Starting phenix.real_space_refine on Mon Aug 25 23:14:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k43_9913/08_2025/6k43_9913_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k43_9913/08_2025/6k43_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6k43_9913/08_2025/6k43_9913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k43_9913/08_2025/6k43_9913.map" model { file = "/net/cci-nas-00/data/ceres_data/6k43_9913/08_2025/6k43_9913_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k43_9913/08_2025/6k43_9913_trim.cif" } 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-2.0-5787/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: 5.35, per 1000 atoms: 0.17 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: 2.21 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.51 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: 3.98 Time building geometry restraints manager: 2.94 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: 0.970 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.970 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- 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 aren 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 : 0.768 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: 0.5502 (mtm) cc_final: 0.5294 (mtm) REVERT: B 105 ILE cc_start: 0.7188 (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: 0.7104 (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: 0.7251 (mt) cc_final: 0.6915 (mt) REVERT: F 130 HIS cc_start: 0.7467 (t-170) cc_final: 0.7206 (m170) REVERT: E 1 MET cc_start: 0.5331 (mtm) cc_final: 0.5069 (mtm) REVERT: E 105 ILE cc_start: 0.7306 (mt) cc_final: 0.6971 (mt) REVERT: G 1 MET cc_start: 0.5342 (mtm) cc_final: 0.5094 (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: 0.7271 (m170) REVERT: H 105 ILE cc_start: 0.7268 (mt) cc_final: 0.6914 (mt) REVERT: H 130 HIS cc_start: 0.7526 (t-170) cc_final: 0.7230 (m170) REVERT: I 105 ILE cc_start: 0.7252 (mt) cc_final: 0.6896 (mt) REVERT: J 105 ILE cc_start: 0.7276 (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: 0.7204 (mt) cc_final: 0.6871 (mt) REVERT: K 126 ASP cc_start: 0.8496 (m-30) cc_final: 0.8134 (t0) REVERT: L 105 ILE cc_start: 0.7282 (mt) cc_final: 0.6931 (mt) REVERT: L 130 HIS cc_start: 0.7611 (t-170) cc_final: 0.7216 (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: 0.7547 (t-170) cc_final: 0.7290 (m170) REVERT: O 1 MET cc_start: 0.5650 (mtm) cc_final: 0.5168 (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: 0.7147 (mt) cc_final: 0.6811 (mt) REVERT: P 130 HIS cc_start: 0.7518 (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: 0.4130 (ptt) REVERT: R 105 ILE cc_start: 0.7150 (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: 0.5023 (mtm) REVERT: T 105 ILE cc_start: 0.7167 (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: 0.7281 (mt) cc_final: 0.6911 (mt) REVERT: V 130 HIS cc_start: 0.7644 (t-170) cc_final: 0.7231 (m170) REVERT: W 1 MET cc_start: 0.4443 (ptm) cc_final: 0.3736 (ptt) REVERT: W 105 ILE cc_start: 0.7164 (mt) cc_final: 0.6807 (mt) REVERT: W 130 HIS cc_start: 0.7568 (t-170) cc_final: 0.7256 (m170) REVERT: X 105 ILE cc_start: 0.7261 (mt) cc_final: 0.6908 (mt) REVERT: X 130 HIS cc_start: 0.7547 (t-170) cc_final: 0.7269 (m170) outliers start: 4 outliers final: 4 residues processed: 1015 average time/residue: 0.1749 time to fit residues: 279.3717 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 : 1.068 ------------------------------------------------------------------------------- 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 aren 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 : 1.303 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: 0.4470 (mtm) REVERT: B 53 ARG cc_start: 0.8273 (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: 0.8583 (mtp85) cc_final: 0.7918 (ttm110) REVERT: G 128 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7950 (mm-30) REVERT: H 1 MET cc_start: 0.4892 (mtm) cc_final: 0.3552 (ptm) REVERT: H 78 ARG cc_start: 0.8584 (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: 0.7904 (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: 0.7821 (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: 0.7850 (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: 0.7429 (mtm110) REVERT: U 53 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7250 (mtm110) outliers start: 92 outliers final: 70 residues processed: 824 average time/residue: 0.2086 time to fit residues: 277.5839 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 : 1.321 ------------------------------------------------------------------------------- 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 aren 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 : 1.298 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: 0.7612 (t0) REVERT: A 132 ASP cc_start: 0.9069 (t70) cc_final: 0.8595 (t0) REVERT: B 1 MET cc_start: 0.5554 (mtm) cc_final: 0.4783 (mtm) REVERT: B 4 ASP cc_start: 0.7894 (m-30) cc_final: 0.7589 (t0) REVERT: C 120 PHE cc_start: 0.7939 (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: 0.7842 (m-30) cc_final: 0.7509 (t0) REVERT: D 60 ASP cc_start: 0.8690 (t70) cc_final: 0.8486 (t70) REVERT: F 126 ASP cc_start: 0.8804 (t0) cc_final: 0.8601 (t0) REVERT: E 1 MET cc_start: 0.5443 (mtm) cc_final: 0.4955 (ptm) REVERT: E 4 ASP cc_start: 0.7849 (m-30) cc_final: 0.7589 (t0) REVERT: G 1 MET cc_start: 0.5462 (mtm) cc_final: 0.3742 (ttp) REVERT: G 4 ASP cc_start: 0.7828 (m-30) cc_final: 0.7584 (t0) REVERT: I 1 MET cc_start: 0.5199 (mtm) cc_final: 0.4809 (ptm) REVERT: J 1 MET cc_start: 0.5444 (mtm) cc_final: 0.4802 (ptm) REVERT: J 4 ASP cc_start: 0.7806 (m-30) cc_final: 0.7594 (t0) REVERT: J 78 ARG cc_start: 0.8672 (mtp85) cc_final: 0.8050 (ttm110) REVERT: J 130 HIS cc_start: 0.8144 (t70) cc_final: 0.7943 (t-90) REVERT: K 1 MET cc_start: 0.5326 (mtm) cc_final: 0.5041 (ptm) REVERT: K 4 ASP cc_start: 0.7817 (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: 0.7808 (mm-30) REVERT: N 78 ARG cc_start: 0.8609 (mtp85) cc_final: 0.7973 (ttm110) REVERT: O 4 ASP cc_start: 0.7842 (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: 0.7899 (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: 0.5338 (mtm) cc_final: 0.4879 (ptm) REVERT: W 4 ASP cc_start: 0.7772 (m-30) cc_final: 0.7515 (t0) outliers start: 133 outliers final: 122 residues processed: 751 average time/residue: 0.2069 time to fit residues: 250.8715 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 : 1.311 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.150205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133693 restraints weight = 48511.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.137515 restraints weight = 26969.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.140059 restraints weight = 17408.