Starting phenix.real_space_refine on Fri Mar 6 12:02:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k3o_9910/03_2026/6k3o_9910.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k3o_9910/03_2026/6k3o_9910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6k3o_9910/03_2026/6k3o_9910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k3o_9910/03_2026/6k3o_9910.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k3o_9910/03_2026/6k3o_9910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k3o_9910/03_2026/6k3o_9910.map" } resolution = 3.4 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= 0.032 sd= 1.138 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 19947 2.51 5 N 5375 2.21 5 O 6054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 157 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31508 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 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: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} 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: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} 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: "H" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} 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: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1301 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 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: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 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: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} 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: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 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: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} 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: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} 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: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1292 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 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: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1295 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 155} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "B" 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: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "R" 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: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "W" 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: "X" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.30, per 1000 atoms: 0.23 Number of scatterers: 31508 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 6054 8.00 N 5375 7.00 C 19947 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.4 seconds 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7292 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 80.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 removed outlier: 3.531A pdb=" N ILE A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 65 removed outlier: 3.635A 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 114 through 145 Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'B' and resid 4 through 34 removed outlier: 3.528A pdb=" N ILE B 8 " --> pdb=" O ASP B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 65 removed outlier: 3.904A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 110 removed outlier: 3.964A pdb=" N MET B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 145 Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'C' and resid 4 through 34 removed outlier: 3.531A pdb=" N ILE C 8 " --> pdb=" O ASP C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 65 removed outlier: 3.637A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 110 removed outlier: 3.930A pdb=" N MET C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 145 Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'D' and resid 4 through 34 removed outlier: 3.525A pdb=" N ILE D 8 " --> pdb=" O ASP D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 65 removed outlier: 3.916A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 110 removed outlier: 4.006A pdb=" N MET D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 145 Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'F' and resid 4 through 34 removed outlier: 3.507A pdb=" N ILE F 8 " --> pdb=" O ASP F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 65 removed outlier: 3.691A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 110 removed outlier: 3.970A pdb=" N MET F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 145 Processing helix chain 'F' and resid 145 through 151 Processing helix chain 'E' and resid 4 through 34 removed outlier: 3.520A pdb=" N ILE E 8 " --> pdb=" O ASP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 65 removed outlier: 3.637A pdb=" N LEU E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 110 removed outlier: 3.893A pdb=" N MET E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 145 Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'G' and resid 4 through 34 removed outlier: 