Starting phenix.real_space_refine on Fri Mar 6 13:55:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k43_9913/03_2026/6k43_9913_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k43_9913/03_2026/6k43_9913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6k43_9913/03_2026/6k43_9913_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k43_9913/03_2026/6k43_9913_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k43_9913/03_2026/6k43_9913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k43_9913/03_2026/6k43_9913.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.030 sd= 1.242 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 36 7.16 5 S 96 5.16 5 C 20132 2.51 5 N 5428 2.21 5 O 6116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 146 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31808 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: "F" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.11, per 1000 atoms: 0.22 Number of scatterers: 31808 At special positions: 0 Unit cell: (132.09, 132.09, 132.09, 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 36 26.01 S 96 16.00 O 6116 8.00 N 5428 7.00 C 20132 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=29, symmetry=0 Number of additional bonds: simple=29, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.3 seconds 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7384 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 81.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 4 through 36 removed outlier: 3.513A pdb=" N ILE A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 65 removed outlier: 3.656A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 110 Processing helix chain 'A' and resid 113 through 145 removed outlier: 3.951A pdb=" N ALA A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'B' and resid 4 through 35 removed outlier: 3.517A pdb=" N ILE B 8 " --> pdb=" O ASP B 4 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 65 removed outlier: 3.552A pdb=" N ALA B 41 " --> pdb=" O TRP B 37 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 110 removed outlier: 3.783A pdb=" N MET B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 145 removed outlier: 3.989A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'C' and resid 4 through 36 removed outlier: 3.547A pdb=" N ILE C 8 " --> pdb=" O ASP C 4 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 65 removed outlier: 3.636A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 110 removed outlier: 3.763A pdb=" N MET C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 145 removed outlier: 3.969A pdb=" N ALA C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 145 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'D' and resid 4 through 35 removed outlier: 3.532A pdb=" N ILE D 8 " --> pdb=" O ASP D 4 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 65 removed outlier: 3.544A pdb=" N ALA D 41 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 110 removed outlier: 3.919A pdb=" N MET D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 145 removed outlier: 3.657A pdb=" N GLY D 145 " --> pdb=" O ILE D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'F' and resid 4 through 35 removed outlier: 3.540A pdb=" N ILE F 8 " --> pdb=" O ASP F 4 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 65 removed outlier: 3.828A pdb=" N ALA F 41 " --> pdb=" O TRP F 37 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 110 removed outlier: 3.904A pdb=" N MET F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 145 removed outlier: 3.973A pdb=" N ALA F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY F 145 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 151 Processing helix chain 'E' and resid 4 through 36 removed outlier: 3.513A pdb=" N ILE E 8 " --> pdb=" O ASP E 4 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 65 removed outlier: 3.683A pdb=" N LEU E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 110 removed outlier: 3.811A pdb=" N MET E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 144 removed outlier: 3.990A 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 'G' and resid 4 through 36 removed outlier: 3.514A pdb=" N ILE G 8 " --> pdb=" O ASP G 4 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY G 36 " --> pdb=" O GLN G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 65 removed outlier: 3.618A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 110 removed outlier: 3.830A pdb=" N MET G 86 " --> pdb=" O SER G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 144 removed outlier: 3.949A 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 36 removed outlier: 3.513A pdb=" N ILE H 8 " --> pdb=" O ASP H 4 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY H 36 " --> pdb=" O GLN H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 65 removed outlier: 3.654A pdb=" N LEU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 110 removed outlier: 3.823A pdb=" N MET H 86 " --> pdb=" O SER H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 145 removed outlier: 3.979A pdb=" N ALA H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY H 145 " --> pdb=" O ILE H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 151 Processing helix chain 'I' and resid 4 through 36 removed outlier: 3.541A pdb=" N ILE I 8 " --> pdb=" O ASP I 4 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS I 35 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY I 36 " --> pdb=" O GLN I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 65 removed outlier: 3.608A pdb=" N LEU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 110 removed outlier: 3.827A pdb=" N MET I 86 " --> pdb=" O SER I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 145 removed outlier: 3.986A pdb=" N ALA I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY I 145 " --> pdb=" O ILE I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 151 Processing helix chain 'J' and resid 4 through 36 removed outlier: 3.508A pdb=" N ILE J 8 " --> pdb=" O ASP J 4 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS J 35 " --> pdb=" O LEU J 31 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY J 36 " --> pdb=" O GLN J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 65 removed outlier: 3.651A pdb=" N LEU J 65 " --> pdb=" O ARG J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 110 removed outlier: 3.910A pdb=" N MET J 86 " --> pdb=" O SER J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 145 removed outlier: 3.652A pdb=" N GLY J 145 " --> pdb=" O ILE J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 151 Processing helix chain 'K' and resid 4 through 35 removed outlier: 3.502A pdb=" N ILE K 8 " --> pdb=" O ASP K 4 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 65 removed outlier: 3.500A pdb=" N ALA K 41 " --> pdb=" O TRP K 37 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 removed outlier: 3.786A pdb=" N MET K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 145 removed outlier: 3.818A pdb=" N ALA K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY K 145 " --> pdb=" O ILE K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'L' and resid 4 through 36 removed outlier: 3.560A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY L 36 " --> pdb=" O GLN L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 65 removed outlier: 3.629A pdb=" N LEU L 65 " --> pdb=" O ARG L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 110 removed outlier: 3.799A pdb=" N MET L 86 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 145 removed outlier: 3.966A pdb=" N ALA L 117 " --> pdb=" O ASP L 113 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY L 145 " --> pdb=" O ILE L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'M' and resid 4 through 36 removed outlier: 3.593A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS M 35 " --> pdb=" O LEU M 31 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY M 36 " --> pdb=" O GLN M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 65 removed outlier: 3.557A pdb=" N ALA M 41 " --> pdb=" O TRP M 37 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR M 43 " --> pdb=" O LYS M 39 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU M 65 " --> pdb=" O ARG M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 110 removed outlier: 3.917A pdb=" N MET M 86 " --> pdb=" O SER M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 145 removed outlier: 3.650A pdb=" N GLY M 145 " --> pdb=" O ILE M 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 151 Processing helix chain 'N' and resid 4 through 35 removed outlier: 3.539A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS N 35 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 65 removed outlier: 3.773A pdb=" N ALA N 41 " --> pdb=" O TRP N 37 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU N 65 " --> pdb=" O ARG N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 110 removed outlier: 3.917A pdb=" N MET N 86 " --> pdb=" O SER N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 145 removed outlier: 3.987A pdb=" N ALA N 117 " --> pdb=" O ASP N 113 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY N 145 " --> pdb=" O ILE N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 151 Processing helix chain 'O' and resid 4 through 36 removed outlier: 3.509A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY O 36 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 65 removed outlier: 3.659A pdb=" N LEU O 65 " --> pdb=" O ARG O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 110 Processing helix chain 'O' and resid 113 through 144 removed outlier: 3.745A 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 removed outlier: 3.515A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS P 35 " --> pdb=" O LEU P 31 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY P 36 " --> pdb=" O GLN P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 65 removed outlier: 3.577A pdb=" N ALA P 41 " --> pdb=" O TRP P 37 