A pdb=" N ALA S 117 " --> pdb=" O ASP S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 151 Processing helix chain 'T' and resid 4 through 35 Processing helix chain 'T' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU T 65 " --> pdb=" O ARG T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 110 removed outlier: 3.549A pdb=" N MET T 86 " --> pdb=" O SER T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 113 through 145 removed outlier: 3.905A pdb=" N ALA T 117 " --> pdb=" O ASP T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 151 Processing helix chain 'U' and resid 4 through 35 removed outlier: 3.542A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 65 removed outlier: 3.608A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU U 65 " --> pdb=" O ARG U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 110 Processing helix chain 'U' and resid 113 through 145 removed outlier: 3.903A pdb=" N ALA U 117 " --> pdb=" O ASP U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 151 Processing helix chain 'V' and resid 4 through 35 removed outlier: 3.541A pdb=" N ILE V 8 " --> pdb=" O ASP V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 65 Processing helix chain 'V' and resid 82 through 111 Processing helix chain 'V' and resid 113 through 145 removed outlier: 3.711A pdb=" N ALA V 117 " --> pdb=" O ASP V 113 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 145 through 151 Processing helix chain 'W' and resid 4 through 36 removed outlier: 3.601A pdb=" N GLY W 36 " --> pdb=" O GLN W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 65 removed outlier: 3.682A pdb=" N ALA W 41 " --> pdb=" O TRP W 37 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS W 42 " --> pdb=" O THR W 38 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 110 removed outlier: 3.553A pdb=" N MET W 86 " --> pdb=" O SER W 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 145 removed outlier: 3.867A pdb=" N ALA W 117 " --> pdb=" O ASP W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 151 Processing helix chain 'X' and resid 4 through 35 Processing helix chain 'X' and resid 37 through 65 removed outlier: 3.570A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 110 removed outlier: 3.574A pdb=" N MET X 86 " --> pdb=" O SER X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 145 removed outlier: 3.879A pdb=" N ALA X 117 " --> pdb=" O ASP X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 151 2579 hydrogen bonds defined for protein. 7737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.50 Time building geometry restraints manager: 8.89 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.070 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 60.840 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.110 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.13), residues: 3724 helix: 3.83 (0.08), residues: 2999 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 37 HIS 0.003 0.001 HIS U 54 PHE 0.062 0.003 PHE F 49 TYR 0.047 0.001 TYR T 71 ARG 0.019 0.000 ARG R 45 Details of bonding type rmsd hydrogen bonds : bond 0.13535 ( 2579) hydrogen bonds : angle 4.25600 ( 7737) covalent geometry : bond 0.00317 (31968) covalent geometry : angle 0.61805 (43354) Misc. bond : bond 0.25639 ( 31) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 712 time to evaluate : 3.463 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: 0.5011 (mtm) REVERT: L 129 HIS cc_start: 0.7173 (m-70) cc_final: 0.6954 (m90) REVERT: S 146 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8137 (mm-30) outliers start: 0 outliers final: 0 residues processed: 712 average time/residue: 1.4197 time to fit residues: 1188.0400 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 : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.7980 chunk 272 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 282 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 171 optimal weight: 0.0870 chunk 210 optimal weight: 9.9990 chunk 326 optimal weight: 7.