3.535A pdb=" N ILE G 8 " --> pdb=" O ASP G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 65 removed outlier: 3.629A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 110 removed outlier: 3.869A pdb=" N MET G 86 " --> pdb=" O SER G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 145 Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'H' and resid 4 through 34 removed outlier: 3.526A pdb=" N ILE H 8 " --> pdb=" O ASP H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 65 removed outlier: 3.630A pdb=" N LEU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 110 removed outlier: 3.927A pdb=" N MET H 86 " --> pdb=" O SER H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 145 Processing helix chain 'H' and resid 145 through 151 Processing helix chain 'I' and resid 4 through 34 removed outlier: 3.557A pdb=" N ILE I 8 " --> pdb=" O ASP I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 65 removed outlier: 3.636A pdb=" N LEU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 110 removed outlier: 3.875A pdb=" N MET I 86 " --> pdb=" O SER I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 145 Processing helix chain 'I' and resid 145 through 151 Processing helix chain 'J' and resid 4 through 34 removed outlier: 3.548A pdb=" N ILE J 8 " --> pdb=" O ASP J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 65 removed outlier: 3.634A pdb=" N LEU J 65 " --> pdb=" O ARG J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 110 removed outlier: 3.948A pdb=" N MET J 86 " --> pdb=" O SER J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 145 Processing helix chain 'J' and resid 145 through 151 Processing helix chain 'K' and resid 4 through 34 removed outlier: 3.519A pdb=" N ILE K 8 " --> pdb=" O ASP K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 65 removed outlier: 3.882A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 removed outlier: 3.962A pdb=" N MET K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 145 Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'L' and resid 4 through 34 removed outlier: 3.615A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 65 removed outlier: 3.608A pdb=" N LEU L 65 " --> pdb=" O ARG L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 110 removed outlier: 3.942A pdb=" N MET L 86 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 145 Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'M' and resid 4 through 34 removed outlier: 3.500A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 65 removed outlier: 3.927A pdb=" N TYR M 43 " --> pdb=" O LYS M 39 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU M 65 " --> pdb=" O ARG M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 110 removed outlier: 3.986A pdb=" N MET M 86 " --> pdb=" O SER M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 145 Processing helix chain 'M' and resid 145 through 151 Processing helix chain 'N' and resid 4 through 35 removed outlier: 3.513A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS N 35 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 65 removed outlier: 3.614A pdb=" N LEU N 65 " --> pdb=" O ARG N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 110 removed outlier: 3.961A pdb=" N MET N 86 " --> pdb=" O SER N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 145 Processing helix chain 'N' and resid 145 through 151 Processing helix chain 'O' and resid 4 through 34 removed outlier: 3.554A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 65 removed outlier: 3.614A 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 114 through 145 Processing helix chain 'O' and resid 145 through 151 Processing helix chain 'P' and resid 4 through 34 removed outlier: 3.523A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 65 removed outlier: 3.895A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU P 65 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 110 removed outlier: 3.964A pdb=" N MET P 86 " --> pdb=" O SER P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 145 Processing helix chain 'P' and resid 145 through 151 Processing helix chain 'Q' and resid 4 through 34 removed outlier: 3.611A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 65 removed outlier: 3.612A pdb=" N LEU Q 65 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 110 removed outlier: 3.930A pdb=" N MET Q 86 " --> pdb=" O SER Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 145 Processing helix chain 'Q' and resid 145 through 151 Processing helix chain 'R' and resid 4 through 34 removed outlier: 3.518A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 65 removed outlier: 3.918A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 110 removed outlier: 4.032A pdb=" N MET R 86 " --> pdb=" O SER R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 145 Processing helix chain 'R' and resid 145 through 151 Processing helix chain 'S' and resid 4 through 35 removed outlier: 3.538A pdb=" N ILE S 8 " --> pdb=" O ASP S 4 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 65 removed outlier: 3.718A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU S 65 " --> pdb=" O ARG S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 110 removed