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU P 65 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 110 removed outlier: 3.787A pdb=" N MET P 86 " --> pdb=" O SER P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 145 removed outlier: 3.937A pdb=" N ALA P 117 " --> pdb=" O ASP P 113 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY P 145 " --> pdb=" O ILE P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 151 Processing helix chain 'Q' and resid 4 through 36 removed outlier: 3.636A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS Q 35 " --> pdb=" O LEU Q 31 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY Q 36 " --> pdb=" O GLN Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 65 removed outlier: 3.667A pdb=" N LEU Q 65 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 110 removed outlier: 3.788A pdb=" N MET Q 86 " --> pdb=" O SER Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 144 removed outlier: 3.983A 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 removed outlier: 3.526A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS R 35 " --> pdb=" O LEU R 31 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY R 36 " --> pdb=" O GLN R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 65 removed outlier: 3.548A pdb=" N ALA R 41 " --> pdb=" O TRP R 37 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 110 removed outlier: 3.892A pdb=" N MET R 86 " --> pdb=" O SER R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 145 removed outlier: 3.944A pdb=" N ALA R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY R 145 " --> pdb=" O ILE R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 151 Processing helix chain 'S' and resid 4 through 35 removed outlier: 3.536A pdb=" N ILE S 8 " --> pdb=" O ASP S 4 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 65 removed outlier: 3.788A pdb=" N ALA S 41 " --> pdb=" O TRP S 37 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU S 65 " --> pdb=" O ARG S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 110 removed outlier: 3.919A pdb=" N MET S 86 " --> pdb=" O SER S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 145 removed outlier: 3.993A pdb=" N ALA S 117 " --> pdb=" O ASP S 113 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY S 145 " --> pdb=" O ILE S 141 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 151 Processing helix chain 'T' and resid 4 through 36 removed outlier: 3.505A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS T 35 " --> pdb=" O LEU T 31 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY T 36 " --> pdb=" O GLN T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 65 removed outlier: 3.645A pdb=" N LEU T 65 " --> pdb=" O ARG T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 110 Processing helix chain 'T' and resid 113 through 144 removed outlier: 3.995A 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 36 removed outlier: 3.537A pdb=" N ILE U 8 " --> pdb=" O ASP U 4 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY U 36 " --> pdb=" O GLN U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 65 removed outlier: 3.543A pdb=" N ALA U 41 " --> pdb=" O TRP U 37 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU U 65 " --> pdb=" O ARG U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 110 removed outlier: 3.822A pdb=" N MET U 86 " --> pdb=" O SER U 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 113 through 145 removed outlier: 3.833A pdb=" N ALA U 117 " --> pdb=" O ASP U 113 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY U 145 " --> pdb=" O ILE U 141 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 151 Processing helix chain 'V' and resid 4 through 36 removed outlier: 3.538A pdb=" N ILE V 8 " --> pdb=" O ASP V 4 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS V 35 " --> pdb=" O LEU V 31 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY V 36 " --> pdb=" O GLN V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 65 removed outlier: 3.670A pdb=" N LEU V 65 " --> pdb=" O ARG V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 82 through 110 removed outlier: 3.784A pdb=" N MET V 86 " --> pdb=" O SER V 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 144 removed outlier: 3.954A pdb=" N ALA V 117 " --> pdb=" O ASP V 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 145 through 151 Processing helix chain 'W' and resid 4 through 36 removed outlier: 3.530A pdb=" N ILE W 8 " --> pdb=" O ASP W 4 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS W 35 " --> pdb=" O LEU W 31 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY W 36 " --> pdb=" O GLN W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 65 removed outlier: 3.539A pdb=" N ALA W 41 " --> pdb=" O TRP W 37 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU W 65 " --> pdb=" O ARG W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 110 removed outlier: 3.918A pdb=" N MET W 86 " --> pdb=" O SER W 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 145 removed outlier: 3.972A pdb=" N ALA W 117 " --> pdb=" O ASP W 113 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY W 145 " --> pdb=" O ILE W 141 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 151 Processing helix chain 'X' and resid 4 through 35 removed outlier: 3.540A pdb=" N ILE X 8 " --> pdb=" O ASP X 4 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS X 35 " --> pdb=" O LEU X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 65 removed outlier: 3.560A pdb=" N ALA X 41 " --> pdb=" O TRP X 37 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU X 65 " --> pdb=" O ARG X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 110 removed outlier: 3.909A pdb=" N MET X 86 " --> pdb=" O SER X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 145 removed outlier: 3.941A pdb=" N ALA X 117 " --> pdb=" O ASP X 113 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY X 145 " --> pdb=" O ILE X 141 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 151 2461 hydrogen bonds defined for protein. 7383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.06 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 13491 1.39 - 1.56: 18653 1.56 - 1.73: 0 1.73 - 1.90: 192 1.90 - 2.07: 48 Bond restraints: 32384 Sorted by residual: bond pdb=" C ASP R 99 " pdb=" O ASP R 99 " ideal model delta sigma weight residual 1.236 1.251 -0.015 1.15e-02 7.56e+03 1.60e+00 bond pdb=" C ASP W 99 " pdb=" O ASP W 99 " ideal model delta sigma weight residual 1.236 1.251 -0.014 1.15e-02 7.56e+03 1.51e+00 bond pdb=" C ASP A 99 " pdb=" O ASP A 99 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.46e+00 bond pdb=" C ASP T 99 " pdb=" O ASP T 99 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.46e+00 bond pdb=" C ASP O 99 " pdb=" O ASP O 99 " ideal model delta sigma weight residual 1.236 1.250 -0.014 1.15e-02 7.56e+03 1.46e+00 ... (remaining 32379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 43673 3.15 - 6.29: 244 6.29 - 9.44: 14 9.44 - 12.58: 2 12.58 - 15.73: 3 Bond angle restraints: 43936 Sorted by residual: angle pdb=" C TYR R 25 " pdb=" N PHE R 26 " pdb=" CA PHE R 26 " ideal model delta sigma weight residual 120.29 116.11 4.18 1.42e+00 4.96e-01 8.65e+00 angle pdb=" C TYR W 25 " pdb=" N PHE W 26 " pdb=" CA PHE W 26 " ideal model delta sigma weight residual 120.29 116.25 4.04 1.42e+00 4.96e-01 8.09e+00 angle pdb=" C TYR I 25 " pdb=" N PHE I 26 " pdb=" CA PHE I 26 " ideal model delta sigma weight residual 120.29 116.26 4.03 1.42e+00 4.96e-01 8.05e+00 angle pdb=" C TYR G 25 " pdb=" N PHE G 26 " pdb=" CA PHE G 26 " ideal model delta sigma weight residual 120.29 116.33 3.96 1.42e+00 4.96e-01 7.76e+00 angle pdb=" C TYR N 25 " pdb=" N PHE N 26 " pdb=" CA PHE N 26 " ideal model delta sigma weight residual 120.29 116.34 3.95 1.42e+00 4.96e-01 7.74e+00 ... (remaining 43931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.74: 16963 18.74 - 37.48: 2063 37.48 - 56.22: 259 56.22 - 74.95: 61 74.95 - 93.69: 38 Dihedral angle restraints: 19384 sinusoidal: 8064 harmonic: 11320 Sorted by residual: dihedral pdb=" C2B HEM K 301 " pdb=" C3B HEM K 301 " pdb=" CAB HEM K 301 " pdb=" CBB HEM K 301 " ideal model delta sinusoidal sigma weight residual -0.00 -39.28 39.28 2 1.00e+01 1.00e-02 1.92e+01 dihedral pdb=" CA PRO T 159 " pdb=" C PRO T 159 " pdb=" N ASP T 160 " pdb=" CA ASP T 160 " ideal model delta harmonic sigma weight residual -180.00 -158.46 -21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" C2C HEM X 201 " pdb=" C3C HEM X 201 " pdb=" CAC HEM X 201 " pdb=" CBC HEM X 201 " ideal model delta sinusoidal sigma weight residual 0.00 37.74 -37.74 2 1.00e+01 1.00e-02 1.80e+01 ... (remaining 19381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 2435 0.024 - 0.049: 1594 0.049 - 0.073: 595 0.073 - 0.097: 161 0.097 - 0.121: 91 Chirality restraints: 4876 Sorted by residual: chirality pdb=" CA PRO J 159 " pdb=" N PRO J 159 " pdb=" C PRO J 159 " pdb=" CB PRO J 159 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA PRO L 161 " pdb=" N PRO L 161 " pdb=" C PRO L 161 " pdb=" CB PRO L 161 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA PRO Q 161 " pdb=" N PRO Q 161 " pdb=" C PRO Q 161 " pdb=" CB PRO Q 161 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 4873 not shown) Planarity restraints: 5680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB HEM K 301 " 0.002 2.00e-02 2.50e+03 1.07e-02 2.58e+00 pdb=" C1B HEM K 301 " -0.008 2.00e-02 2.50e+03 pdb=" C2B HEM K 301 " 0.009 2.00e-02 2.50e+03 pdb=" C3B HEM K 301 " -0.019 2.00e-02 2.50e+03 pdb=" C4B HEM K 301 " -0.008 2.00e-02 2.50e+03 pdb=" CAB HEM K 301 " 0.016 2.00e-02 2.50e+03 pdb=" CHB HEM K 301 " 0.011 2.00e-02 2.50e+03 pdb=" CHC HEM K 301 " 0.004 2.00e-02 2.50e+03 pdb=" CMB HEM K 301 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 37 " -0.016 2.00e-02 2.50e+03 9.74e-03 2.37e+00 pdb=" CG TRP G 37 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP G 37 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP G 37 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 