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- 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** J 112 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 156 GLN Q 112 HIS T 70 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.162134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.156549 restraints weight = 25809.926| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 0.32 r_work: 0.3496 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.459 31999 Z= 0.165 Angle : 0.517 11.350 43354 Z= 0.247 Chirality : 0.032 0.132 4806 Planarity : 0.003 0.086 5596 Dihedral : 6.890 83.297 4204 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.94 % Allowed : 7.66 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.69 (0.13), residues: 3724 helix: 4.18 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.49 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 37 HIS 0.004 0.000 HIS Q 129 PHE 0.039 0.002 PHE F 49 TYR 0.041 0.001 TYR T 71 ARG 0.003 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.08735 ( 2579) hydrogen bonds : angle 3.45109 ( 7737) covalent geometry : bond 0.00292 (31968) covalent geometry : angle 0.51732 (43354) Misc. bond : bond 0.13943 ( 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 686 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 655 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7814 (mt-10) REVERT: L 155 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7842 (mt-10) REVERT: V 155 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7717 (mt-10) outliers start: 31 outliers final: 1 residues processed: 659 average time/residue: 1.4952 time to fit residues: 1154.0914 Evaluate side-chains 629 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 628 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 302 optimal weight: 6.9990 chunk 335 optimal weight: 30.0000 chunk 73 optimal weight: 0.9990 chunk 273 optimal weight: 0.9980 chunk 308 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 chunk 350 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 310 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 HIS ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 156 GLN T 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.156534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.150962 restraints weight = 25692.043| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 0.31 r_work: 0.3426 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.458 31999 Z= 0.176 Angle : 0.537 21.741 43354 Z= 0.250 Chirality : 0.032 0.117 4806 Planarity : 0.003 0.070 5596 Dihedral : 7.031 86.573 4204 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.90 % Allowed : 8.21 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.74 (0.13), residues: 3724 helix: 4.22 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.50 (0.19), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 37 HIS 0.003 0.001 HIS Q 129 PHE 0.024 0.002 PHE O 120 TYR 0.029 0.001 TYR T 71 ARG 0.003 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.09564 ( 2579) hydrogen bonds : angle 3.43284 ( 7737) covalent geometry : bond 0.00311 (31968) covalent geometry : angle 0.53713 (43354) Misc. bond : bond 0.16015 ( 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 704 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 641 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8160 (t0) cc_final: 0.7895 (t0) REVERT: B 81 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: C 66 ASP cc_start: 0.8189 (t0) cc_final: 0.7929 (t0) REVERT: F 81 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: H 66 ASP cc_start: 0.8176 (t0) cc_final: 0.7912 (t0) REVERT: L 155 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7675 (mt-10) REVERT: N 81 GLN cc_start: 0.8291 (mt0) cc_final: 0.8043 (mt0) REVERT: P 66 ASP cc_start: 0.8124 (t0) cc_final: 0.7876 (t0) REVERT: S 81 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7532 (mt0) outliers start: 63 outliers final: 5 residues processed: 646 average time/residue: 1.5079 time to fit residues: 1134.2706 Evaluate side-chains 632 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 624 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain S residue 81 GLN Chi-restraints excluded: chain V residue 60 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 71 optimal weight: 9.9990 chunk 324 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 chunk 176 optimal weight: 0.1980 chunk 355 optimal weight: 9.9990 chunk 333 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 290 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.147295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.139944 restraints weight = 24184.170| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 0.41 r_work: 0.3361 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.464 31999 Z= 0.190 Angle : 0.536 22.427 43354 Z= 0.257 Chirality : 0.032 0.119 4806 Planarity : 0.003 0.059 5596 Dihedral : 7.139 87.571 4204 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.63 % Allowed : 10.41 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.81 (0.13), residues: 3724 helix: 4.19 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.04 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 37 HIS 0.004 0.001 HIS Q 129 PHE 0.024 0.002 PHE O 120 TYR 0.029 0.001 TYR T 71 ARG 0.003 0.000 ARG S 45 Details of bonding type rmsd hydrogen bonds : bond 0.10589 ( 2579) hydrogen bonds : angle 3.51725 ( 7737) covalent geometry : bond 0.00334 (31968) covalent geometry : angle 0.53626 (43354) Misc. bond : bond 0.16322 ( 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 704 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 650 time to evaluate : 3.