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.141832 restraints weight = 12440.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.143113 restraints weight = 9541.173| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.511 32413 Z= 0.143 Angle : 0.559 10.581 43936 Z= 0.272 Chirality : 0.033 0.131 4876 Planarity : 0.003 0.030 5680 Dihedral : 6.986 86.175 4280 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.61 % Allowed : 20.16 % Favored : 78.23 % 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 aren not related in a simple way. whole: 3.77 (0.14), residues: 3792 helix: 3.89 (0.08), residues: 2952 sheet: None (None), residues: 0 loop : -3.26 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 73 TYR 0.004 0.001 TYR T 71 PHE 0.016 0.001 PHE V 26 TRP 0.008 0.001 TRP A 37 HIS 0.017 0.001 HIS P 28 Details of bonding type rmsd covalent geometry : bond 0.00284 (32384) covalent geometry : angle 0.55866 (43936) hydrogen bonds : bond 0.07089 ( 2461) hydrogen bonds : angle 3.26593 ( 7383) Misc. bond : bond 0.09489 ( 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 723 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 669 time to evaluate : 1.265 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 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: A 132 ASP cc_start: 0.8997 (t70) cc_final: 0.8552 (t0) REVERT: B 1 MET cc_start: 0.5707 (mtm) cc_final: 0.5207 (mtm) REVERT: B 2 GLN cc_start: 0.8428 (tt0) cc_final: 0.8194 (mt0) REVERT: B 32 GLN cc_start: 0.8954 (mt0) cc_final: 0.8711 (mt0) REVERT: B 81 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7514 (mt0) REVERT: B 120 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.7063 (m-10) REVERT: B 137 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8278 (tp-100) REVERT: C 32 GLN cc_start: 0.8856 (mt0) cc_final: 0.8630 (mt0) REVERT: C 128 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8026 (tp30) REVERT: C 130 HIS cc_start: 0.7845 (t-90) cc_final: 0.6876 (m170) REVERT: C 137 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8448 (tp40) REVERT: D 32 GLN cc_start: 0.8957 (mt0) cc_final: 0.8729 (mt0) REVERT: D 132 ASP cc_start: 0.8996 (t70) cc_final: 0.8473 (t0) REVERT: D 137 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8495 (tp40) REVERT: F 32 GLN cc_start: 0.8862 (mt0) cc_final: 0.8629 (mt0) REVERT: F 126 ASP cc_start: 0.8504 (t0) cc_final: 0.8232 (t0) REVERT: F 130 HIS cc_start: 0.7738 (t-90) cc_final: 0.6723 (m170) REVERT: E 120 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7036 (m-10) REVERT: E 130 HIS cc_start: 0.7922 (t-90) cc_final: 0.6913 (m170) REVERT: E 132 ASP cc_start: 0.9006 (t70) cc_final: 0.8495 (t0) REVERT: E 137 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8504 (tp40) REVERT: G 1 MET cc_start: 0.5398 (mtm) cc_final: 0.4754 (ptm) REVERT: G 32 GLN cc_start: 0.8846 (mt0) cc_final: 0.8639 (mt0) REVERT: G 137 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8484 (tp40) REVERT: H 130 HIS cc_start: 0.7895 (t-90) cc_final: 0.6933 (m170) REVERT: H 137 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8495 (tp40) REVERT: I 120 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7145 (m-10) REVERT: I 130 HIS cc_start: 0.7883 (t-90) cc_final: 0.6938 (m170) REVERT: I 137 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8502 (tp40) REVERT: J 32 GLN cc_start: 0.8885 (mt0) cc_final: 0.8681 (mt0) REVERT: J 78 ARG cc_start: 0.8595 (mtp85) cc_final: 0.8050 (ttm110) REVERT: J 137 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8403 (tp-100) REVERT: K 32 GLN cc_start: 0.8964 (mt0) cc_final: 0.8741 (mt0) REVERT: K 81 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7478 (mt0) REVERT: K 120 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7149 (m-10) REVERT: K 126 ASP cc_start: 0.8060 (m-30) cc_final: 0.7481 (t0) REVERT: K 130 HIS cc_start: 0.7773 (t-90) cc_final: 0.6974 (m170) REVERT: L 120 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7234 (m-10) REVERT: M 32 GLN cc_start: 0.8958 (mt0) cc_final: 0.8748 (mt0) REVERT: M 137 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8534 (tp40) REVERT: N 32 GLN cc_start: 0.8846 (mt0) cc_final: 0.8634 (mt0) REVERT: N 78 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8037 (ttm110) REVERT: N 130 HIS cc_start: 0.7863 (t-90) cc_final: 0.6961 (m170) REVERT: N 132 ASP cc_start: 0.8981 (t70) cc_final: 0.8489 (t0) REVERT: O 1 MET cc_start: 0.5302 (mtm) cc_final: 0.5022 (ptm) REVERT: O 120 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7126 (m-10) REVERT: O 130 HIS cc_start: 0.7913 (t-90) cc_final: 0.6979 (m170) REVERT: O 137 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8340 (tp-100) REVERT: P 32 GLN cc_start: 0.8943 (mt0) cc_final: 0.8711 (mt0) REVERT: P 81 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7531 (mt0) REVERT: P 120 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7123 (m-10) REVERT: P 130 HIS cc_start: 0.7804 (t-90) cc_final: 0.7063 (m170) REVERT: Q 32 GLN cc_start: 0.8874 (mt0) cc_final: 0.8660 (mt0) REVERT: Q 120 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7129 (m-10) REVERT: Q 137 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8397 (tp40) REVERT: R 32 GLN cc_start: 0.8949 (mt0) cc_final: 0.8729 (mt0) REVERT: R 130 HIS cc_start: 0.7642 (t-90) cc_final: 0.6703 (m170) REVERT: R 132 ASP cc_start: 0.8989 (t70) cc_final: 0.8505 (t0) REVERT: S 22 ILE cc_start: 0.8800 (mt) cc_final: 0.8558 (mm) REVERT: S 120 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7173 (m-10) REVERT: S 130 HIS cc_start: 0.7849 (t-90) cc_final: 0.6822 (m170) REVERT: T 1 MET cc_start: 0.5797 (OUTLIER) cc_final: 0.5404 (ptm) REVERT: T 130 HIS cc_start: 0.7911 (t-90) cc_final: 0.6993 (m170) REVERT: T 132 ASP cc_start: 0.8944 (t70) cc_final: 0.8478 (t0) REVERT: U 120 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7113 (m-10) REVERT: U 130 HIS cc_start: 0.7875 (t-90) cc_final: 0.6983 (m170) REVERT: U 137 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8605 (tp40) REVERT: V 120 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7046 (m-10) REVERT: V 130 HIS cc_start: 0.7884 (t-90) cc_final: 0.6862 (m170) REVERT: V 137 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8482 (tp40) REVERT: W 32 GLN cc_start: 0.8927 (mt0) cc_final: 0.8715 (mt0) REVERT: W 120 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7035 (m-10) REVERT: W 130 HIS cc_start: 0.7641 (t-90) cc_final: 0.6673 (m170) REVERT: W 132 ASP cc_start: 0.8984 (t70) cc_final: 0.8493 (t0) REVERT: X 32 GLN cc_start: 0.8928 (mt0) cc_final: 0.8697 (mt0) REVERT: X 130 HIS cc_start: 0.7878 (t-90) cc_final: 0.6954 (m170) outliers start: 54 outliers final: 29 residues processed: 695 average time/residue: 0.1929 time to fit residues: 222.6198 Evaluate side-chains 656 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 613 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1 MET Chi-restraints excluded: chain T residue 59 THR 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 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: 9.9990 chunk 134 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 252 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 346 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.142921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126837 restraints weight = 48844.