37 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 37 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP G 37 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 37 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 37 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP G 37 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM O 202 " -0.024 2.00e-02 2.50e+03 1.03e-02 2.37e+00 pdb=" C1B HEM O 202 " 0.005 2.00e-02 2.50e+03 pdb=" C2B HEM O 202 " 0.006 2.00e-02 2.50e+03 pdb=" C3B HEM O 202 " -0.005 2.00e-02 2.50e+03 pdb=" C4B HEM O 202 " 0.000 2.00e-02 2.50e+03 pdb=" CAB HEM O 202 " -0.001 2.00e-02 2.50e+03 pdb=" CHB HEM O 202 " 0.010 2.00e-02 2.50e+03 pdb=" CHC HEM O 202 " 0.013 2.00e-02 2.50e+03 pdb=" CMB HEM O 202 " -0.004 2.00e-02 2.50e+03 ... (remaining 5677 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.99: 26 1.99 - 2.72: 2821 2.72 - 3.45: 46863 3.45 - 4.17: 62685 4.17 - 4.90: 122097 Nonbonded interactions: 234492 Sorted by model distance: nonbonded pdb=" OE1 GLU J 18 " pdb=" OE1 GLU J 51 " model vdw 1.266 3.040 nonbonded pdb=" OE1 GLU B 18 " pdb=" OE1 GLU B 51 " model vdw 1.287 3.040 nonbonded pdb=" OE1 GLU T 18 " pdb=" OE1 GLU T 51 " model vdw 1.303 3.040 nonbonded pdb=" OE1 GLU P 18 " pdb=" OE1 GLU P 51 " model vdw 1.308 3.040 nonbonded pdb=" OE1 GLU L 18 " pdb=" OE1 GLU L 51 " model vdw 1.319 3.040 ... (remaining 234487 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 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'B' and resid 1 through 157) selection = (chain 'C' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'D' and resid 1 through 157) selection = (chain 'E' and resid 1 through 157) selection = (chain 'F' and resid 1 through 157) selection = (chain 'G' and resid 1 through 157) selection = (chain 'H' and resid 1 through 157) selection = (chain 'I' and resid 1 through 157) selection = (chain 'J' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'K' and resid 1 through 157) selection = (chain 'L' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'M' and resid 1 through 157) selection = (chain 'N' and resid 1 through 157) selection = (chain 'O' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'P' and resid 1 through 157) selection = (chain 'Q' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'R' and resid 1 through 157) selection = (chain 'S' and resid 1 through 157) selection = (chain 'T' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'U' and resid 1 through 157) selection = (chain 'V' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'W' and resid 1 through 157) selection = (chain 'X' and resid 1 through 157) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 26.420 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 : 0.008 0.277 32413 Z= 0.335 Angle : 0.716 15.729 43936 Z= 0.393 Chirality : 0.037 0.121 4876 Planarity : 0.003 0.027 5680 Dihedral : 15.849 93.692 12000 Min Nonbonded Distance : 1.266 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.12 % Allowed : 7.78 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.11), residues: 3792 helix: -0.37 (0.08), residues: 2888 sheet: None (None), residues: 0 loop : -4.43 (0.15), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 103 TYR 0.008 0.001 TYR C 71 PHE 0.025 0.003 PHE T 120 TRP 0.025 0.003 TRP G 37 HIS 0.005 0.001 HIS U 54 Details of bonding type rmsd covalent geometry : bond 0.00736 (32384) covalent geometry : angle 0.71553 (43936) hydrogen bonds : bond 0.14321 ( 2461) hydrogen bonds : angle 5.90145 ( 7383) Misc. bond : bond 0.06322 ( 29) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1011 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.7144 (mt) cc_final: 0.6787 (mt) REVERT: B 1 MET cc_start: 0.5501 (mtm) cc_final: 0.5292 (mtm) REVERT: B 105 ILE cc_start: 0.7189 (mt) cc_final: 0.6844 (mt) REVERT: C 105 ILE cc_start: 0.7282 (mt) cc_final: 0.6922 (mt) REVERT: C 130 HIS cc_start: 0.7478 (t-170) cc_final: 0.7105 (m170) REVERT: D 105 ILE cc_start: 0.7115 (mt) cc_final: 0.6723 (mt) REVERT: D 130 HIS cc_start: 0.7503 (t-170) cc_final: 0.7254 (m170) REVERT: F 105 ILE cc_start: 0.7252 (mt) cc_final: 0.6916 (mt) REVERT: F 130 HIS cc_start: 0.7467 (t-170) cc_final: 0.7205 (m170) REVERT: E 1 MET cc_start: 0.5331 (mtm) cc_final: 0.5069 (mtm) REVERT: E 105 ILE cc_start: 0.7307 (mt) cc_final: 0.6971 (mt) REVERT: G 1 MET cc_start: 0.5342 (mtm) cc_final: 0.5093 (mtm) REVERT: G 105 ILE cc_start: 0.7284 (mt) cc_final: 0.6932 (mt) REVERT: G 130 HIS cc_start: 0.7560 (t-170) cc_final: 0.7270 (m170) REVERT: H 105 ILE cc_start: 0.7254 (mt) cc_final: 0.6901 (mt) REVERT: H 130 HIS cc_start: 0.7525 (t-170) cc_final: 0.7229 (m170) REVERT: I 105 ILE cc_start: 0.7252 (mt) cc_final: 0.6896 (mt) REVERT: J 105 ILE cc_start: 0.7275 (mt) cc_final: 0.6917 (mt) REVERT: J 130 HIS cc_start: 0.7582 (t-170) cc_final: 0.7297 (m170) REVERT: K 105 ILE cc_start: 0.7205 (mt) cc_final: 0.6872 (mt) REVERT: K 126 ASP cc_start: 0.8495 (m-30) cc_final: 0.8134 (t0) REVERT: L 105 ILE cc_start: 0.7282 (mt) cc_final: 0.6930 (mt) REVERT: L 130 HIS cc_start: 0.7612 (t-170) cc_final: 0.7217 (m170) REVERT: M 1 MET cc_start: 0.4551 (mtp) cc_final: 0.3689 (mtm) REVERT: M 105 ILE cc_start: 0.7112 (mt) cc_final: 0.6736 (mt) REVERT: M 130 HIS cc_start: 0.7472 (t-170) cc_final: 0.7238 (m170) REVERT: N 105 ILE cc_start: 0.7250 (mt) cc_final: 0.6916 (mt) REVERT: N 130 HIS cc_start: 0.7548 (t-170) cc_final: 0.7289 (m170) REVERT: O 1 MET cc_start: 0.5649 (mtm) cc_final: 0.5169 (mtm) REVERT: O 105 ILE cc_start: 0.7355 (mt) cc_final: 0.7043 (mt) REVERT: O 130 HIS cc_start: 0.7585 (t-170) cc_final: 0.7278 (m170) REVERT: P 105 ILE cc_start: 0.7148 (mt) cc_final: 0.6812 (mt) REVERT: P 130 HIS cc_start: 0.7519 (t-170) cc_final: 0.7225 (m170) REVERT: Q 105 ILE cc_start: 0.7282 (mt) cc_final: 0.6919 (mt) REVERT: R 1 MET cc_start: 0.4463 (ptm) cc_final: 0.4131 (ptt) REVERT: R 105 ILE cc_start: 0.7151 (mt) cc_final: 0.6767 (mt) REVERT: R 130 HIS cc_start: 0.7528 (t-170) cc_final: 0.7245 (m170) REVERT: S 105 ILE cc_start: 0.7276 (mt) cc_final: 0.6920 (mt) REVERT: T 1 MET cc_start: 0.5351 (mtm) cc_final: 0.5022 (mtm) REVERT: T 105 ILE cc_start: 0.7168 (mt) cc_final: 0.6804 (mt) REVERT: T 130 HIS cc_start: 0.7503 (t-170) cc_final: 0.7087 (m170) REVERT: U 105 ILE cc_start: 0.7236 (mt) cc_final: 0.6901 (mt) REVERT: U 156 GLN cc_start: 0.8417 (tp-100) cc_final: 0.8154 (mm-40) REVERT: V 105 ILE cc_start: 0.7282 (mt) cc_final: 0.6912 (mt) REVERT: V 130 HIS cc_start: 0.7643 (t-170) cc_final: 0.7231 (m170) REVERT: W 1 MET cc_start: 0.4442 (ptm) cc_final: 0.3736 (ptt) REVERT: W 105 ILE cc_start: 0.7164 (mt) cc_final: 0.6806 (mt) REVERT: W 130 HIS cc_start: 0.7568 (t-170) cc_final: 0.7256 (m170) REVERT: X 105 ILE cc_start: 0.7262 (mt) cc_final: 0.6908 (mt) REVERT: X 130 HIS cc_start: 0.7548 (t-170) cc_final: 0.7269 (m170) outliers start: 4 outliers final: 4 residues processed: 1015 average time/residue: 0.2191 time to fit residues: 348.1585 Evaluate side-chains 681 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 677 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain V residue 160 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN B 130 HIS C 24 GLN C 130 HIS D 24 GLN D 130 HIS F 24 GLN F 118 ASN F 130 HIS F 156 GLN E 24 GLN E 130 HIS G 24 GLN G 130 HIS H 24 GLN H 130 HIS I 24 GLN J 24 GLN J 130 HIS K 24 GLN L 24 GLN L 130 HIS M 24 GLN M 130 HIS N 24 GLN N 118 ASN N 130 HIS O 24 GLN O 130 HIS P 130 HIS Q 24 GLN R 24 GLN R 130 HIS S 24 GLN S 118 ASN S 130 HIS S 156 GLN T 24 GLN T 130 HIS U 24 GLN U 130 HIS V 24 GLN V 130 HIS W 24 GLN W 130 HIS X 118 ASN X 130 HIS X 156 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.140276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.123915 restraints weight = 48920.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.127781 restraints weight = 27175.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.130389 restraints weight = 17469.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.132246 restraints weight = 12360.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.133559 restraints weight = 9350.587| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.246 32413 Z= 0.187 Angle : 0.649 12.343 43936 Z= 0.315 Chirality : 0.034 0.136 4876 Planarity : 0.003 0.021 5680 Dihedral : 7.129 89.487 4280 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.75 % Allowed : 12.35 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.13), residues: 3792 helix: 2.90 (0.08), residues: 2920 sheet: None (None), residues: 0 loop : -3.99 (0.15), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 78 TYR 0.006 0.001 TYR T 71 PHE 0.028 0.001 PHE N 26 TRP 0.014 0.002 TRP Q 37 HIS 0.004 0.001 HIS Q 130 Details of bonding type rmsd covalent geometry : bond 0.00378 (32384) covalent geometry : angle 0.64873 (43936) hydrogen bonds : bond 0.09954 ( 2461) hydrogen bonds : angle 3.92516 ( 7383) Misc. bond : bond 0.04579 ( 29) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 817 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5174 (mtm) cc_final: 0.4468 (mtm) REVERT: B 53 ARG cc_start: 0.8272 (mtm-85) cc_final: 0.7280 (mtm110) REVERT: B 128 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7921 (mm-30) REVERT: E 78 ARG cc_start: 0.8584 (mtp85) cc_final: 0.7919 (ttm110) REVERT: G 128 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7949 (mm-30) REVERT: H 1 MET cc_start: 0.4893 (mtm) cc_final: 0.3553 (ptm) REVERT: H 78 ARG cc_start: 0.8585 (mtp85) cc_final: 0.7906 (ttm110) REVERT: I 128 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7880 (mm-30) REVERT: I 130 HIS cc_start: 0.7903 (t-90) cc_final: 0.6960 (m170) REVERT: J 78 ARG cc_start: 0.8626 (mtp85) cc_final: 0.7938 (ttm110) REVERT: K 126 ASP cc_start: 0.8283 (m-30) cc_final: 0.7820 (t0) REVERT: N 53 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7867 (ttp-110) REVERT: N 78 ARG cc_start: 0.8583 (mtp85) cc_final: 0.7849 (ttm110) REVERT: O 32 GLN cc_start: 0.8887 (mt0) cc_final: 0.8656 (mt0) REVERT: P 53 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.7428 (mtm110) REVERT: U 53 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7249 (mtm110) outliers start: 92 outliers final: 70 residues processed: 824 average time/residue: 0.2016 time to fit residues: 270.0393 Evaluate side-chains 777 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 707 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 115 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain V residue 160 ASP Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 100 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 324 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 321 optimal weight: 5.9990 chunk 210 optimal weight: 0.0470 chunk 18 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 282 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 HIS C 72 GLN D 72 GLN F 72 GLN E 28 HIS H 28 HIS J 158 GLN L 28 HIS M 72 GLN N 72 GLN P 28 HIS Q 72 GLN R 72 GLN U 28 HIS V 28 HIS V 72 GLN W 72 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118035 restraints weight = 49329.