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 GLN cc_start: 0.8346 (mt0) cc_final: 0.8064 (mt0) REVERT: E 81 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: G 81 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: I 81 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: J 81 GLN cc_start: 0.8323 (mt0) cc_final: 0.8071 (mt0) REVERT: L 155 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7701 (mt-10) REVERT: M 1 MET cc_start: 0.5989 (mmp) cc_final: 0.5550 (mmm) REVERT: Q 81 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7773 (mt0) REVERT: S 81 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: U 81 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7729 (mt0) outliers start: 54 outliers final: 3 residues processed: 654 average time/residue: 1.5955 time to fit residues: 1215.1703 Evaluate side-chains 646 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 637 time to evaluate : 3.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain S residue 81 GLN Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain V residue 60 ASP 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 283 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 206 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.140259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.132670 restraints weight = 23897.927| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 0.41 r_work: 0.3242 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.434 31999 Z= 0.218 Angle : 0.607 25.563 43354 Z= 0.280 Chirality : 0.034 0.122 4806 Planarity : 0.003 0.056 5596 Dihedral : 7.267 87.611 4204 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.48 % Allowed : 11.50 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.66 (0.13), residues: 3724 helix: 4.05 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -1.95 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 37 HIS 0.004 0.001 HIS Q 129 PHE 0.020 0.002 PHE F 49 TYR 0.032 0.002 TYR T 71 ARG 0.003 0.000 ARG S 45 Details of bonding type rmsd hydrogen bonds : bond 0.12237 ( 2579) hydrogen bonds : angle 3.66673 ( 7737) covalent geometry : bond 0.00396 (31968) covalent geometry : angle 0.60668 (43354) Misc. bond : bond 0.16146 ( 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 728 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 679 time to evaluate : 3.526 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: 0.8234 (OUTLIER) cc_final: 0.7790 (mt0) REVERT: D 81 GLN cc_start: 0.8422 (mt0) cc_final: 0.8129 (mt0) REVERT: E 68 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8432 (mt) REVERT: E 81 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7649 (mt0) REVERT: G 81 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: I 81 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: J 81 GLN cc_start: 0.8398 (mt0) cc_final: 0.8052 (mt0) REVERT: L 66 ASP cc_start: 0.8118 (t70) cc_final: 0.7735 (t0) REVERT: M 1 MET cc_start: 0.6333 (mmp) cc_final: 0.5787 (mmm) REVERT: N 66 ASP cc_start: 0.8228 (t0) cc_final: 0.7874 (t0) REVERT: N 81 GLN cc_start: 0.8370 (mt0) cc_final: 0.8073 (mt0) REVERT: P 81 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: Q 66 ASP cc_start: 0.8273 (t0) cc_final: 0.7907 (t0) REVERT: Q 81 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: S 66 ASP cc_start: 0.8253 (t0) cc_final: 0.7902 (t0) REVERT: T 68 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8376 (mt) REVERT: U 68 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8434 (mt) REVERT: W 66 ASP cc_start: 0.8298 (t0) cc_final: 0.7948 (t0) outliers start: 49 outliers final: 3 residues processed: 685 average time/residue: 1.5106 time to fit residues: 1207.2329 Evaluate side-chains 690 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 678 time to evaluate : 3.