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130380 restraints weight = 28040.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132806 restraints weight = 18514.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134508 restraints weight = 13388.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135735 restraints weight = 10352.098| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.542 32413 Z= 0.166 Angle : 0.581 14.811 43936 Z= 0.279 Chirality : 0.033 0.133 4876 Planarity : 0.002 0.028 5680 Dihedral : 6.817 86.614 4280 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.57 % Allowed : 19.74 % Favored : 77.69 % 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 aren not related in a simple way. whole: 3.81 (0.14), residues: 3792 helix: 3.88 (0.08), residues: 2952 sheet: None (None), residues: 0 loop : -3.11 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 53 TYR 0.007 0.001 TYR I 149 PHE 0.029 0.001 PHE N 26 TRP 0.007 0.001 TRP J 37 HIS 0.004 0.001 HIS M 130 Details of bonding type rmsd covalent geometry : bond 0.00344 (32384) covalent geometry : angle 0.58113 (43936) hydrogen bonds : bond 0.08654 ( 2461) hydrogen bonds : angle 3.46146 ( 7383) Misc. bond : bond 0.10069 ( 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 684 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 598 time to evaluate : 1.342 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: A 120 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7358 (m-10) REVERT: A 132 ASP cc_start: 0.8936 (t70) cc_final: 0.8508 (t0) REVERT: B 1 MET cc_start: 0.5901 (mtm) cc_final: 0.5285 (mtm) REVERT: B 2 GLN cc_start: 0.8499 (tt0) cc_final: 0.8293 (mt0) REVERT: B 32 GLN cc_start: 0.9109 (mt0) cc_final: 0.8875 (mt0) REVERT: B 137 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8507 (tp-100) REVERT: C 120 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7467 (m-10) REVERT: C 128 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8005 (tp30) REVERT: C 130 HIS cc_start: 0.7845 (t-90) cc_final: 0.6945 (m170) REVERT: D 132 ASP cc_start: 0.8936 (t70) cc_final: 0.8433 (t0) REVERT: F 126 ASP cc_start: 0.8551 (t0) cc_final: 0.8308 (t0) REVERT: F 130 HIS cc_start: 0.7832 (t-90) cc_final: 0.6927 (m170) REVERT: F 132 ASP cc_start: 0.8920 (t70) cc_final: 0.8435 (t0) REVERT: E 78 ARG cc_start: 0.8545 (mtp85) cc_final: 0.8144 (ttm110) REVERT: E 120 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7553 (m-10) REVERT: E 130 HIS cc_start: 0.7925 (t-90) cc_final: 0.7002 (m170) REVERT: E 132 ASP cc_start: 0.8928 (t70) cc_final: 0.8440 (t0) REVERT: H 78 ARG cc_start: 0.8521 (mtp85) cc_final: 0.8144 (ttm110) REVERT: I 130 HIS cc_start: 0.7797 (t-90) cc_final: 0.7030 (m170) REVERT: J 78 ARG cc_start: 0.8567 (mtp85) cc_final: 0.8113 (ttm110) REVERT: K 32 GLN cc_start: 0.9073 (mt0) cc_final: 0.8873 (mt0) REVERT: K 126 ASP cc_start: 0.8070 (m-30) cc_final: 0.7563 (t0) REVERT: K 130 HIS cc_start: 0.7752 (t-90) cc_final: 0.6959 (m170) REVERT: L 120 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7512 (m-10) REVERT: N 78 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8099 (ttm110) REVERT: N 130 HIS cc_start: 0.7927 (t-90) cc_final: 0.6981 (m170) REVERT: P 32 GLN cc_start: 0.9076 (mt0) cc_final: 0.8844 (mt0) REVERT: P 126 ASP cc_start: 0.8526 (t0) cc_final: 0.8267 (t0) REVERT: P 130 HIS cc_start: 0.7826 (t-90) cc_final: 0.7014 (m170) REVERT: Q 120 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: R 130 HIS cc_start: 0.7852 (t-90) cc_final: 0.6911 (m170) REVERT: R 132 ASP cc_start: 0.8937 (t70) cc_final: 0.8459 (t0) REVERT: S 130 HIS cc_start: 0.7909 (t-90) cc_final: 0.6962 (m170) REVERT: T 120 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7183 (m-10) REVERT: T 130 HIS cc_start: 0.7964 (t-90) cc_final: 0.7180 (m170) REVERT: U 120 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7621 (m-10) REVERT: U 130 HIS cc_start: 0.7986 (t-90) cc_final: 0.7083 (m170) REVERT: V 120 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7530 (m-10) REVERT: V 130 HIS cc_start: 0.7961 (t-90) cc_final: 0.7025 (m170) REVERT: W 130 HIS cc_start: 0.7847 (t-90) cc_final: 0.6895 (m170) REVERT: W 132 ASP cc_start: 0.8936 (t70) cc_final: 0.8453 (t0) REVERT: X 32 GLN cc_start: 0.9068 (mt0) cc_final: 0.8861 (mt0) REVERT: X 120 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7270 (m-10) REVERT: X 130 HIS cc_start: 0.7908 (t-90) cc_final: 0.7036 (m170) outliers start: 86 outliers final: 66 residues processed: 629 average time/residue: 0.2130 time to fit residues: 214.4932 Evaluate side-chains 657 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 581 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 57 VAL 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 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 57 VAL 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 57 VAL 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 57 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 120 PHE Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 57 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 131 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 5 optimal weight: 40.0000 chunk 84 optimal weight: 0.0070 chunk 344 optimal weight: 0.0870 chunk 279 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 137 GLN U 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.142595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125982 restraints weight = 48818.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129733 restraints weight = 27481.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132249 restraints weight = 17848.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.134016 restraints weight = 12779.