outlier: 3.975A pdb=" N MET S 86 " --> pdb=" O SER S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 145 Processing helix chain 'S' and resid 145 through 151 Processing helix chain 'T' and resid 4 through 35 removed outlier: 3.551A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS T 35 " --> pdb=" O LEU T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 65 removed outlier: 3.642A 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 114 through 145 Processing helix chain 'T' and resid 145 through 151 Processing helix chain 'U' and resid 4 through 34 removed outlier: 3.521A pdb=" N ILE U 8 " --> pdb=" O ASP U 4 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 65 removed outlier: 3.879A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU U 65 " --> pdb=" O ARG U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 110 removed outlier: 3.929A pdb=" N MET U 86 " --> pdb=" O SER U 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 145 Processing helix chain 'U' and resid 145 through 151 Processing helix chain 'V' and resid 4 through 34 removed outlier: 3.533A pdb=" N ILE V 8 " --> pdb=" O ASP V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 65 removed outlier: 3.619A pdb=" N LEU V 65 " --> pdb=" O ARG V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 82 through 110 removed outlier: 3.959A pdb=" N MET V 86 " --> pdb=" O SER V 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 114 through 145 Processing helix chain 'V' and resid 145 through 151 Processing helix chain 'W' and resid 4 through 34 removed outlier: 3.518A pdb=" N ILE W 8 " --> pdb=" O ASP W 4 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 65 removed outlier: 3.844A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU W 65 " --> pdb=" O ARG W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 110 removed outlier: 3.992A pdb=" N MET W 86 " --> pdb=" O SER W 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 114 through 145 Processing helix chain 'W' and resid 145 through 151 Processing helix chain 'X' and resid 4 through 34 removed outlier: 3.511A pdb=" N ILE X 8 " --> pdb=" O ASP X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 65 removed outlier: 3.772A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU X 65 " --> pdb=" O ARG X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 110 removed outlier: 4.004A pdb=" N MET X 86 " --> pdb=" O SER X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 145 Processing helix chain 'X' and resid 145 through 151 2494 hydrogen bonds defined for protein. 7482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 13390 1.40 - 1.57: 18442 1.57 - 1.75: 0 1.75 - 1.92: 192 1.92 - 2.09: 48 Bond restraints: 32072 Sorted by residual: bond pdb=" CA GLN S 158 " pdb=" C GLN S 158 " ideal model delta sigma weight residual 1.534 1.524 0.010 9.50e-03 1.11e+04 1.17e+00 bond pdb=" CA ALA O 110 " pdb=" C ALA O 110 " ideal model delta sigma weight residual 1.523 1.543 -0.019 1.80e-02 3.09e+03 1.14e+00 bond pdb=" CA GLN N 158 " pdb=" C GLN N 158 " ideal model delta sigma weight residual 1.534 1.524 0.010 9.50e-03 1.11e+04 1.07e+00 bond pdb=" CA ALA P 110 " pdb=" C ALA P 110 " ideal model delta sigma weight residual 1.523 1.542 -0.018 1.80e-02 3.09e+03 1.05e+00 bond pdb=" CA ALA H 110 " pdb=" C ALA H 110 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.80e-02 3.09e+03 1.02e+00 ... (remaining 32067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 42848 1.83 - 3.67: 579 3.67 - 5.50: 27 5.50 - 7.34: 40 7.34 - 9.17: 6 Bond angle restraints: 43500 Sorted by residual: angle pdb=" C ARG A 109 " pdb=" N ALA A 110 " pdb=" CA ALA A 110 " ideal model delta sigma weight residual 122.31 115.44 6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" C ARG E 109 " pdb=" N ALA E 110 " pdb=" CA ALA E 110 " ideal model delta sigma weight residual 122.31 115.47 6.84 2.00e+00 2.50e-01 1.17e+01 angle pdb=" C ARG R 109 " pdb=" N ALA R 110 " pdb=" CA ALA R 110 " ideal model delta sigma weight residual 122.31 115.47 6.84 2.00e+00 2.50e-01 1.17e+01 angle pdb=" C ARG T 109 " pdb=" N ALA T 110 " pdb=" CA ALA T 110 " ideal model delta sigma weight residual 122.31 115.50 6.81 2.00e+00 2.50e-01 1.16e+01 angle pdb=" C ARG W 109 " pdb=" N ALA W 110 " pdb=" CA ALA W 110 " ideal model delta sigma weight residual 122.31 115.51 6.80 2.00e+00 2.50e-01 1.16e+01 ... (remaining 43495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 17020 17.69 - 35.38: 1797 35.38 - 53.07: 270 53.07 - 70.76: 73 70.76 - 88.45: 20 Dihedral angle restraints: 19180 sinusoidal: 8002 harmonic: 11178 Sorted by residual: 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 38.65 -38.65 2 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" C2D HEM S 202 " pdb=" C3D HEM S 202 " pdb=" CAD HEM S 202 " pdb=" CBD HEM S 202 " ideal model delta sinusoidal sigma weight residual 180.00 91.55 88.45 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C2A HEM F 202 " pdb=" CAA HEM F 202 " pdb=" CBA HEM F 202 " pdb=" CGA HEM F 202 " ideal model delta sinusoidal sigma weight residual 0.00 -86.17 86.17 2 2.00e+01 2.50e-03 1.19e+01 ... (remaining 19177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 2942 0.021 - 0.042: 1100 0.042 - 0.064: 