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121609 restraints weight = 28183.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124085 restraints weight = 18405.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125875 restraints weight = 13171.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127140 restraints weight = 9992.981| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.249 32413 Z= 0.223 Angle : 0.669 19.137 43936 Z= 0.331 Chirality : 0.035 0.131 4876 Planarity : 0.003 0.022 5680 Dihedral : 7.066 88.197 4280 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.98 % Allowed : 14.80 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.14), residues: 3792 helix: 3.32 (0.08), residues: 2920 sheet: None (None), residues: 0 loop : -3.11 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 73 TYR 0.009 0.001 TYR I 149 PHE 0.021 0.001 PHE N 26 TRP 0.007 0.002 TRP O 37 HIS 0.005 0.001 HIS G 130 Details of bonding type rmsd covalent geometry : bond 0.00486 (32384) covalent geometry : angle 0.66941 (43936) hydrogen bonds : bond 0.11350 ( 2461) hydrogen bonds : angle 4.25120 ( 7383) Misc. bond : bond 0.04632 ( 29) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 683 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 4 ASP cc_start: 0.7871 (m-30) cc_final: 0.7611 (t0) REVERT: A 132 ASP cc_start: 0.9069 (t70) cc_final: 0.8596 (t0) REVERT: B 1 MET cc_start: 0.5555 (mtm) cc_final: 0.4784 (mtm) REVERT: B 4 ASP cc_start: 0.7893 (m-30) cc_final: 0.7589 (t0) REVERT: C 120 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7627 (m-10) REVERT: C 128 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8035 (tp30) REVERT: D 4 ASP cc_start: 0.7843 (m-30) cc_final: 0.7509 (t0) REVERT: D 60 ASP cc_start: 0.8691 (t70) cc_final: 0.8486 (t70) REVERT: F 126 ASP cc_start: 0.8804 (t0) cc_final: 0.8601 (t0) REVERT: F 130 HIS cc_start: 0.8111 (t70) cc_final: 0.7911 (t-90) REVERT: E 1 MET cc_start: 0.5442 (mtm) cc_final: 0.4954 (ptm) REVERT: E 4 ASP cc_start: 0.7849 (m-30) cc_final: 0.7589 (t0) REVERT: G 1 MET cc_start: 0.5461 (mtm) cc_final: 0.3742 (ttp) REVERT: G 4 ASP cc_start: 0.7827 (m-30) cc_final: 0.7584 (t0) REVERT: I 1 MET cc_start: 0.5199 (mtm) cc_final: 0.4808 (ptm) REVERT: J 1 MET cc_start: 0.5445 (mtm) cc_final: 0.4802 (ptm) REVERT: J 4 ASP cc_start: 0.7806 (m-30) cc_final: 0.7593 (t0) REVERT: J 78 ARG cc_start: 0.8672 (mtp85) cc_final: 0.8050 (ttm110) REVERT: J 130 HIS cc_start: 0.8145 (t70) cc_final: 0.7944 (t-90) REVERT: K 1 MET cc_start: 0.5327 (mtm) cc_final: 0.5041 (ptm) REVERT: K 4 ASP cc_start: 0.7816 (m-30) cc_final: 0.7527 (t0) REVERT: K 126 ASP cc_start: 0.8429 (m-30) cc_final: 0.7928 (t0) REVERT: M 128 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7809 (mm-30) REVERT: N 78 ARG cc_start: 0.8609 (mtp85) cc_final: 0.7973 (ttm110) REVERT: O 4 ASP cc_start: 0.7843 (m-30) cc_final: 0.7594 (t0) REVERT: P 1 MET cc_start: 0.5379 (mtm) cc_final: 0.4984 (ptm) REVERT: P 4 ASP cc_start: 0.7900 (m-30) cc_final: 0.7587 (t0) REVERT: R 4 ASP cc_start: 0.7745 (m-30) cc_final: 0.7500 (t0) REVERT: T 4 ASP cc_start: 0.7840 (m-30) cc_final: 0.7609 (t0) REVERT: U 1 MET cc_start: 0.5337 (mtm) cc_final: 0.4879 (ptm) REVERT: W 4 ASP cc_start: 0.7773 (m-30) cc_final: 0.7515 (t0) outliers start: 133 outliers final: 122 residues processed: 751 average time/residue: 0.1981 time to fit residues: 240.7729 Evaluate side-chains 771 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 647 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 28 HIS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 28 HIS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 28 HIS Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 28 HIS Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 115 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 28 HIS Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 28 HIS Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain V residue 160 ASP Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 115 THR Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 346 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 335 optimal weight: 0.0060 chunk 161 optimal weight: 0.8980 chunk 348 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 54 HIS U 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.149141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.131890 restraints weight = 48801.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.135937 restraints weight = 26530.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.138619 restraints weight = 16904.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140467 restraints weight = 11984.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141797 restraints weight = 9156.069| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.494 32413 Z= 0.148 Angle : 0.563 10.803 43936 Z= 0.274 Chirality : 0.033 0.134 4876 Planarity : 0.003 0.029 5680 Dihedral : 6.988 85.184 4280 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.73 % Allowed : 20.13 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.79 (0.14), residues: 3792 helix: 3.90 (0.08), residues: 2948 sheet: None (None), residues: 0 loop : -3.22 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 73 TYR 0.004 0.001 TYR I 149 PHE 0.017 0.001 PHE V 26 TRP 0.007 0.001 TRP A 37 HIS 0.010 0.001 HIS P 28 Details of bonding type rmsd covalent geometry : bond 0.00287 (32384) covalent geometry : angle 0.56279 (43936) hydrogen bonds : bond 0.07254 ( 2461) hydrogen bonds : angle 3.29522 ( 7383) Misc. bond : bond 0.09182 ( 29) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 668 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP C 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP V 160 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 132 ASP cc_start: 0.9045 (t70) cc_final: 0.8584 (t0) REVERT: B 1 MET cc_start: 0.5706 (mtm) cc_final: 0.5184 (mtm) REVERT: B 2 GLN cc_start: 0.8456 (tt0) cc_final: 0.8190 (mt0) REVERT: B 32 GLN cc_start: 0.8877 (mt0) cc_final: 0.8629 (mt0) REVERT: B 81 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7487 (mt0) REVERT: B 120 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.6976 (m-10) REVERT: B 137 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8231 (tp-100) REVERT: C 32 GLN cc_start: 0.8770 (mt0) cc_final: 0.8542 (mt0) REVERT: C 128 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8103 (tp30) REVERT: C 130 HIS cc_start: 0.7788 (t-90) cc_final: 0.6779 (m170) REVERT: C 137 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8376 (tp40) REVERT: D 32 GLN cc_start: 0.8895 (mt0) cc_final: 0.8657 (mt0) REVERT: D 132 ASP cc_start: 0.9035 (t70) cc_final: 0.8523 (t0) REVERT: D 137 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8433 (tp40) REVERT: F 32 GLN cc_start: 0.8780 (mt0) cc_final: 0.8554 (mt0) REVERT: F 126 ASP cc_start: 0.8584 (t0) cc_final: 0.8358 (t0) REVERT: E 120 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6979 (m-10) REVERT: E 130 HIS cc_start: 0.7887 (t-90) cc_final: 0.6823 (m170) REVERT: E 132 ASP cc_start: 0.9065 (t70) cc_final: 0.8556 (t0) REVERT: E 137 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8439 (tp40) REVERT: G 1 MET cc_start: 0.5316 (mtm) cc_final: 0.4667 (ptm) REVERT: G 32 GLN cc_start: 0.8757 (mt0) cc_final: 0.8531 (mt0) REVERT: H 130 HIS cc_start: 0.7864 (t-90) cc_final: 0.6849 (m170) REVERT: H 137 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8423 (tp40) REVERT: I 120 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7004 (m-10) REVERT: I 130 HIS cc_start: 0.7861 (t-90) cc_final: 0.6856 (m170) REVERT: I 137 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8436 (tp40) REVERT: J 32 GLN cc_start: 0.8811 (mt0) cc_final: 0.8598 (mt0) REVERT: J 78 ARG cc_start: 0.8614 (mtp85) cc_final: 0.7990 (ttm110) REVERT: J 137 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8344 (tp-100) REVERT: K 32 GLN cc_start: 0.8906 (mt0) cc_final: 0.8670 (mt0) REVERT: K 81 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7478 (mt0) REVERT: K 120 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.7024 (m-10) REVERT: K 126 ASP cc_start: 0.8134 (m-30) cc_final: 0.7466 (t0) REVERT: K 130 HIS cc_start: 0.7761 (t-90) cc_final: 0.6882 (m170) REVERT: L 120 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7047 (m-10) REVERT: M 32 GLN cc_start: 0.8892 (mt0) cc_final: 0.8676 (mt0) REVERT: M 137 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8471 (tp40) REVERT: N 32 GLN cc_start: 0.8758 (mt0) cc_final: 0.8532 (mt0) REVERT: N 78 ARG cc_start: 0.8611 (mtp85) cc_final: 0.7975 (ttm110) REVERT: N 130 HIS cc_start: 0.7831 (t-90) cc_final: 0.6870 (m170) REVERT: N 132 ASP cc_start: 0.9030 (t70) cc_final: 0.8544 (t0) REVERT: O 1 MET cc_start: 0.5244 (mtm) cc_final: 0.4939 (ptm) REVERT: O 120 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6955 (m-10) REVERT: O 130 HIS cc_start: 0.7871 (t-90) cc_final: 0.6883 (m170) REVERT: O 137 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8273 (tp-100) REVERT: P 32 GLN cc_start: 