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.135277 restraints weight = 9792.736| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.506 32413 Z= 0.169 Angle : 0.593 17.911 43936 Z= 0.284 Chirality : 0.032 0.149 4876 Planarity : 0.003 0.118 5680 Dihedral : 6.757 86.014 4272 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.83 % Allowed : 19.53 % Favored : 76.64 % 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 aren not related in a simple way. whole: 3.87 (0.14), residues: 3792 helix: 3.91 (0.08), residues: 2948 sheet: None (None), residues: 0 loop : -2.99 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG L 53 TYR 0.006 0.001 TYR I 149 PHE 0.024 0.001 PHE N 26 TRP 0.004 0.001 TRP J 37 HIS 0.004 0.001 HIS G 130 Details of bonding type rmsd covalent geometry : bond 0.00352 (32384) covalent geometry : angle 0.59270 (43936) hydrogen bonds : bond 0.08660 ( 2461) hydrogen bonds : angle 3.47130 ( 7383) Misc. bond : bond 0.09411 ( 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 708 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 580 time to evaluate : 1.335 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: 0.8867 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 132 ASP cc_start: 0.9039 (t70) cc_final: 0.8602 (t0) REVERT: B 1 MET cc_start: 0.5777 (mtm) cc_final: 0.5197 (mtm) REVERT: B 32 GLN cc_start: 0.9024 (mt0) cc_final: 0.8805 (mt0) REVERT: B 120 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7440 (m-10) REVERT: B 137 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8435 (tp-100) REVERT: C 128 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8092 (tp30) REVERT: C 130 HIS cc_start: 0.7877 (t-90) cc_final: 0.6882 (m170) REVERT: D 1 MET cc_start: 0.6912 (pmm) cc_final: 0.6699 (ptm) REVERT: D 53 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.7494 (mtm110) REVERT: F 120 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7037 (m-10) REVERT: F 126 ASP cc_start: 0.8650 (t0) cc_final: 0.8377 (t0) REVERT: F 130 HIS cc_start: 0.7769 (t-90) cc_final: 0.6850 (m170) REVERT: E 120 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7394 (m-10) REVERT: E 130 HIS cc_start: 0.7937 (t-90) cc_final: 0.6878 (m170) REVERT: E 132 ASP cc_start: 0.9036 (t70) cc_final: 0.8557 (t0) REVERT: H 78 ARG cc_start: 0.8530 (mtp85) cc_final: 0.8014 (ttm110) REVERT: H 120 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7044 (m-10) REVERT: H 130 HIS cc_start: 0.7897 (t-90) cc_final: 0.6822 (m170) REVERT: I 120 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7356 (m-10) REVERT: I 126 ASP cc_start: 0.8641 (t0) cc_final: 0.8363 (t0) REVERT: I 130 HIS cc_start: 0.7750 (t-90) cc_final: 0.6854 (m170) REVERT: J 78 ARG cc_start: 0.8612 (mtp85) cc_final: 0.8080 (ttm110) REVERT: J 120 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7120 (m-10) REVERT: K 120 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7350 (m-10) REVERT: K 126 ASP cc_start: 0.8133 (m-30) cc_final: 0.7512 (t0) REVERT: K 130 HIS cc_start: 0.7777 (t-90) cc_final: 0.6846 (m170) REVERT: L 120 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7367 (m-10) REVERT: N 78 ARG cc_start: 0.8627 (mtp85) cc_final: 0.8062 (ttm110) REVERT: N 130 HIS cc_start: 0.7926 (t-90) cc_final: 0.6875 (m170) REVERT: N 132 ASP cc_start: 0.9020 (t70) cc_final: 0.8516 (t0) REVERT: O 120 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7335 (m-10) REVERT: O 130 HIS cc_start: 0.7956 (t-90) cc_final: 0.6900 (m170) REVERT: P 32 GLN cc_start: 0.8985 (mt0) cc_final: 0.8779 (mt0) REVERT: P 52 MET cc_start: 0.8685 (mtm) cc_final: 0.8409 (mtt) REVERT: P 120 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7413 (m-10) REVERT: P 126 ASP cc_start: 0.8659 (t0) cc_final: 0.8371 (t0) REVERT: P 130 HIS cc_start: 0.7783 (t-90) cc_final: 0.6848 (m170) REVERT: Q 120 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7313 (m-10) REVERT: R 52 MET cc_start: 0.8759 (mtm) cc_final: 0.8534 (ttm) REVERT: R 130 HIS cc_start: 0.7728 (t-90) cc_final: 0.6767 (m170) REVERT: R 132 ASP cc_start: 0.9016 (t70) cc_final: 0.8551 (t0) REVERT: S 120 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7373 (m-10) REVERT: S 130 HIS cc_start: 0.7936 (t-90) cc_final: 0.6823 (m170) REVERT: T 130 HIS cc_start: 0.8043 (t-90) cc_final: 0.7062 (m170) REVERT: U 120 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7414 (m-10) REVERT: U 130 HIS cc_start: 0.8027 (t-90) cc_final: 0.7001 (m170) REVERT: U 132 ASP cc_start: 0.8963 (t70) cc_final: 0.8551 (t0) REVERT: V 120 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7377 (m-10) REVERT: V 130 HIS cc_start: 0.7944 (t-90) cc_final: 0.6897 (m170) REVERT: W 130 HIS cc_start: 0.7736 (t-90) cc_final: 0.6750 (m170) REVERT: W 132 ASP cc_start: 0.9019 (t70) cc_final: 0.8547 (t0) REVERT: X 32 GLN cc_start: 0.8999 (mt0) cc_final: 0.8787 (mt0) REVERT: X 120 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7057 (m-10) REVERT: X 130 HIS cc_start: 0.7901 (t-90) cc_final: 0.6915 (m170) outliers start: 128 outliers final: 84 residues processed: 644 average time/residue: 0.2105 time to fit residues: 217.8232 Evaluate side-chains 672 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 572 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 115 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 59 THR 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 57 VAL Chi-restraints excluded: chain D residue 141 ILE 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 115 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 115 THR 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 115 THR 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 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 115 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 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 115 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 57 VAL 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 353 optimal weight: 0.9980 chunk 368 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 350 optimal weight: 1.9990 chunk 148 optimal weight: 0.4980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135176 restraints weight = 48569.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.138815 restraints weight = 27945.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.141266 restraints weight = 18506.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.142949 restraints weight = 13402.