482 0.064 - 0.085: 173 0.085 - 0.106: 132 Chirality restraints: 4829 Sorted by residual: chirality pdb=" CA VAL U 77 " pdb=" N VAL U 77 " pdb=" C VAL U 77 " pdb=" CB VAL U 77 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.82e-01 chirality pdb=" CA VAL J 77 " pdb=" N VAL J 77 " pdb=" C VAL J 77 " pdb=" CB VAL J 77 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.79e-01 chirality pdb=" CA ILE U 154 " pdb=" N ILE U 154 " pdb=" C ILE U 154 " pdb=" CB ILE U 154 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.78e-01 ... (remaining 4826 not shown) Planarity restraints: 5615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 37 " -0.012 2.00e-02 2.50e+03 8.48e-03 1.80e+00 pdb=" CG TRP A 37 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 37 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 37 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 37 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 37 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 37 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 37 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 37 " -0.011 2.00e-02 2.50e+03 7.75e-03 1.50e+00 pdb=" CG TRP O 37 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP O 37 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP O 37 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP O 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP O 37 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP O 37 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 37 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 37 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP O 37 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP T 37 " 0.011 2.00e-02 2.50e+03 7.72e-03 1.49e+00 pdb=" CG TRP T 37 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP T 37 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP T 37 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP T 37 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP T 37 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP T 37 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP T 37 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP T 37 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP T 37 " 0.001 2.00e-02 2.50e+03 ... (remaining 5612 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.84: 24 1.84 - 2.61: 537 2.61 - 3.37: 44106 3.37 - 4.14: 64131 4.14 - 4.90: 124870 Nonbonded interactions: 233668 Sorted by model distance: nonbonded pdb=" OE2 GLU O 127 " pdb="FE FE2 O 201 " model vdw 1.077 3.000 nonbonded pdb=" OE1 GLU K 18 " pdb=" OE1 GLU K 51 " model vdw 1.308 3.040 nonbonded pdb=" OE1 GLU M 18 " pdb=" OE1 GLU M 51 " model vdw 1.322 3.040 nonbonded pdb=" OE1 GLU U 18 " pdb=" OE1 GLU U 51 " model vdw 1.335 3.040 nonbonded pdb=" OE1 GLU S 18 " pdb=" OE1 GLU S 51 " model vdw 1.342 3.040 ... (remaining 233663 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 157) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.970 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 0.662 32104 Z= 0.547 Angle : 0.557 9.174 43500 Z= 0.325 Chirality : 0.031 0.106 4829 Planarity : 0.002 0.024 5615 Dihedral : 14.463 88.447 11888 Min Nonbonded Distance : 1.077 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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 are not related in a simple way. whole: -1.52 (0.11), residues: 3742 helix: 0.08 (0.08), residues: 2922 sheet: None (None), residues: 0 loop : -4.98 (0.11), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 73 TYR 0.005 0.001 TYR L 43 PHE 0.017 0.001 PHE I 26 TRP 0.023 0.003 TRP A 37 HIS 0.002 0.000 HIS M 129 Details of bonding type rmsd covalent geometry : bond 0.00334 (32072) covalent geometry : angle 0.55738 (43500) hydrogen bonds : bond 0.10712 ( 2494) hydrogen bonds : angle 4.72604 ( 7482) Misc. bond : bond 0.22825 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 1.321 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: C 132 ASP cc_start: 0.8847 (t0) cc_final: 0.8620 (t0) REVERT: F 132 ASP cc_start: 0.8863 (t0) cc_final: 0.8644 (t0) REVERT: E 132 ASP cc_start: 0.8859 (t0) cc_final: 0.8620 (t0) REVERT: L 132 ASP cc_start: 0.8875 (t0) cc_final: 0.8651 (t0) REVERT: P 132 ASP cc_start: 0.8901 (t0) cc_final: 0.8663 (t0) REVERT: Q 132 ASP cc_start: 0.8861 (t0) cc_final: 0.8616 (t0) REVERT: T 132 ASP cc_start: 0.8833 (t0) cc_final: 0.8633 (t0) REVERT: U 132 ASP cc_start: 0.8872 (t0) cc_final: 0.8628 (t0) REVERT: U 156 GLN cc_start: 0.8525 (tp-100) cc_final: 0.8228 (mm-40) outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.1908 time to fit residues: 176.5564 Evaluate side-chains 463 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 156 GLN C 24 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN F 118 ASN F 156 GLN E 24 GLN E 130 HIS G 24 GLN G 130 HIS H 24 GLN ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 GLN J 24 GLN K 24 GLN ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN M 24 GLN ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN N 118 ASN N 130 HIS N 156 GLN O 24 GLN P 24 GLN P 130 HIS P 156 GLN Q 24 GLN Q 130 HIS R 24 GLN S 24 GLN S 118 ASN ** S 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 