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain W residue 44 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 207 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 277 optimal weight: 0.2980 chunk 345 optimal weight: 2.9990 chunk 278 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 354 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 339 optimal weight: 5.9990 chunk 254 optimal weight: 0.9980 chunk 292 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.139970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.132366 restraints weight = 23982.377| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 0.41 r_work: 0.3233 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.437 31999 Z= 0.219 Angle : 0.619 30.558 43354 Z= 0.289 Chirality : 0.034 0.121 4806 Planarity : 0.003 0.050 5596 Dihedral : 7.383 86.984 4204 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.69 % Allowed : 11.68 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.60 (0.13), residues: 3724 helix: 4.02 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -1.99 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 37 HIS 0.004 0.001 HIS Q 129 PHE 0.027 0.002 PHE F 49 TYR 0.030 0.002 TYR T 71 ARG 0.004 0.000 ARG T 73 Details of bonding type rmsd hydrogen bonds : bond 0.12265 ( 2579) hydrogen bonds : angle 3.68124 ( 7737) covalent geometry : bond 0.00395 (31968) covalent geometry : angle 0.61884 (43354) Misc. bond : bond 0.15902 ( 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 747 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 691 time to evaluate : 3.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4655 (OUTLIER) cc_final: 0.4292 (mmm) REVERT: B 68 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8419 (mt) REVERT: B 81 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7709 (mt0) REVERT: D 68 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8427 (mt) REVERT: D 81 GLN cc_start: 0.8423 (mt0) cc_final: 0.8162 (mt0) REVERT: E 81 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: F 1 MET cc_start: 0.4592 (OUTLIER) cc_final: 0.3961 (mmm) REVERT: F 68 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8466 (mt) REVERT: G 68 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8443 (mt) REVERT: G 81 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: I 68 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8437 (mt) REVERT: I 81 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: J 81 GLN cc_start: 0.8388 (mt0) cc_final: 0.8069 (mt0) REVERT: K 68 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8429 (mt) REVERT: K 81 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: L 66 ASP cc_start: 0.8191 (t70) cc_final: 0.7792 (t0) REVERT: M 1 MET cc_start: 0.6499 (mmp) cc_final: 0.5936 (mmm) REVERT: N 1 MET cc_start: 0.4642 (OUTLIER) cc_final: 0.3981 (mmm) REVERT: N 66 ASP cc_start: 0.8262 (t0) cc_final: 0.7897 (t0) REVERT: N 81 GLN cc_start: 0.8401 (mt0) cc_final: 0.8100 (mt0) REVERT: P 81 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7659 (mt0) REVERT: Q 66 ASP cc_start: 0.8305 (t0) cc_final: 0.7952 (t0) REVERT: Q 81 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: R 68 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8424 (mt) REVERT: R 155 GLU cc_start: 0.7784 (tt0) cc_final: 0.7582 (tt0) REVERT: S 66 ASP cc_start: 0.8287 (t0) cc_final: 0.7936 (t0) REVERT: T 68 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8433 (mt) REVERT: U 68 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8458 (mt) REVERT: W 66 ASP cc_start: 0.8337 (t0) cc_final: 0.7984 (t0) outliers start: 56 outliers final: 7 residues processed: 696 average time/residue: 1.5025 time to fit residues: 1226.6941 Evaluate side-chains 708 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 682 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 81 GLN 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 M residue 93 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain W residue 44 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 336 optimal weight: 10.0000 chunk 284 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 321 optimal weight: 0.0870 chunk 351 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 241 optimal weight: 0.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.138699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.131068 restraints weight = 23779.743| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 0.41 r_work: 0.3218 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.468 31999 Z= 0.225 Angle : 0.613 24.547 43354 Z= 0.287 Chirality : 0.034 0.157 4806 Planarity : 0.003 0.061 5596 Dihedral : 7.412 89.824 4204 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.60 % Allowed : 12.52 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.53 (0.13), residues: 3724 helix: 3.97 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.02 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 37 HIS 0.004 0.001 HIS H 54 PHE 0.023 0.002 PHE F 49 TYR 0.030 0.002 TYR T 71 ARG 0.004 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.12566 ( 2579) hydrogen bonds : angle 3.71252 ( 7737) covalent geometry : bond 0.00405 (31968) covalent geometry : angle 0.61321 (43354) Misc. bond : bond 0.16145 ( 