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.144225 restraints weight = 10373.470| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.523 32413 Z= 0.142 Angle : 0.573 15.629 43936 Z= 0.270 Chirality : 0.032 0.132 4876 Planarity : 0.003 0.071 5680 Dihedral : 6.668 88.985 4272 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.06 % Allowed : 21.89 % Favored : 76.05 % 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 aren not related in a simple way. whole: 4.21 (0.14), residues: 3792 helix: 4.14 (0.08), residues: 2948 sheet: None (None), residues: 0 loop : -2.79 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG L 53 TYR 0.005 0.001 TYR J 43 PHE 0.023 0.001 PHE N 26 TRP 0.004 0.001 TRP J 37 HIS 0.004 0.001 HIS M 130 Details of bonding type rmsd covalent geometry : bond 0.00291 (32384) covalent geometry : angle 0.57345 (43936) hydrogen bonds : bond 0.06628 ( 2461) hydrogen bonds : angle 3.12321 ( 7383) Misc. bond : bond 0.09718 ( 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 629 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 560 time to evaluate : 1.288 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: A 72 GLN cc_start: 0.8770 (tm-30) cc_final: 0.7968 (tm-30) REVERT: A 132 ASP cc_start: 0.8963 (t70) cc_final: 0.8544 (t0) REVERT: B 1 MET cc_start: 0.5966 (mtm) cc_final: 0.5466 (mtm) REVERT: B 32 GLN cc_start: 0.8956 (mt0) cc_final: 0.8742 (mt0) REVERT: B 137 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8356 (tp-100) REVERT: C 22 ILE cc_start: 0.8930 (mt) cc_final: 0.8636 (mm) REVERT: C 120 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7200 (m-10) REVERT: C 128 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8034 (tp30) REVERT: C 130 HIS cc_start: 0.7734 (t-90) cc_final: 0.6802 (m170) REVERT: D 1 MET cc_start: 0.7002 (pmm) cc_final: 0.6638 (ptm) REVERT: D 137 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8528 (tp40) REVERT: F 126 ASP cc_start: 0.8570 (t0) cc_final: 0.8324 (t0) REVERT: F 130 HIS cc_start: 0.7768 (t-90) cc_final: 0.6816 (m170) REVERT: E 78 ARG cc_start: 0.8553 (mtp85) cc_final: 0.8112 (ttm110) REVERT: E 120 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.7100 (m-10) REVERT: E 130 HIS cc_start: 0.7811 (t-90) cc_final: 0.6853 (m170) REVERT: G 22 ILE cc_start: 0.9091 (mt) cc_final: 0.8868 (mm) REVERT: H 53 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.6991 (mtm110) REVERT: H 78 ARG cc_start: 0.8554 (mtp85) cc_final: 0.8105 (ttm110) REVERT: H 130 HIS cc_start: 0.7750 (t-90) cc_final: 0.6844 (m170) REVERT: I 130 HIS cc_start: 0.7720 (t-90) cc_final: 0.6893 (m170) REVERT: J 72 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8346 (tm-30) REVERT: J 78 ARG cc_start: 0.8593 (mtp85) cc_final: 0.8067 (ttm110) REVERT: K 126 ASP cc_start: 0.8058 (m-30) cc_final: 0.7432 (t0) REVERT: K 130 HIS cc_start: 0.7770 (t-90) cc_final: 0.6880 (m170) REVERT: K 135 GLU cc_start: 0.7877 (tt0) cc_final: 0.7671 (tt0) REVERT: L 72 GLN cc_start: 0.8697 (tp40) cc_final: 0.8440 (tp-100) REVERT: L 120 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7246 (m-10) REVERT: N 78 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8051 (ttm110) REVERT: N 130 HIS cc_start: 0.7746 (t-90) cc_final: 0.6881 (m170) REVERT: N 132 ASP cc_start: 0.8918 (t70) cc_final: 0.8422 (t0) REVERT: O 120 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7069 (m-10) REVERT: O 130 HIS cc_start: 0.7922 (t-90) cc_final: 0.6882 (m170) REVERT: O 137 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8386 (tp40) REVERT: P 32 GLN cc_start: 0.8911 (mt0) cc_final: 0.8705 (mt0) REVERT: P 52 MET cc_start: 0.8521 (mtm) cc_final: 0.8195 (mtt) REVERT: P 120 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7212 (m-10) REVERT: P 126 ASP cc_start: 0.8519 (t0) cc_final: 0.8255 (t0) REVERT: P 130 HIS cc_start: 0.7670 (t-90) cc_final: 0.6780 (m170) REVERT: R 52 MET cc_start: 0.8734 (mtm) cc_final: 0.8531 (ttm) REVERT: R 130 HIS cc_start: 0.7688 (t-90) cc_final: 0.6760 (m170) REVERT: S 120 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7162 (m-10) REVERT: S 130 HIS cc_start: 0.7974 (t-90) cc_final: 0.6848 (m170) REVERT: T 130 HIS cc_start: 0.7983 (t-90) cc_final: 0.7036 (m170) REVERT: U 120 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7172 (m-10) REVERT: U 130 HIS cc_start: 0.7962 (t-90) cc_final: 0.6901 (m170) REVERT: V 120 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7125 (m-10) REVERT: V 130 HIS cc_start: 0.7827 (t-90) cc_final: 0.6877 (m170) REVERT: W 120 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7103 (m-10) REVERT: W 130 HIS cc_start: 0.7656 (t-90) cc_final: 0.6761 (m170) REVERT: X 130 HIS cc_start: 0.7864 (t-90) cc_final: 0.6926 (m170) outliers start: 69 outliers final: 54 residues processed: 590 average time/residue: 0.1960 time to fit residues: 192.2116 Evaluate side-chains 605 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 541 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 57 VAL 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 115 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 141 ILE 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 115 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 115 THR 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 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 115 THR Chi-restraints excluded: chain N residue 141 ILE 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 115 THR Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 141 ILE 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 115 THR Chi-restraints excluded: chain S residue 120 PHE 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 120 PHE Chi-restraints excluded: chain V residue 141 ILE 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 57 VAL Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 239 optimal weight: 1.9990 chunk 314 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 276 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 351 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 289 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.141226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122244 restraints weight = 50542.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.126577 restraints weight = 26436.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129561 restraints weight = 16434.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.131559 restraints weight = 11331.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133075 restraints weight = 8445.929| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.483 32413 Z= 0.204 Angle : 0.658 13.616 43936 Z= 0.319 Chirality : 0.034 0.148 4876 Planarity : 0.003 0.073 5680 Dihedral : 6.855 89.027 4272 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.35 % Allowed : 21.08 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.74 (0.14), residues: 3792 helix: 3.77 (0.08), residues: 2944 sheet: None (None), residues: 0 loop : -2.78 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG L 53 TYR 0.007 0.001 TYR I 149 PHE 0.020 0.001 PHE N 26 TRP 0.006 0.001 TRP F 37 HIS 0.004 0.001 HIS M 130 Details of bonding type rmsd covalent geometry : bond 0.00441 (32384) covalent geometry : angle 0.65767 (43936) hydrogen bonds : bond 0.10259 ( 2461) hydrogen bonds : angle 3.82264 ( 7383) Misc. bond : bond 0.08973 ( 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 708 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 596 time to evaluate : 1.328 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: 0.8966 (tm-30) cc_final: 0.8479 (tm-30) REVERT: A 120 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7158 (m-10) REVERT: A 132 ASP cc_start: 0.9072 (t70) cc_final: 0.8672 (t0) REVERT: B 1 MET cc_start: 0.6116 (mtm) cc_final: 0.5566 (mtm) REVERT: B 32 GLN