0.8884 (mt0) cc_final: 0.8646 (mt0) REVERT: P 81 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7544 (mt0) REVERT: P 120 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7018 (m-10) REVERT: P 130 HIS cc_start: 0.7806 (t-90) cc_final: 0.6979 (m170) REVERT: Q 32 GLN cc_start: 0.8782 (mt0) cc_final: 0.8560 (mt0) REVERT: Q 120 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.7051 (m-10) REVERT: Q 137 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8334 (tp40) REVERT: R 32 GLN cc_start: 0.8886 (mt0) cc_final: 0.8658 (mt0) REVERT: R 130 HIS cc_start: 0.7622 (t-90) cc_final: 0.6612 (m170) REVERT: R 132 ASP cc_start: 0.9016 (t70) cc_final: 0.8544 (t0) REVERT: S 22 ILE cc_start: 0.8659 (mt) cc_final: 0.8412 (mm) REVERT: S 32 GLN cc_start: 0.8811 (mt0) cc_final: 0.8608 (mt0) REVERT: S 120 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.6995 (m-10) REVERT: S 130 HIS cc_start: 0.7828 (t-90) cc_final: 0.6815 (m170) REVERT: T 130 HIS cc_start: 0.7897 (t-90) cc_final: 0.6923 (m170) REVERT: T 132 ASP cc_start: 0.8976 (t70) cc_final: 0.8525 (t0) REVERT: U 120 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.7023 (m-10) REVERT: U 130 HIS cc_start: 0.7852 (t-90) cc_final: 0.6893 (m170) REVERT: V 32 GLN cc_start: 0.8745 (mt0) cc_final: 0.8538 (mt0) REVERT: V 120 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6962 (m-10) REVERT: V 130 HIS cc_start: 0.7837 (t-90) cc_final: 0.6765 (m170) REVERT: V 137 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8419 (tp40) REVERT: W 32 GLN cc_start: 0.8870 (mt0) cc_final: 0.8641 (mt0) REVERT: W 120 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.6930 (m-10) REVERT: W 130 HIS cc_start: 0.7620 (t-90) cc_final: 0.6595 (m170) REVERT: W 132 ASP cc_start: 0.9027 (t70) cc_final: 0.8553 (t0) REVERT: X 32 GLN cc_start: 0.8857 (mt0) cc_final: 0.8619 (mt0) REVERT: X 130 HIS cc_start: 0.7832 (t-90) cc_final: 0.6857 (m170) outliers start: 58 outliers final: 32 residues processed: 696 average time/residue: 0.1800 time to fit residues: 207.1082 Evaluate side-chains 651 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 606 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 120 PHE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 120 PHE Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 120 PHE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 120 PHE Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 120 PHE Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 120 PHE Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 28 HIS Chi-restraints excluded: chain U residue 120 PHE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain V residue 160 ASP Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 120 PHE Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 109 optimal weight: 0.0170 chunk 134 optimal weight: 5.9990 chunk 308 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 chunk 346 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 243 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN M 156 GLN U 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130324 restraints weight = 48689.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134135 restraints weight = 27413.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136660 restraints weight = 17781.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.138466 restraints weight = 12778.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.139732 restraints weight = 9762.658| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.546 32413 Z= 0.148 Angle : 0.557 15.110 43936 Z= 0.265 Chirality : 0.032 0.132 4876 Planarity : 0.002 0.028 5680 Dihedral : 6.786 84.890 4280 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.15 % Allowed : 19.71 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.96 (0.14), residues: 3792 helix: 4.00 (0.08), residues: 2948 sheet: None (None), residues: 0 loop : -3.06 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 53 TYR 0.006 0.001 TYR I 149 PHE 0.031 0.001 PHE N 26 TRP 0.007 0.001 TRP J 37 HIS 0.004 0.001 HIS F 130 Details of bonding type rmsd covalent geometry : bond 0.00300 (32384) covalent geometry : angle 0.55708 (43936) hydrogen bonds : bond 0.07640 ( 2461) hydrogen bonds : angle 3.27581 ( 7383) Misc. bond : bond 0.10143 ( 29) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 596 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.9014 (t70) cc_final: 0.8586 (t0) REVERT: B 1 MET cc_start: 0.5808 (mtm) cc_final: 0.5183 (mtm) REVERT: B 2 GLN cc_start: 0.8524 (tt0) cc_final: 0.8302 (mt0) REVERT: B 32 GLN cc_start: 0.9003 (mt0) cc_final: 0.8762 (mt0) REVERT: B 81 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7443 (mt0) REVERT: B 137 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8370 (tp-100) REVERT: C 32 GLN cc_start: 0.8861 (mt0) cc_final: 0.8651 (mt0) REVERT: C 128 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8158 (tp30) REVERT: D 32 GLN cc_start: 0.8955 (mt0) cc_final: 0.8742 (mt0) REVERT: F 32 GLN cc_start: 0.8908 (mt0) cc_final: 0.8695 (mt0) REVERT: F 126 ASP cc_start: 0.8635 (t0) cc_final: 0.8422 (t0) REVERT: E 78 ARG cc_start: 0.8577 (mtp85) cc_final: 0.8076 (ttm110) REVERT: E 120 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7188 (m-10) REVERT: E 130 HIS cc_start: 0.7912 (t-90) cc_final: 0.6880 (m170) REVERT: E 132 ASP cc_start: 0.9020 (t70) cc_final: 0.8541 (t0) REVERT: H 78 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8091 (ttm110) REVERT: H 130 HIS cc_start: 0.7908 (t-90) cc_final: 0.6820 (m170) REVERT: H 137 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8576 (tp40) REVERT: I 130 HIS cc_start: 0.7743 (t-90) cc_final: 0.6906 (m170) REVERT: I 137 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8578 (tp40) REVERT: J 78 ARG cc_start: 0.8602 (mtp85) cc_final: 0.8057 (ttm110) REVERT: K 32 GLN cc_start: 0.8981 (mt0) cc_final: 0.8774 (mt0) REVERT: K 81 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7467 (mt0) REVERT: K 126 ASP cc_start: 0.8150 (m-30) cc_final: 0.7515 (t0) REVERT: K 130 HIS cc_start: 0.7726 (t-90) cc_final: 0.6842 (m170) REVERT: L 120 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7253 (m-10) REVERT: N 78 ARG cc_start: 0.8613 (mtp85) cc_final: 0.8038 (ttm110) REVERT: N 130 HIS cc_start: 0.7882 (t-90) cc_final: 0.6857 (m170) REVERT: N 132 ASP cc_start: 0.8993 (t70) cc_final: 0.8486 (t0) REVERT: O 130 HIS cc_start: 0.7893 (t-90) cc_final: 0.6865 (m170) REVERT: O 137 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8426 (tp-100) REVERT: P 32 GLN cc_start: 0.8978 (mt0) cc_final: 0.8732 (mt0) REVERT: P 81 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7599 (mt0) REVERT: P 126 ASP cc_start: 0.8591 (t0) cc_final: 0.8291 (t0) REVERT: P 130 HIS cc_start: 0.7848 (t-90) cc_final: 0.6956 (m170) REVERT: Q 120 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7208 (m-10) REVERT: R 130 HIS cc_start: 0.7776 (t-90) cc_final: 0.6764 (m170) REVERT: R 132 ASP cc_start: 0.9005 (t70) cc_final: 0.8522 (t0) REVERT: S 130 HIS cc_start: 0.7827 (t-90) cc_final: 0.6802 (m170) REVERT: T 130 HIS cc_start: 0.7994 (t-90) cc_final: 0.7050 (m170) REVERT: U 120 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7226 (m-10) REVERT: U 130 HIS cc_start: 0.7971 (t-90) cc_final: 0.6958 (m170) REVERT: V 32 GLN cc_start: 0.8882 (mt0) cc_final: 0.8652 (mt0) REVERT: V 120 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7210 (m-10) REVERT: V 130 HIS cc_start: 0.7908 (t-90) cc_final: 0.6858 (m170) REVERT: W 130 HIS cc_start: 0.7800 (t-90) cc_final: 0.6721 (m170) REVERT: W 132 ASP cc_start: 0.9000 (t70) cc_final: 0.8515 (t0) REVERT: X 32 GLN cc_start: 0.8924 (mt0) cc_final: 0.8722 (mt0) REVERT: X 120 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7206 (m-10) REVERT: X 130 HIS cc_start: 0.7851 (t-90) cc_final: 0.6888 (m170) outliers start: 72 outliers final: 56 residues processed: 623 average time/residue: 0.1960 time to fit residues: 198.0672 Evaluate side-chains 636 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 573 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 120 PHE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 120 PHE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 120 PHE Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 120 PHE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 120 PHE Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 131 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 84 optimal weight: 0.0470 chunk 344 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 137 GLN U 137 GLN U 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.142178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123329 restraints weight = 50191.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127729 restraints weight = 26062.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130752 restraints weight = 16108.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.132774 restraints weight = 11072.