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 760 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 707 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4724 (OUTLIER) cc_final: 0.4290 (mmm) REVERT: A 68 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8472 (mt) REVERT: B 68 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8411 (mt) REVERT: B 81 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: C 68 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8412 (mt) REVERT: D 68 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8420 (mt) REVERT: D 81 GLN cc_start: 0.8486 (mt0) cc_final: 0.8169 (mt0) REVERT: E 68 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8446 (mt) REVERT: E 81 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: F 1 MET cc_start: 0.4685 (OUTLIER) cc_final: 0.4042 (mmm) REVERT: F 68 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8458 (mt) REVERT: G 68 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8441 (mt) REVERT: G 81 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7694 (mt0) REVERT: H 1 MET cc_start: 0.4648 (OUTLIER) cc_final: 0.4236 (mmm) REVERT: H 68 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8455 (mt) REVERT: I 68 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8431 (mt) REVERT: I 81 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: J 68 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8417 (mt) REVERT: J 81 GLN cc_start: 0.8364 (mt0) cc_final: 0.8043 (mt0) REVERT: K 68 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8428 (mt) REVERT: K 81 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7724 (mt0) REVERT: L 66 ASP cc_start: 0.8209 (t70) cc_final: 0.7793 (t0) REVERT: M 1 MET cc_start: 0.6323 (mmp) cc_final: 0.5966 (mmm) REVERT: N 1 MET cc_start: 0.4560 (OUTLIER) cc_final: 0.4005 (mmm) REVERT: N 66 ASP cc_start: 0.8243 (t0) cc_final: 0.7880 (t0) REVERT: N 81 GLN cc_start: 0.8391 (mt0) cc_final: 0.8084 (mt0) REVERT: P 68 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8453 (mt) REVERT: P 81 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: Q 81 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: Q 86 MET cc_start: 0.7835 (mtt) cc_final: 0.7589 (mtt) REVERT: R 68 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8417 (mt) REVERT: R 155 GLU cc_start: 0.7844 (tt0) cc_final: 0.7643 (tt0) REVERT: S 66 ASP cc_start: 0.8278 (t0) cc_final: 0.7916 (t0) REVERT: T 68 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8428 (mt) REVERT: U 68 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8449 (mt) REVERT: W 66 ASP cc_start: 0.8334 (t0) cc_final: 0.7969 (t0) REVERT: X 35 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8366 (mtmm) outliers start: 53 outliers final: 6 residues processed: 713 average time/residue: 1.4956 time to fit residues: 1245.1962 Evaluate side-chains 740 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 707 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D 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 1 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain J residue 68 LEU 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 N residue 1 MET Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 35 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 46 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 327 optimal weight: 4.9990 chunk 333 optimal weight: 0.0020 chunk 65 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 280 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 overall best weight: 2.3594 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.143958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.136613 restraints weight = 23888.279| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 0.40 r_work: 0.3281 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.561 31999 Z= 0.204 Angle : 0.613 35.351 43354 Z= 0.281 Chirality : 0.033 0.214 4806 Planarity : 0.003 0.051 5596 Dihedral : 7.439 89.209 4204 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.69 % Allowed : 13.