cc_start: 0.8845 (mt0) cc_final: 0.8644 (mt0) REVERT: B 116 SER cc_start: 0.7008 (OUTLIER) cc_final: 0.6602 (p) REVERT: B 126 ASP cc_start: 0.8761 (t0) cc_final: 0.8538 (t0) REVERT: C 120 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.7131 (m-10) REVERT: C 128 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8179 (tp30) REVERT: C 130 HIS cc_start: 0.7723 (t-90) cc_final: 0.6667 (m170) REVERT: D 1 MET cc_start: 0.7253 (pmm) cc_final: 0.6960 (pmm) REVERT: F 120 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6849 (m-10) REVERT: F 126 ASP cc_start: 0.8758 (t0) cc_final: 0.8552 (t0) REVERT: E 53 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7157 (mtm110) REVERT: E 120 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7227 (m-10) REVERT: E 130 HIS cc_start: 0.7915 (t-90) cc_final: 0.6707 (m170) REVERT: G 120 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.6848 (m-10) REVERT: G 126 ASP cc_start: 0.8779 (t0) cc_final: 0.8567 (t0) REVERT: H 78 ARG cc_start: 0.8538 (mtp85) cc_final: 0.7889 (ttm110) REVERT: H 120 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.6790 (m-10) REVERT: I 53 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7328 (mtm110) REVERT: I 116 SER cc_start: 0.6997 (OUTLIER) cc_final: 0.6335 (p) REVERT: I 120 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6959 (m-10) REVERT: I 126 ASP cc_start: 0.8744 (t0) cc_final: 0.8391 (t0) REVERT: I 130 HIS cc_start: 0.7694 (t-90) cc_final: 0.6753 (m170) REVERT: J 4 ASP cc_start: 0.7784 (m-30) cc_final: 0.7326 (t0) REVERT: J 72 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8475 (tm-30) REVERT: J 78 ARG cc_start: 0.8566 (mtp85) cc_final: 0.7894 (ttm110) REVERT: J 120 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6885 (m-10) REVERT: K 126 ASP cc_start: 0.8372 (m-30) cc_final: 0.7690 (t0) REVERT: L 120 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7232 (m-10) REVERT: M 126 ASP cc_start: 0.8789 (t0) cc_final: 0.8571 (t0) REVERT: N 78 ARG cc_start: 0.8566 (mtp85) cc_final: 0.7868 (ttm110) REVERT: N 120 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6865 (m-10) REVERT: N 130 HIS cc_start: 0.7691 (t-90) cc_final: 0.6724 (m170) REVERT: O 4 ASP cc_start: 0.7720 (m-30) cc_final: 0.7269 (t0) REVERT: O 120 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7186 (m-10) REVERT: O 130 HIS cc_start: 0.7892 (t-90) cc_final: 0.6729 (m170) REVERT: P 4 ASP cc_start: 0.7590 (m-30) cc_final: 0.7269 (t0) REVERT: P 32 GLN cc_start: 0.8840 (mt0) cc_final: 0.8623 (mt0) REVERT: P 52 MET cc_start: 0.8591 (mtm) cc_final: 0.8107 (mtt) REVERT: P 120 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.7112 (m-10) REVERT: P 126 ASP cc_start: 0.8770 (t0) cc_final: 0.8440 (t0) REVERT: P 130 HIS cc_start: 0.7722 (t-90) cc_final: 0.6688 (m170) REVERT: Q 120 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7114 (m-10) REVERT: R 52 MET cc_start: 0.8833 (mtm) cc_final: 0.8462 (ttm) REVERT: R 120 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7142 (m-10) REVERT: S 120 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7108 (m-10) REVERT: S 130 HIS cc_start: 0.7865 (t-90) cc_final: 0.6672 (m170) REVERT: T 4 ASP cc_start: 0.7832 (m-30) cc_final: 0.7434 (t0) REVERT: T 120 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7265 (m-10) REVERT: T 126 ASP cc_start: 0.8866 (t0) cc_final: 0.8504 (t0) REVERT: T 130 HIS cc_start: 0.7947 (t-90) cc_final: 0.6867 (m170) REVERT: U 120 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.7122 (m-10) REVERT: U 130 HIS cc_start: 0.7954 (t-90) cc_final: 0.6733 (m170) REVERT: V 81 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7821 (mt0) REVERT: V 120 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7188 (m-10) REVERT: V 130 HIS cc_start: 0.7858 (t-90) cc_final: 0.6748 (m170) REVERT: W 120 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.7109 (m-10) REVERT: X 120 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.6854 (m-10) REVERT: X 130 HIS cc_start: 0.7813 (t-90) cc_final: 0.6737 (m170) outliers start: 112 outliers final: 71 residues processed: 645 average time/residue: 0.2174 time to fit residues: 223.0903 Evaluate side-chains 680 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 586 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 116 SER 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 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 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 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 57 VAL 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 116 SER 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 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 141 ILE Chi-restraints excluded: chain L residue 54 HIS 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 141 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 120 PHE Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 57 VAL 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 115 THR Chi-restraints excluded: chain P residue 116 SER 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 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 52 MET 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 59 THR Chi-restraints excluded: chain U residue 115 THR 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 180 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 302 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 275 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.140136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123859 restraints weight = 48714.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127362 restraints weight = 28420.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.129712 restraints weight = 18932.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.131397 restraints weight = 13816.