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134227 restraints weight = 8222.497| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.543 32413 Z= 0.195 Angle : 0.627 17.917 43936 Z= 0.303 Chirality : 0.033 0.148 4876 Planarity : 0.003 0.126 5680 Dihedral : 6.748 87.818 4272 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.07 % Allowed : 19.77 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.14), residues: 3792 helix: 3.76 (0.08), residues: 2956 sheet: None (None), residues: 0 loop : -3.07 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG L 53 TYR 0.007 0.001 TYR I 149 PHE 0.021 0.001 PHE N 26 TRP 0.004 0.001 TRP P 37 HIS 0.005 0.001 HIS F 130 Details of bonding type rmsd covalent geometry : bond 0.00417 (32384) covalent geometry : angle 0.62724 (43936) hydrogen bonds : bond 0.09840 ( 2461) hydrogen bonds : angle 3.70734 ( 7383) Misc. bond : bond 0.10102 ( 29) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 580 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.7161 (m-10) REVERT: A 132 ASP cc_start: 0.9071 (t70) cc_final: 0.8654 (t0) REVERT: B 1 MET cc_start: 0.5886 (mtm) cc_final: 0.5192 (mtm) REVERT: B 120 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.7235 (m-10) REVERT: B 126 ASP cc_start: 0.8759 (t0) cc_final: 0.8549 (t0) REVERT: B 137 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8318 (tp-100) REVERT: C 120 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7229 (m-10) REVERT: C 128 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8147 (tp30) REVERT: C 130 HIS cc_start: 0.7748 (t-90) cc_final: 0.6695 (m170) REVERT: D 53 ARG cc_start: 0.8172 (mtm-85) cc_final: 0.7177 (mtm110) REVERT: F 120 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6927 (m-10) REVERT: F 126 ASP cc_start: 0.8723 (t0) cc_final: 0.8511 (t0) REVERT: E 120 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7261 (m-10) REVERT: E 130 HIS cc_start: 0.7874 (t-90) cc_final: 0.6690 (m170) REVERT: E 132 ASP cc_start: 0.9106 (t70) cc_final: 0.8613 (t0) REVERT: G 116 SER cc_start: 0.6820 (OUTLIER) cc_final: 0.6215 (p) REVERT: G 120 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6950 (m-10) REVERT: G 126 ASP cc_start: 0.8749 (t0) cc_final: 0.8544 (t0) REVERT: H 52 MET cc_start: 0.8088 (mtm) cc_final: 0.7824 (ttm) REVERT: H 78 ARG cc_start: 0.8524 (mtp85) cc_final: 0.7884 (ttm110) REVERT: H 116 SER cc_start: 0.6826 (OUTLIER) cc_final: 0.6225 (p) REVERT: H 120 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6861 (m-10) REVERT: I 120 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.7215 (m-10) REVERT: I 126 ASP cc_start: 0.8748 (t0) cc_final: 0.8541 (t0) REVERT: J 4 ASP cc_start: 0.7783 (m-30) cc_final: 0.7359 (t0) REVERT: J 78 ARG cc_start: 0.8582 (mtp85) cc_final: 0.7879 (ttm110) REVERT: J 116 SER cc_start: 0.6938 (OUTLIER) cc_final: 0.6308 (p) REVERT: J 120 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6978 (m-10) REVERT: K 32 GLN cc_start: 0.8845 (mt0) cc_final: 0.8627 (mt0) REVERT: K 120 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7302 (m-10) REVERT: K 126 ASP cc_start: 0.8292 (m-30) cc_final: 0.7666 (t0) REVERT: L 120 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7248 (m-10) REVERT: M 116 SER cc_start: 0.7016 (OUTLIER) cc_final: 0.6304 (p) REVERT: N 78 ARG cc_start: 0.8571 (mtp85) cc_final: 0.7858 (ttm110) REVERT: N 130 HIS cc_start: 0.7836 (t-90) cc_final: 0.6693 (m170) REVERT: O 4 ASP cc_start: 0.7640 (m-30) cc_final: 0.7295 (t0) REVERT: O 120 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.7244 (m-10) REVERT: P 52 MET cc_start: 0.8740 (mtm) cc_final: 0.8366 (mtt) REVERT: P 120 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.7259 (m-10) REVERT: P 126 ASP cc_start: 0.8783 (t0) cc_final: 0.8534 (t0) REVERT: Q 120 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7275 (m-10) REVERT: R 120 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7076 (m-10) REVERT: R 130 HIS cc_start: 0.7631 (t-90) cc_final: 0.6694 (m170) REVERT: S 120 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7294 (m-10) REVERT: S 130 HIS cc_start: 0.7855 (t-90) cc_final: 0.6644 (m170) REVERT: T 120 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.7099 (m-10) REVERT: T 130 HIS cc_start: 0.7986 (t-90) cc_final: 0.6903 (m170) REVERT: U 120 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.7257 (m-10) REVERT: U 130 HIS cc_start: 0.7934 (t-90) cc_final: 0.6807 (m170) REVERT: V 120 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7224 (m-10) REVERT: V 130 HIS cc_start: 0.7848 (t-90) cc_final: 0.6722 (m170) REVERT: W 52 MET cc_start: 0.8860 (ttm) cc_final: 0.8590 (ttm) REVERT: W 120 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7199 (m-10) REVERT: W 132 ASP cc_start: 0.9062 (t70) cc_final: 0.8615 (t0) REVERT: X 32 GLN cc_start: 0.8786 (mt0) cc_final: 0.8557 (mt0) REVERT: X 116 SER cc_start: 0.6863 (OUTLIER) cc_final: 0.6262 (p) REVERT: X 120 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7073 (m-10) REVERT: X 130 HIS cc_start: 0.7790 (t-90) cc_final: 0.6720 (m170) outliers start: 136 outliers final: 80 residues processed: 651 average time/residue: 0.1952 time to fit residues: 204.6500 Evaluate side-chains 681 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 574 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 120 PHE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 120 PHE Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 120 PHE Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 120 PHE Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 120 PHE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 120 PHE Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 120 PHE Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 120 PHE Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 120 PHE Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 120 PHE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 156 GLN Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 120 PHE Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 120 PHE Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 353 optimal weight: 0.0980 chunk 368 optimal weight: 3.9990 chunk 50 optimal weight: 0.0670 chunk 170 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 350 optimal weight: 6.9990 chunk 148 optimal weight: 0.0770 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS J 54 HIS P 156 GLN X 54 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.155935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.139623 restraints weight = 48753.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143326 restraints weight = 27928.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.145767 restraints weight = 18434.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.147532 restraints weight = 13376.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.148819 restraints weight = 10316.303| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.559 32413 Z= 0.136 Angle : 0.583 16.137 43936 Z= 0.272 Chirality : 0.032 0.141 4876 Planarity : 0.003 0.071 5680 Dihedral : 6.631 89.801 4272 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.53 % Allowed : 22.46 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.19 (0.14), residues: 3792 helix: 4.12 (0.08), residues: 2964 sheet: None (None), residues: 0 loop : -2.95 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.000 ARG L 53 TYR 0.005 0.001 TYR J 43 PHE 0.017 0.001 PHE N 26 TRP 0.003 0.001 TRP J 37 HIS 0.004 0.001 HIS M 130 Details of bonding type rmsd covalent geometry : bond 0.00283 (32384) covalent geometry : angle 0.58336 (43936) hydrogen bonds : bond 0.05703 ( 2461) hydrogen bonds : angle 3.00759 ( 7383) Misc. bond : bond 0.10397 ( 29) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 583 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8030 (tm-30) REVERT: A 132 ASP cc_start: 0.8943 (t70) cc_final: 0.8526 (t0) REVERT: B 137 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8365 (tp-100) REVERT: C 120 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.7026 (m-10) REVERT: C 130 HIS cc_start: 0.7760 (t-90) cc_final: 0.6818 (m170) REVERT: D 53 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7261 (mtm110) REVERT: F 32 GLN cc_start: 0.8791 (mt0) cc_final: 0.8590 (mt0) REVERT: F 53 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.7418 (mtm110) REVERT: E 78 ARG cc_start: 0.8474 (mtp85) cc_final: 0.8026 (ttm110) REVERT: E 120 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6995 (m-10) REVERT: E 130 HIS cc_start: 0.7790 (t-90) cc_final: 0.6847 (m170) REVERT: H 52 MET cc_start: 0.7991 (mtm) cc_final: 0.7789 (mtm) REVERT: H 53 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.7094 (mtm110) REVERT: H 78 ARG cc_start: 0.8549 (mtp85) cc_final: 0.8079 (ttm110) REVERT: I 120 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6943 (m-10) REVERT: I 130 HIS cc_start: 0.7677 (t-90) cc_final: 0.6803 (m170) REVERT: J 72 GLN cc_start: 0.8792 (tm-30) cc_final: 0.7981 (tm-30) REVERT: J 78 ARG cc_start: 0.8581 (mtp85) cc_final: 0.8039 (ttm110) REVERT: K 126 ASP cc_start: 0.7984 (m-30) cc_final: 0.7511 (t0) REVERT: K 130 HIS cc_start: 0.7627 (t-90) cc_final: 0.6770 (m170) REVERT: L 72 GLN cc_start: 0.8684 (tp40) cc_final: 0.8432 (tp-100) REVERT: L 120 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.7060 (m-10) REVERT: M 130 HIS cc_start: 0.7824 (t70) cc_final: 0.6934 (m170) REVERT: N 78 ARG cc_start: 0.8563 (mtp85) cc_final: 0.8039 (ttm110) REVERT: N 130 HIS cc_start: 0.7704 (t-90) cc_final: 0.6846 (m170) REVERT: O 130 HIS cc_start: 0.7909 (t-90) cc_final: 0.6882 (m170) REVERT: O 137 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8378 (tp40) REVERT: P 32 GLN cc_start: 0.8834 (mt0) cc_final: 0.8617 (mt0) REVERT: P 52 MET cc_start: 0.8616 (mtm) cc_final: 0.8273 (mtt) REVERT: P 120 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6970 (m-10) REVERT: P 126 ASP cc_start: 0.8472 (t0) cc_final: 0.8182 (t0) REVERT: P 130 HIS cc_start: 0.7683 (t-90) cc_final: 0.6825 (m170) REVERT: Q 120 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.7016 (m-10) REVERT: R 130 HIS cc_start: 0.7630 (t-90) cc_final: 0.6712 (m170) REVERT: S 120 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7113 (m-10) REVERT: S 130 HIS cc_start: 0.7854 (t-90) cc_final: 0.6805 (m170) REVERT: T 130 HIS cc_start: 0.7913 (t-90) cc_final: 0.7081 (m170) REVERT: U 120 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6998 (m-10) REVERT: U 130 HIS cc_start: 0.7837 (t-90) cc_final: 0.6928 (m170) REVERT: V 30 LYS cc_start: 0.8586 (tptt) cc_final: 0.8385 (tptp) REVERT: V 120 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.6958 (m-10) REVERT: V 130 HIS cc_start: 0.7805 (t-90) cc_final: 0.6838 (m170) REVERT: W 52 MET cc_start: 0.9035 (ttm) cc_final: 0.8708 (ttt) REVERT: W 130 HIS cc_start: 0.7626 (t-90) cc_final: 0.6698 (m170) REVERT: X 130 HIS cc_start: 0.7854 (t-90) cc_final: 0.6919 (m170) outliers start: 51 outliers final: 33 residues processed: 608 average time/residue: 0.1815 time to fit residues: 184.0371 Evaluate side-chains 573 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 531 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 120 PHE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 54 HIS Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 120 PHE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 120 PHE Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 120 PHE Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain U residue 120 PHE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 59 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 239 optimal weight: 6.9990 chunk 314 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 351 optimal weight: 8.9990 chunk 330 optimal weight: 6.9990 chunk 283 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.144078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127364 restraints weight = 48448.