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.67 (0.13), residues: 3724 helix: 4.06 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -1.95 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 37 HIS 0.004 0.001 HIS Q 129 PHE 0.030 0.001 PHE F 49 TYR 0.025 0.001 TYR T 71 ARG 0.003 0.000 ARG T 73 Details of bonding type rmsd hydrogen bonds : bond 0.11334 ( 2579) hydrogen bonds : angle 3.61994 ( 7737) covalent geometry : bond 0.00367 (31968) covalent geometry : angle 0.61297 (43354) Misc. bond : bond 0.16919 ( 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 712 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 656 time to evaluate : 3.799 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: A 1 MET cc_start: 0.4593 (OUTLIER) cc_final: 0.4126 (mmm) REVERT: A 81 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7394 (mt0) REVERT: B 81 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: C 35 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8184 (mtmm) REVERT: C 81 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: D 81 GLN cc_start: 0.8385 (mt0) cc_final: 0.8085 (mt0) REVERT: E 68 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8434 (mt) REVERT: E 81 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7679 (mt0) REVERT: F 1 MET cc_start: 0.4575 (OUTLIER) cc_final: 0.4007 (mmm) REVERT: G 68 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8435 (mt) REVERT: G 81 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: H 1 MET cc_start: 0.4641 (OUTLIER) cc_final: 0.4121 (mmm) REVERT: I 81 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: J 68 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8409 (mt) REVERT: J 81 GLN cc_start: 0.8337 (mt0) cc_final: 0.8003 (mt0) REVERT: K 81 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7730 (mt0) REVERT: L 66 ASP cc_start: 0.8093 (t70) cc_final: 0.7714 (t0) REVERT: L 81 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7743 (mt0) REVERT: M 1 MET cc_start: 0.6228 (mmp) cc_final: 0.5968 (mmm) REVERT: N 1 MET cc_start: 0.4471 (OUTLIER) cc_final: 0.3894 (mmm) REVERT: N 66 ASP cc_start: 0.8149 (t0) cc_final: 0.7795 (t0) REVERT: N 81 GLN cc_start: 0.8357 (mt0) cc_final: 0.8054 (mt0) REVERT: P 81 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7616 (mt0) REVERT: Q 66 ASP cc_start: 0.8119 (t70) cc_final: 0.7764 (t0) REVERT: Q 81 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: R 155 GLU cc_start: 0.7841 (tt0) cc_final: 0.7633 (tt0) REVERT: S 66 ASP cc_start: 0.8199 (t0) cc_final: 0.7849 (t0) REVERT: T 81 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: W 66 ASP cc_start: 0.8251 (t0) cc_final: 0.7925 (t0) outliers start: 56 outliers final: 6 residues processed: 664 average time/residue: 1.4751 time to fit residues: 1146.5093 Evaluate side-chains 678 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 653 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain T residue 81 GLN Chi-restraints excluded: chain W residue 44 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 88 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 96 optimal weight: 0.0270 chunk 82 optimal weight: 0.8980 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 245 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 303 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 overall best weight: 1.9442 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.147407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.140097 restraints weight = 24215.934| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 0.40 r_work: 0.3333 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.579 31999 Z= 0.191 Angle : 0.654 34.285 43354 Z= 0.280 Chirality : 0.033 0.301 4806 Planarity : 0.003 0.056 5596 Dihedral : 7.435 88.974 4204 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.33 % Allowed : 14.60 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.74 (0.13), residues: 3724 helix: 4.13 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.02 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 37 HIS 0.003 0.001 HIS Q 129 PHE 0.028 0.001 PHE F 49 TYR 0.017 0.001 TYR T 71 ARG 0.004 0.000 ARG J 73 Details of bonding type rmsd hydrogen bonds : bond 0.10470 ( 2579) hydrogen bonds : angle 3.55548 ( 7737) covalent geometry : bond 0.00349 (31968) covalent geometry : angle 0.65357 (43354) Misc. bond : bond 0.16886 ( 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 693 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 649 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7341 (mt0) REVERT: B 81 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: C 35 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8210 (mtmm) REVERT: D 81 GLN cc_start: 0.8309 (mt0) cc_final: 0.8029 (mt0) REVERT: E 81 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: G 1 MET cc_start: 0.6068 (mtm) cc_final: 0.5837 (mtm) REVERT: H 1 MET cc_start: 0.4579 (OUTLIER) cc_final: 0.4064 (mmm) REVERT: J 68 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8420 (mt) REVERT: J 81 GLN cc_start: 0.8274 (mt0) cc_final: 0.7955 (mt0) REVERT: K 1 MET cc_start: 0.6063 (mtm) cc_final: 0.5769 (mtm) REVERT: K 81 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7685 (mt0) REVERT: L 81 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: M 1 MET cc_start: 0.6316 (mmp) cc_final: 0.6009 (mmm) REVERT: N 81 