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.132612 restraints weight = 10758.745| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.485 32413 Z= 0.184 Angle : 0.642 13.307 43936 Z= 0.309 Chirality : 0.033 0.156 4876 Planarity : 0.003 0.071 5680 Dihedral : 6.849 87.400 4272 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.57 % Allowed : 22.91 % Favored : 74.52 % 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 aren not related in a simple way. whole: 3.90 (0.14), residues: 3792 helix: 3.92 (0.08), residues: 2912 sheet: None (None), residues: 0 loop : -2.58 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG L 53 TYR 0.006 0.001 TYR I 149 PHE 0.014 0.001 PHE M 26 TRP 0.004 0.001 TRP F 37 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00392 (32384) covalent geometry : angle 0.64198 (43936) hydrogen bonds : bond 0.09353 ( 2461) hydrogen bonds : angle 3.67341 ( 7383) Misc. bond : bond 0.09008 ( 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 655 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 569 time to evaluate : 1.338 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: 0.8817 (tm-30) cc_final: 0.8404 (tm-30) REVERT: A 132 ASP cc_start: 0.8981 (t70) cc_final: 0.8567 (t0) REVERT: B 1 MET cc_start: 0.6037 (mtm) cc_final: 0.5622 (mtm) REVERT: B 32 GLN cc_start: 0.9072 (mt0) cc_final: 0.8870 (mt0) REVERT: B 120 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7464 (m-10) REVERT: B 137 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8575 (tp-100) REVERT: C 120 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7557 (m-10) REVERT: C 128 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7950 (tp30) REVERT: C 130 HIS cc_start: 0.7885 (t-90) cc_final: 0.6926 (m170) REVERT: D 1 MET cc_start: 0.7031 (pmm) cc_final: 0.6819 (pmm) REVERT: F 120 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7580 (m-10) REVERT: E 120 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7542 (m-10) REVERT: E 130 HIS cc_start: 0.7965 (t-90) cc_final: 0.6967 (m170) REVERT: G 22 ILE cc_start: 0.9177 (mt) cc_final: 0.8949 (mm) REVERT: G 120 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7567 (m-10) REVERT: H 78 ARG cc_start: 0.8538 (mtp85) cc_final: 0.8080 (ttm110) REVERT: I 116 SER cc_start: 0.6957 (OUTLIER) cc_final: 0.6247 (p) REVERT: I 126 ASP cc_start: 0.8586 (t0) cc_final: 0.8292 (t0) REVERT: I 130 HIS cc_start: 0.7797 (t-90) cc_final: 0.6958 (m170) REVERT: J 72 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8371 (tm-30) REVERT: J 78 ARG cc_start: 0.8557 (mtp85) cc_final: 0.8047 (ttm110) REVERT: K 126 ASP cc_start: 0.8175 (m-30) cc_final: 0.7579 (t0) REVERT: K 130 HIS cc_start: 0.7831 (t-90) cc_final: 0.6975 (m170) REVERT: L 52 MET cc_start: 0.6434 (mtp) cc_final: 0.6201 (mtp) REVERT: L 120 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7663 (m-10) REVERT: M 120 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7628 (m-10) REVERT: N 78 ARG cc_start: 0.8585 (mtp85) cc_final: 0.8058 (ttm110) REVERT: N 130 HIS cc_start: 0.7862 (t-90) cc_final: 0.6943 (m170) REVERT: N 132 ASP cc_start: 0.8940 (t70) cc_final: 0.8451 (t0) REVERT: O 120 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7584 (m-10) REVERT: O 130 HIS cc_start: 0.8017 (t-90) cc_final: 0.7006 (m170) REVERT: P 32 GLN cc_start: 0.9080 (mt0) cc_final: 0.8854 (mt0) REVERT: P 52 MET cc_start: 0.8601 (mtm) cc_final: 0.8297 (mtt) REVERT: P 120 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: P 126 ASP cc_start: 0.8594 (t0) cc_final: 0.8320 (t0) REVERT: P 130 HIS cc_start: 0.7811 (t-90) cc_final: 0.6941 (m170) REVERT: Q 120 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7665 (m-10) REVERT: R 52 MET cc_start: 0.8864 (mtm) cc_final: 0.8593 (ttm) REVERT: R 130 HIS cc_start: 0.7797 (t-90) cc_final: 0.6841 (m170) REVERT: S 120 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7599 (m-10) REVERT: S 130 HIS cc_start: 0.7978 (t-90) cc_final: 0.6995 (m170) REVERT: T 116 SER cc_start: 0.6945 (OUTLIER) cc_final: 0.6193 (p) REVERT: T 130 HIS cc_start: 0.8002 (t-90) cc_final: 0.7104 (m170) REVERT: U 120 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7510 (m-10) REVERT: U 130 HIS cc_start: 0.8052 (t-90) cc_final: 0.7017 (m170) REVERT: V 81 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7749 (mt0) REVERT: V 120 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7607 (m-10) REVERT: V 130 HIS cc_start: 0.8001 (t-90) cc_final: 0.7000 (m170) REVERT: W 120 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7591 (m-10) REVERT: X 120 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7594 (m-10) REVERT: X 130 HIS cc_start: 0.7992 (t-90) cc_final: 0.6994 (m170) outliers start: 86 outliers final: 65 residues processed: 594 average time/residue: 0.2163 time to fit residues: 205.0199 Evaluate side-chains 655 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 572 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 141 ILE 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 57 VAL Chi-restraints excluded: chain C residue 59 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 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 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 57 VAL 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 116 SER Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 57 VAL 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 141 ILE Chi-restraints excluded: chain L residue 54 HIS 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 120 PHE 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 57 VAL 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 115 THR Chi-restraints excluded: chain P residue 120 PHE Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 59 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 141 ILE Chi-restraints excluded: chain S residue 52 MET 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 116 SER 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 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: 0.0570 chunk 335 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 316 optimal weight: 7.9990 chunk 366 optimal weight: 4.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126779 restraints weight = 48560.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.130420 restraints weight = 27577.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.132974 restraints weight = 18147.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.134756 restraints weight = 13054.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136078 restraints weight = 9996.835| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.493 32413 Z= 0.167 Angle : 0.632 16.028 43936 Z= 0.300 Chirality : 0.033 0.135 4876 Planarity : 0.003 0.069 5680 Dihedral : 6.849 89.290 4272 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.51 % Allowed : 22.82 % Favored : 74.67 % 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 aren not related in a simple way. whole: 4.02 (0.14), residues: 3792 helix: 4.00 (0.08), residues: 2924 sheet: None (None), residues: 0 loop : -2.65 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG L 53 TYR 0.005 0.001 TYR I 149 PHE 0.019 0.001 PHE N 26 TRP 0.003 0.001 TRP G 37 HIS 0.004 0.001 HIS M 130 Details of bonding type rmsd covalent geometry : bond 0.00346 (32384) covalent geometry : angle 0.63160 (43936) hydrogen bonds : bond 0.08407 ( 2461) hydrogen bonds : angle 3.48737 ( 7383) Misc. bond : bond 0.09160 ( 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 641 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 557 time to evaluate : 1.412 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: 0.8852 (tm-30) cc_final: 0.8403 (tm-30) REVERT: A 108 MET cc_start: 0.8507 (tmm) cc_final: 0.8235 (ttp) REVERT: A 120 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7433 (m-10) REVERT: A 132 ASP cc_start: 0.8990 (t70) cc_final: 0.8583 (t0) REVERT: B 1 MET cc_start: 0.6154 (mtm) cc_final: 0.5690 (mtm) REVERT: B 32 GLN cc_start: 0.9005 (mt0) cc_final: 0.8790 (mt0) REVERT: B 120 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7431 (m-10) REVERT: B 137 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8452 (tp-100) REVERT: C 22 ILE cc_start: 0.8938 (mt) cc_final: 0.8654 (mm) REVERT: C 120 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7384 (m-10) REVERT: C 128 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8149 (tp30) REVERT: C 130 HIS cc_start: 0.7841 (t-90) cc_final: 0.6818 (m170) REVERT: D 1 MET cc_start: 0.7084 (pmm) cc_final: 0.6869 (pmm) REVERT: D 4 ASP cc_start: 0.7166 (t0) cc_final: 0.6785 (m-30) REVERT: E 72 GLN cc_start: 0.8783 (tp40) cc_final: 0.8557 (tp-100) REVERT: E 120 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7418 (m-10) REVERT: E 130 HIS cc_start: 0.8004 (t-90) cc_final: 0.6908 (m170) REVERT: G 22 ILE cc_start: 0.9079 (mt) cc_final: 0.8871 (mm) REVERT: H 72 GLN cc_start: 0.8772 (tp40) cc_final: 0.8571 (tp40) REVERT: H 130 HIS cc_start: 0.7836 (t-90) cc_final: 0.6786 (m170) REVERT: I 108 MET cc_start: 0.8469 (tmm) cc_final: 0.8246 (ttp) REVERT: I 120 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7476 (m-10) REVERT: I 126 ASP cc_start: 0.8618 (t0) cc_final: 0.8310 (t0) REVERT: I 130 HIS cc_start: 0.7716 (t-90) cc_final: 0.6809 (m170) REVERT: J 72 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8424 (tm-30) REVERT: J 78 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8022 (ttm110) REVERT: K 120 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7064 (m-10) REVERT: K 126 ASP cc_start: 0.8198 (m-30) cc_final: 0.7504 (t0) REVERT: K 130 HIS cc_start: 0.7793 (t-90) cc_final: 0.6891 (m170) REVERT: L 108 MET cc_start: 0.8445 (tmm) cc_final: 0.8224 (ttp) REVERT: L 120 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7490 (m-10) REVERT: N 78 ARG cc_start: 0.8588 (mtp85) cc_final: 0.8014 (ttm110) REVERT: N 130 HIS cc_start: 0.7968 (t-90) cc_final: 0.6868 (m170) REVERT: N 132 ASP cc_start: 0.8970 (t70) cc_final: 0.8472 (t0) REVERT: O 120 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7333 (m-10) REVERT: O 130 HIS cc_start: 0.7965 (t-90) cc_final: 0.6904 (m170) REVERT: P 32 GLN cc_start: 0.9020 (mt0) cc_final: 0.8755 (mt0) REVERT: P 52 MET cc_start: 0.8600 (mtm) cc_final: 0.8186 (mtt) REVERT: P 120 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7056 (m-10) REVERT: P 126 ASP cc_start: 0.8625 (t0) cc_final: 0.8318 (t0) REVERT: P 130 HIS cc_start: 0.7771 (t-90) cc_final: 0.6872 (m170) REVERT: R 52 MET cc_start: 0.8843 (mtm) cc_final: 0.8523 (ttm) REVERT: R 130 HIS cc_start: 0.7725 (t-90) cc_final: 0.6764 (m170) REVERT: S 108 MET cc_start: 0.8511 (tmm) cc_final: 0.8254 (ttp) REVERT: S 120 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7479 (m-10) REVERT: S 130 HIS cc_start: 0.7951 (t-90) cc_final: 0.6899 (m170) REVERT: T 108 MET cc_start: 0.8471 (tmm) cc_final: 0.8207 (ttp) REVERT: T 120 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7472 (m-10) REVERT: T 130 HIS cc_start: 0.7975 (t-90) cc_final: 0.7017 (m170) REVERT: U 120 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7362 (m-10) REVERT: U 130 HIS cc_start: 0.7996 (t-90) cc_final: 0.6965 (m170) REVERT: U 137 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8532 (tp40) REVERT: V 81 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7688 (mt0) REVERT: V 120 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7430 (m-10) REVERT: V 130 HIS cc_start: 0.7967 (t-90) cc_final: 0.6903 (m170) REVERT: W 120 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7400 (m-10) REVERT: X 130 HIS cc_start: 0.7936 (t-90) cc_final: 0.6892 (m170) outliers start: 84 outliers final: 64 residues processed: 581 average time/residue: 0.2094 time to fit residues: 199.6141 Evaluate side-chains 629 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 549 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL 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 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 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 141 ILE Chi-restraints excluded: chain F residue 57 VAL 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 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 141 ILE Chi-restraints excluded: chain H residue 57 VAL 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 57 VAL Chi-restraints excluded: chain J residue 59 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 120 PHE 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 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 141 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 57 VAL 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 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 141 ILE Chi-restraints excluded: chain R residue 57 VAL 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 57 VAL Chi-restraints excluded: chain S residue 59 THR 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 120 PHE Chi-restraints excluded: chain U residue 137 GLN 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 141 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 17 optimal weight: 3.9990 chunk 342 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 268 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.143543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127208 restraints weight = 48508.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.130744 restraints weight = 28165.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.133098 restraints weight = 18736.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.134799 restraints weight = 13677.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136041 restraints weight = 10633.193| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.492 32413 Z= 0.194 Angle : 0.748 59.084 43936 Z= 0.382 Chirality : 0.034 0.641 4876 Planarity : 0.003 0.069 5680 Dihedral : 6.851 89.299 4272 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.60 % Allowed : 23.15 % Favored : 74.25 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.02 (0.14), residues: 3792 helix: 4.01 (0.08), residues: 2924 sheet: None (None), residues: 0 loop : -2.65 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG L 53 TYR 0.008 0.001 TYR P 149 PHE 0.018 0.001 PHE N 26 TRP 0.003 0.001 TRP B 37 HIS 0.004 0.001 HIS M 130 Details of bonding type rmsd covalent geometry : bond 0.00410 (32384) covalent geometry : angle 0.74799 (43936) hydrogen bonds : bond 0.08450 ( 2461) hydrogen bonds : angle 3.49864 ( 7383) Misc. bond : bond 0.09146 ( 29) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5122.66 seconds wall clock time: 89 minutes 44.30 seconds (5384.30 seconds total)