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.131049 restraints weight = 27989.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133503 restraints weight = 18486.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135255 restraints weight = 13419.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136522 restraints weight = 10350.851| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.589 32413 Z= 0.172 Angle : 0.614 15.135 43936 Z= 0.291 Chirality : 0.033 0.134 4876 Planarity : 0.003 0.081 5680 Dihedral : 6.726 86.016 4272 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.63 % Allowed : 20.84 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.12 (0.14), residues: 3792 helix: 4.04 (0.08), residues: 2940 sheet: None (None), residues: 0 loop : -2.60 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG L 53 TYR 0.006 0.001 TYR I 149 PHE 0.019 0.001 PHE N 26 TRP 0.005 0.001 TRP P 37 HIS 0.004 0.001 HIS F 130 Details of bonding type rmsd covalent geometry : bond 0.00367 (32384) covalent geometry : angle 0.61450 (43936) hydrogen bonds : bond 0.08559 ( 2461) hydrogen bonds : angle 3.44995 ( 7383) Misc. bond : bond 0.10948 ( 29) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 553 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8276 (tm-30) REVERT: A 132 ASP cc_start: 0.8894 (t70) cc_final: 0.8487 (t0) REVERT: B 1 MET cc_start: 0.6016 (mtm) cc_final: 0.5350 (mtm) REVERT: B 120 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7633 (m-10) REVERT: B 126 ASP cc_start: 0.8542 (t0) cc_final: 0.8327 (t0) REVERT: B 137 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8588 (tp-100) REVERT: C 120 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7598 (m-10) REVERT: C 128 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8047 (tp30) REVERT: C 130 HIS cc_start: 0.7868 (t-90) cc_final: 0.6974 (m170) REVERT: D 53 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.7518 (mtm110) REVERT: F 120 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7474 (m-10) REVERT: E 78 ARG cc_start: 0.8488 (mtp85) cc_final: 0.8093 (ttm110) REVERT: E 120 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7614 (m-10) REVERT: E 130 HIS cc_start: 0.7993 (t-90) cc_final: 0.7094 (m170) REVERT: H 53 ARG cc_start: 0.8353 (mtm-85) cc_final: 0.7224 (mtm110) REVERT: H 78 ARG cc_start: 0.8486 (mtp85) cc_final: 0.8081 (ttm110) REVERT: I 120 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7591 (m-10) REVERT: I 126 ASP cc_start: 0.8623 (t0) cc_final: 0.8267 (t0) REVERT: I 130 HIS cc_start: 0.7801 (t-90) cc_final: 0.6992 (m170) REVERT: J 72 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8287 (tm-30) REVERT: J 78 ARG cc_start: 0.8521 (mtp85) cc_final: 0.8073 (ttm110) REVERT: K 120 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7559 (m-10) REVERT: K 126 ASP cc_start: 0.8165 (m-30) cc_final: 0.7589 (t0) REVERT: K 130 HIS cc_start: 0.7761 (t-90) cc_final: 0.6983 (m170) REVERT: L 120 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7622 (m-10) REVERT: N 78 ARG cc_start: 0.8541 (mtp85) cc_final: 0.8065 (ttm110) REVERT: N 120 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7495 (m-10) REVERT: N 130 HIS cc_start: 0.7851 (t-90) cc_final: 0.6993 (m170) REVERT: O 130 HIS cc_start: 0.8005 (t-90) cc_final: 0.7042 (m170) REVERT: P 52 MET cc_start: 0.8566 (mtm) cc_final: 0.8272 (mtt) REVERT: P 126 ASP cc_start: 0.8532 (t0) cc_final: 0.8286 (t0) REVERT: P 130 HIS cc_start: 0.7772 (t-90) cc_final: 0.6969 (m170) REVERT: Q 120 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7639 (m-10) REVERT: R 130 HIS cc_start: 0.7733 (t-90) cc_final: 0.6889 (m170) REVERT: S 120 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7649 (m-10) REVERT: S 130 HIS cc_start: 0.8025 (t-90) cc_final: 0.6973 (m170) REVERT: T 130 HIS cc_start: 0.7944 (t-90) cc_final: 0.7099 (m170) REVERT: U 120 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7614 (m-10) REVERT: U 130 HIS cc_start: 0.8079 (t-90) cc_final: 0.7069 (m170) REVERT: V 120 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7612 (m-10) REVERT: V 130 HIS cc_start: 0.7965 (t-90) cc_final: 0.7026 (m170) REVERT: W 52 MET cc_start: 0.9010 (ttm) cc_final: 0.8738 (ttt) REVERT: W 130 HIS cc_start: 0.7738 (t-90) cc_final: 0.6897 (m170) REVERT: X 120 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7566 (m-10) REVERT: X 130 HIS cc_start: 0.7909 (t-90) cc_final: 0.7047 (m170) outliers start: 88 outliers final: 66 residues processed: 595 average time/residue: 0.1999 time to fit residues: 190.6185 Evaluate side-chains 634 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 554 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 120 PHE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 120 PHE Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 120 PHE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 120 PHE Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 120 PHE Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 120 PHE Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 116 SER Chi-restraints excluded: chain U residue 120 PHE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 120 PHE Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 180 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 302 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 275 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.140092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123641 restraints weight = 48324.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.127135 restraints weight = 28333.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.129535 restraints weight = 18958.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131220 restraints weight = 13830.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.132477 restraints weight = 10759.849| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.548 32413 Z= 0.189 Angle : 0.667 19.634 43936 Z= 0.316 Chirality : 0.033 0.144 4876 Planarity : 0.003 0.069 5680 Dihedral : 6.774 88.060 4272 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.93 % Allowed : 21.38 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.92 (0.14), residues: 3792 helix: 3.89 (0.08), residues: 2928 sheet: None (None), residues: 0 loop : -2.55 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG L 53 TYR 0.008 0.001 TYR J 149 PHE 0.018 0.001 PHE N 26 TRP 0.004 0.001 TRP F 37 HIS 0.004 0.001 HIS M 130 Details of bonding type rmsd covalent geometry : bond 0.00407 (32384) covalent geometry : angle 0.66671 (43936) hydrogen bonds : bond 0.09398 ( 2461) hydrogen bonds : angle 3.68401 ( 7383) Misc. bond : bond 0.10187 ( 29) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 568 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8346 (tm-30) REVERT: A 120 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7669 (m-10) REVERT: A 132 ASP cc_start: 0.8944 (t70) cc_final: 0.8522 (t0) REVERT: B 116 SER cc_start: 0.6649 (OUTLIER) cc_final: 0.6227 (p) REVERT: B 120 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7537 (m-10) REVERT: B 137 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8621 (tp-100) REVERT: C 120 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7672 (m-10) REVERT: C 130 HIS cc_start: 0.7867 (t-90) cc_final: 0.6984 (m170) REVERT: D 120 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7649 (m-10) REVERT: E 120 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7603 (m-10) REVERT: E 130 HIS cc_start: 0.8071 (t-90) cc_final: 0.7068 (m170) REVERT: G 22 ILE cc_start: 0.9195 (mt) cc_final: 0.8949 (mm) REVERT: G 120 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7363 (m-10) REVERT: H 120 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7522 (m-10) REVERT: I 53 ARG cc_start: 0.8386 (mtm-85) cc_final: 0.7615 (mtm110) REVERT: I 120 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7536 (m-10) REVERT: I 126 ASP cc_start: 0.8625 (t0) cc_final: 0.8289 (t0) REVERT: I 130 HIS cc_start: 0.7801 (t-90) cc_final: 0.7004 (m170) REVERT: J 52 MET cc_start: 0.8500 (ttp) cc_final: 0.8165 (ttp) REVERT: J 72 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8345 (tm-30) REVERT: J 78 ARG cc_start: 0.8543 (mtp85) cc_final: 0.8064 (ttm110) REVERT: J 120 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7545 (m-10) REVERT: K 120 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7611 (m-10) REVERT: K 126 ASP cc_start: 0.8117 (m-30) cc_final: 0.7612 (t0) REVERT: L 120 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7746 (m-10) REVERT: M 120 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7561 (m-10) REVERT: N 78 ARG cc_start: 0.8561 (mtp85) cc_final: 0.8058 (ttm110) REVERT: N 130 HIS cc_start: 0.7876 (t-90) cc_final: 0.6988 (m170) REVERT: N 132 ASP cc_start: 0.8848 (t70) cc_final: 0.8399 (t0) REVERT: O 120 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7519 (m-10) REVERT: O 130 HIS cc_start: 0.8010 (t-90) cc_final: 0.7040 (m170) REVERT: P 52 MET cc_start: 0.8589 (mtm) cc_final: 0.8270 (mtt) REVERT: P 120 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7360 (m-10) REVERT: P 126 ASP cc_start: 0.8591 (t0) cc_final: 0.8316 (t0) REVERT: P 130 HIS cc_start: 0.7845 (t-90) cc_final: 0.6992 (m170) REVERT: Q 120 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7675 (m-10) REVERT: R 52 MET cc_start: 0.8807 (ttm) cc_final: 0.8586 (ttp) REVERT: R 130 HIS cc_start: 0.7785 (t-90) cc_final: 0.6855 (m170) REVERT: S 120 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7559 (m-10) REVERT: S 130 HIS cc_start: 0.7964 (t-90) cc_final: 0.6924 (m170) REVERT: T 120 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7536 (m-10) REVERT: T 130 HIS cc_start: 0.8064 (t-90) cc_final: 0.7163 (m170) REVERT: U 120 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7648 (m-10) REVERT: U 130 HIS cc_start: 0.8089 (t-90) cc_final: 0.7058 (m170) REVERT: V 120 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7579 (m-10) REVERT: V 130 HIS cc_start: 0.7990 (t-90) cc_final: 0.7018 (m170) REVERT: W 52 MET cc_start: 0.8986 (ttm) cc_final: 0.8699 (ttt) REVERT: W 120 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7501 (m-10) REVERT: W 130 HIS cc_start: 0.7770 (t-90) cc_final: 0.6914 (m170) REVERT: X 120 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7695 (m-10) REVERT: X 130 HIS cc_start: 0.7949 (t-90) cc_final: 0.7044 (m170) outliers start: 98 outliers final: 61 residues processed: 615 average time/residue: 0.1989 time to fit residues: 195.2653 Evaluate side-chains 651 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 568 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 120 PHE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 120 PHE Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 120 PHE Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 120 PHE Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 120 PHE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 120 PHE Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 120 PHE Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 120 PHE Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 120 PHE Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 120 PHE Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain U residue 120 PHE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 120 PHE Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 120 PHE Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 235 optimal weight: 2.9990 chunk 335 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 316 optimal weight: 8.9990 chunk 366 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.145103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128372 restraints weight = 48518.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132057 restraints weight = 27984.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.134497 restraints weight = 18509.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136293 restraints weight = 13384.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137559 restraints weight = 10371.776| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.602 32413 Z= 0.163 Angle : 0.637 18.621 43936 Z= 0.299 Chirality : 0.032 0.141 4876 Planarity : 0.003 0.071 5680 Dihedral : 6.757 88.650 4272 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.15 % Allowed : 23.03 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.08 (0.14), residues: 3792 helix: 4.01 (0.08), residues: 2932 sheet: None (None), residues: 0 loop : -2.56 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG L 53 TYR 0.007 0.001 TYR J 149 PHE 0.017 0.001 PHE N 26 TRP 0.003 0.001 TRP J 37 HIS 0.004 0.001 HIS M 130 Details of bonding type rmsd covalent geometry : bond 0.00342 (32384) covalent geometry : angle 0.63680 (43936) hydrogen bonds : bond 0.08072 ( 2461) hydrogen bonds : angle 3.42831 ( 7383) Misc. bond : bond 0.11183 ( 29) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 540 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8666 (tm-30) cc_final: 0.7929 (tm-30) REVERT: A 132 ASP cc_start: 0.8857 (t70) cc_final: 0.8448 (t0) REVERT: B 120 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7539 (m-10) REVERT: B 137 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8588 (tp-100) REVERT: C 108 MET cc_start: 0.8484 (tmm) cc_final: 0.8284 (ttp) REVERT: C 120 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7722 (m-10) REVERT: C 130 HIS cc_start: 0.7925 (t-90) cc_final: 0.6879 (m170) REVERT: D 120 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7552 (m-10) REVERT: F 108 MET cc_start: 0.8539 (tmm) cc_final: 0.8237 (ttp) REVERT: E 120 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7682 (m-10) REVERT: E 130 HIS cc_start: 0.8011 (t-90) cc_final: 0.7024 (m170) REVERT: G 22 ILE cc_start: 0.9189 (mt) cc_final: 0.8954 (mm) REVERT: G 120 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7462 (m-10) REVERT: H 120 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7498 (m-10) REVERT: I 53 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7691 (mtm110) REVERT: I 120 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7536 (m-10) REVERT: I 126 ASP cc_start: 0.8586 (t0) cc_final: 0.8255 (t0) REVERT: I 130 HIS cc_start: 0.7718 (t-90) cc_final: 0.6910 (m170) REVERT: J 52 MET cc_start: 0.8367 (ttp) cc_final: 0.8123 (ttp) REVERT: J 72 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8297 (tm-30) REVERT: J 78 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8080 (ttm110) REVERT: J 120 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7548 (m-10) REVERT: K 52 MET cc_start: 0.8463 (ttm) cc_final: 0.8223 (ttp) REVERT: K 120 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7567 (m-10) REVERT: K 126 ASP cc_start: 0.8083 (m-30) cc_final: 0.7612 (t0) REVERT: L 120 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7674 (m-10) REVERT: M 120 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7541 (m-10) REVERT: N 78 ARG cc_start: 0.8544 (mtp85) cc_final: 0.8067 (ttm110) REVERT: N 108 MET cc_start: 0.8552 (tmm) cc_final: 0.8220 (ttp) REVERT: N 130 HIS cc_start: 0.7921 (t-90) cc_final: 0.7006 (m170) REVERT: O 120 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7467 (m-10) REVERT: O 130 HIS cc_start: 0.7982 (t-90) cc_final: 0.7029 (m170) REVERT: P 52 MET cc_start: 0.8514 (mtm) cc_final: 0.8246 (mtt) REVERT: P 120 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: P 126 ASP cc_start: 0.8494 (t0) cc_final: 0.8224 (t0) REVERT: P 130 HIS cc_start: 0.7772 (t-90) cc_final: 0.6964 (m170) REVERT: Q 108 MET cc_start: 0.8503 (tmm) cc_final: 0.8231 (ttp) REVERT: Q 120 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7668 (m-10) REVERT: R 52 MET cc_start: 0.8801 (ttm) cc_final: 0.8588 (ttp) REVERT: R 130 HIS cc_start: 0.7700 (t-90) cc_final: 0.6870 (m170) REVERT: S 108 MET cc_start: 0.8525 (tmm) cc_final: 0.8266 (ttp) REVERT: S 120 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7597 (m-10) REVERT: S 130 HIS cc_start: 0.7967 (t-90) cc_final: 0.7014 (m170) REVERT: T 120 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7665 (m-10) REVERT: T 130 HIS cc_start: 0.7903 (t-90) cc_final: 0.7107 (m170) REVERT: U 120 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7550 (m-10) REVERT: U 130 HIS cc_start: 0.8028 (t-90) cc_final: 0.7062 (m170) REVERT: V 120 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7576 (m-10) REVERT: V 130 HIS cc_start: 0.7976 (t-90) cc_final: 0.7012 (m170) REVERT: W 52 MET cc_start: 0.9033 (ttm) cc_final: 0.8743 (ttt) REVERT: W 130 HIS cc_start: 0.7709 (t-90) cc_final: 0.6884 (m170) REVERT: X 120 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7538 (m-10) REVERT: X 130 HIS cc_start: 0.7926 (t-90) cc_final: 0.7045 (m170) outliers start: 72 outliers final: 45 residues processed: 568 average time/residue: 0.1833 time to fit residues: 171.3457 Evaluate side-chains 593 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 529 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 120 PHE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 120 PHE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 120 PHE Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 120 PHE Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 120 PHE Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 120 PHE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 59 THR Chi-restraints excluded: chain M residue 120 PHE Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 120 PHE Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 120 PHE Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 120 PHE Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 120 PHE Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 120 PHE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 120 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 17 optimal weight: 4.9990 chunk 342 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 344 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.152349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135148 restraints weight = 48574.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.138932 restraints weight = 27805.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141537 restraints weight = 18338.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143283 restraints weight = 13257.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.144627 restraints weight = 10285.745| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.642 32413 Z= 0.145 Angle : 0.617 15.584 43936 Z= 0.290 Chirality : 0.032 0.129 4876 Planarity : 0.003 0.071 5680 Dihedral : 6.706 89.614 4272 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.29 % Allowed : 24.31 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.34 (0.14), residues: 3792 helix: 4.17 (0.08), residues: 2932 sheet: None (None), residues: 0 loop : -2.35 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG L 53 TYR 0.007 0.001 TYR J 149 PHE 0.017 0.001 PHE N 26 TRP 0.005 0.001 TRP J 37 HIS 0.004 0.001 HIS F 130 Details of bonding type rmsd covalent geometry : bond 0.00300 (32384) covalent geometry : angle 0.61734 (43936) hydrogen bonds : bond 0.06507 ( 2461) hydrogen bonds : angle 3.13466 ( 7383) Misc. bond : bond 0.11920 ( 29) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4855.74 seconds wall clock time: 84 minutes 51.18 seconds (5091.18 seconds total)