GLN cc_start: 0.8290 (mt0) cc_final: 0.7964 (mt0) REVERT: R 155 GLU cc_start: 0.7874 (tt0) cc_final: 0.7658 (tt0) REVERT: T 81 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7354 (mt0) REVERT: U 1 MET cc_start: 0.6044 (mtm) cc_final: 0.5719 (mtt) outliers start: 44 outliers final: 5 residues processed: 660 average time/residue: 1.4722 time to fit residues: 1133.7095 Evaluate side-chains 656 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 642 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain T residue 81 GLN 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 33 optimal weight: 0.9980 chunk 279 optimal weight: 2.9990 chunk 307 optimal weight: 4.9990 chunk 354 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 342 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.145129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.137695 restraints weight = 24048.438| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 0.40 r_work: 0.3300 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.589 31999 Z= 0.206 Angle : 0.707 38.891 43354 Z= 0.296 Chirality : 0.033 0.300 4806 Planarity : 0.003 0.052 5596 Dihedral : 7.453 88.360 4204 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.10 % Favored : 98.87 % Rotamer: Outliers : 0.60 % Allowed : 15.39 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.69 (0.13), residues: 3724 helix: 4.07 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -1.93 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 37 HIS 0.003 0.001 HIS Q 129 PHE 0.037 0.001 PHE F 49 TYR 0.018 0.001 TYR T 71 ARG 0.004 0.000 ARG J 73 Details of bonding type rmsd hydrogen bonds : bond 0.10950 ( 2579) hydrogen bonds : angle 3.61675 ( 7737) covalent geometry : bond 0.00391 (31968) covalent geometry : angle 0.70680 (43354) Misc. bond : bond 0.17306 ( 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 665 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 645 time to evaluate : 3.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7354 (mt0) REVERT: C 35 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8236 (mtmm) REVERT: C 81 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7824 (mt0) REVERT: D 81 GLN cc_start: 0.8345 (mt0) cc_final: 0.8020 (mt0) REVERT: E 68 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8420 (mt) REVERT: E 81 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7675 (mt0) REVERT: H 1 MET cc_start: 0.4598 (OUTLIER) cc_final: 0.4088 (mmm) REVERT: J 68 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8416 (mt) REVERT: J 81 GLN cc_start: 0.8327 (mt0) cc_final: 0.8005 (mt0) REVERT: K 1 MET cc_start: 0.5945 (mtm) cc_final: 0.5648 (mtm) REVERT: K 81 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7698 (mt0) REVERT: N 81 GLN cc_start: 0.8245 (mt0) cc_final: 0.7932 (mt0) REVERT: R 155 GLU cc_start: 0.7854 (tt0) cc_final: 0.7641 (tt0) REVERT: U 1 MET cc_start: 0.5920 (mtm) cc_final: 0.5619 (mtm) outliers start: 20 outliers final: 7 residues processed: 651 average time/residue: 1.4985 time to fit residues: 1140.8056 Evaluate side-chains 661 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 646 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain T residue 66 ASP 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 195 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 247 optimal weight: 6.9990 chunk 324 optimal weight: 7.9990 chunk 273 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 268 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 125 optimal weight: 0.0980 chunk 209 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.159032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.153493 restraints weight = 25736.414| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 0.31 r_work: 0.3470 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.600 31999 Z= 0.169 Angle : 0.655 36.384 43354 Z= 0.273 Chirality : 0.032 0.182 4806 Planarity : 0.003 0.050 5596 Dihedral : 7.488 89.972 4204 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.36 % Allowed : 15.66 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.78 (0.13), residues: 3724 helix: 4.23 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.42 (0.19), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 37 HIS 0.004 0.000 HIS S 54 PHE 0.035 0.001 PHE F 49 TYR 0.012 0.001 TYR T 71 ARG 0.004 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.08749 ( 2579) hydrogen bonds : angle 3.43582 ( 7737) covalent geometry : bond 0.00312 (31968) covalent geometry : angle 0.65504 (43354) Misc. bond : bond 0.18037 ( 31) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23804.12 seconds wall clock time: 408 minutes 53.70 seconds (24533.70 seconds total)