156 GLN T 24 GLN ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 24 GLN W 24 GLN X 24 GLN X 118 ASN X 156 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.150783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.137450 restraints weight = 47498.505| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.56 r_work: 0.3685 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.397 32104 Z= 0.195 Angle : 0.663 23.232 43500 Z= 0.313 Chirality : 0.035 0.133 4829 Planarity : 0.003 0.021 5615 Dihedral : 6.385 88.986 4222 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.08 % Allowed : 12.11 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.13), residues: 3742 helix: 2.65 (0.09), residues: 2898 sheet: None (None), residues: 0 loop : -3.33 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 53 TYR 0.018 0.001 TYR I 25 PHE 0.018 0.001 PHE G 26 TRP 0.012 0.002 TRP S 37 HIS 0.004 0.001 HIS L 54 Details of bonding type rmsd covalent geometry : bond 0.00398 (32072) covalent geometry : angle 0.66330 (43500) hydrogen bonds : bond 0.09935 ( 2494) hydrogen bonds : angle 3.86149 ( 7482) Misc. bond : bond 0.07684 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 613 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7599 (mm-30) REVERT: B 18 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7849 (mm-30) REVERT: B 130 HIS cc_start: 0.7426 (t-170) cc_final: 0.7176 (m170) REVERT: C 18 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7682 (mm-30) REVERT: C 132 ASP cc_start: 0.8932 (t0) cc_final: 0.8640 (t0) REVERT: D 18 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7618 (mm-30) REVERT: F 18 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7760 (mm-30) REVERT: F 132 ASP cc_start: 0.8884 (t0) cc_final: 0.8627 (t0) REVERT: E 18 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7704 (mm-30) REVERT: E 132 ASP cc_start: 0.8855 (t0) cc_final: 0.8582 (t0) REVERT: G 18 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7597 (mm-30) REVERT: H 18 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7789 (mm-30) REVERT: I 18 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7452 (mm-30) REVERT: J 18 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7407 (mm-30) REVERT: K 18 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7691 (mm-30) REVERT: L 18 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7703 (mm-30) REVERT: L 132 ASP cc_start: 0.9045 (t0) cc_final: 0.8791 (t0) REVERT: L 155 GLU cc_start: 0.8110 (tt0) cc_final: 0.7686 (mt-10) REVERT: M 18 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7673 (mm-30) REVERT: N 18 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7686 (mm-30) REVERT: O 2 GLN cc_start: 0.8540 (mt0) cc_final: 0.8312 (mt0) REVERT: O 18 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7612 (mm-30) REVERT: P 18 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7775 (mm-30) REVERT: P 132 ASP cc_start: 0.8917 (t0) cc_final: 0.8629 (t0) REVERT: Q 132 ASP cc_start: 0.8962 (t0) cc_final: 0.8680 (t0) REVERT: R 18 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7527 (mm-30) REVERT: S 18 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7714 (mm-30) REVERT: T 18 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7689 (mm-30) REVERT: T 132 ASP cc_start: 0.8911 (t0) cc_final: 0.8681 (t0) REVERT: U 18 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7686 (mm-30) REVERT: U 132 ASP cc_start: 0.8877 (t0) cc_final: 0.8585 (t0) REVERT: V 18 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7476 (mm-30) REVERT: W 18 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7548 (mm-30) REVERT: W 130 HIS cc_start: 0.7452 (t-170) cc_final: 0.7090 (m170) REVERT: X 18 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7398 (mm-30) REVERT: X 155 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8095 (mm-30) outliers start: 36 outliers final: 34 residues processed: 616 average time/residue: 0.1842 time to fit residues: 186.4736 Evaluate side-chains 580 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 546 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 151 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 158 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 348 optimal weight: 6.9990 chunk 331 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN C 130 HIS ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS G 130 HIS ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 HIS ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN M 130 HIS N 130 HIS P 130 HIS Q 130 HIS ** S 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 130 HIS V 24 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.143779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130323 restraints weight = 47577.901| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.60 r_work: 0.3594 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.330 32104 Z= 0.239 Angle : 0.656 21.375 43500 Z= 0.320 Chirality : 0.035 0.146 4829 Planarity : 0.003 0.020 5615 Dihedral : 6.678 87.900 4222 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.13 % Allowed : 13.92 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.13), residues: 3742 helix: 2.96 (0.08), residues: 2880 sheet: None (None), residues: 0 loop : -2.65 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 53 TYR 0.014 0.002 TYR J 25 PHE 0.018 0.002 PHE G 26 TRP 0.010 0.002 TRP T 37 HIS 0.003 0.001 HIS G 130 Details of bonding type rmsd covalent geometry : bond 0.00527 (32072) covalent geometry : angle 0.65567 (43500) hydrogen bonds : bond 0.11996 ( 2494) hydrogen bonds : angle 4.08903 ( 7482) Misc. bond : bond 0.06582 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 563 time to evaluate : 1.256 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: B 130 HIS cc_start: 0.7602 (t-170) cc_final: 0.7246 (m170) REVERT: C 132 ASP cc_start: 0.9033 (t0) cc_final: 0.8719 (t0) REVERT: D 18 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7872 (mm-30) REVERT: F 132 ASP cc_start: 0.8999 (t0) cc_final: 0.8684 (t0) REVERT: E 132 ASP cc_start: 0.8962 (t0) cc_final: 0.8672 (t0) REVERT: G 18 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7743 (mm-30) REVERT: H 18 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7858 (mm-30) REVERT: I 18 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7703 (mm-30) REVERT: J 18 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7668 (mm-30) REVERT: L 65 LEU cc_start: 0.8415 (mt) cc_final: 0.8147 (tp) REVERT: L 130 HIS cc_start: 0.7504 (t70) cc_final: 0.7088 (m170) REVERT: L 132 ASP cc_start: 0.9142 (t0) cc_final: 0.8839 (t0) REVERT: P 132 ASP cc_start: 0.8996 (t0) cc_final: 0.8685 (t0) REVERT: Q 132 ASP cc_start: 0.9028 (t0) cc_final: 0.8725 (t0) REVERT: R 18 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7744 (mm-30) REVERT: T 52 MET cc_start: 0.8974 (mtt) cc_final: 0.8759 (mtt) REVERT: T 132 ASP cc_start: 0.9026 (t0) cc_final: 0.8748 (t0) REVERT: U 130 HIS cc_start: 0.7573 (t-170) cc_final: 0.7315 (m170) REVERT: U 132 ASP cc_start: 0.8971 (t0) cc_final: 0.8644 (t0) REVERT: V 128 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8263 (mm-30) REVERT: W 18 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7728 (mm-30) REVERT: W 130 HIS cc_start: 0.7514 (t-170) cc_final: 0.7239 (m170) REVERT: X 155 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8093 (mm-30) outliers start: 104 outliers final: 90 residues processed: 602 average time/residue: 0.1939 time to fit residues: 191.2182 Evaluate side-chains 635 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 544 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 151 SER Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 2 GLN Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 151 SER Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain V residue 128 GLU Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 141 ILE Chi-restraints excluded: chain X residue 151 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 37 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 342 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS D 130 HIS E 130 HIS G 130 HIS H 130 HIS K 130 HIS M 130 HIS N 130 HIS O 130 HIS P 130 HIS Q 130 HIS S 130 HIS T 130 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.142572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129171 restraints weight = 47179.331| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.59 r_work: 0.3591 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.324 32104 Z= 0.233 Angle : 0.630 14.188 43500 Z= 0.315 Chirality : 0.034 0.138 4829 Planarity : 0.003 0.021 5615 Dihedral : 6.674 89.502 4222 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.04 % Allowed : 15.15 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.13), residues: 3742 helix: 3.14 (0.08), residues: 2889 sheet: None (None), residues: 0 loop : -2.40 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 53 TYR 0.013 0.001 TYR B 25 PHE 0.017 0.001 PHE G 26 TRP 0.005 0.001 TRP I 37 HIS 0.003 0.001 HIS G 130 Details of bonding type rmsd covalent geometry : bond 0.00508 (32072) covalent geometry : angle 0.63014 (43500) hydrogen bonds : bond 0.12170 ( 2494) hydrogen bonds : angle 4.10115 ( 7482) Misc. bond : bond 0.06568 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 544 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8322 (t0) cc_final: 0.8098 (t0) REVERT: B 130 HIS cc_start: 0.7638 (t-170) cc_final: 0.7289 (m170) REVERT: C 132 ASP cc_start: 0.9035 (t0) cc_final: 0.8723 (t0) REVERT: C 139 ASP cc_start: 0.8362 (t0) cc_final: 0.8130 (t0) REVERT: D 18 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7754 (mm-30) REVERT: F 132 ASP cc_start: 0.9013 (t0) cc_final: 0.8691 (t0) REVERT: F 139 ASP cc_start: 0.8309 (t0) cc_final: 0.8057 (t0) REVERT: E 132 ASP cc_start: 0.8981 (t0) cc_final: 0.8688 (t0) REVERT: G 18 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7778 (mm-30) REVERT: H 18 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7779 (mm-30) REVERT: I 18 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7722 (mm-30) REVERT: J 18 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7662 (mm-30) REVERT: K 128 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8290 (tp30) REVERT: L 130 HIS cc_start: 0.7569 (t70) cc_final: 0.7179 (m170) REVERT: L 132 ASP cc_start: 0.9139 (t0) cc_final: 0.8829 (t0) REVERT: L 139 ASP cc_start: 0.8395 (t0) cc_final: 0.8174 (t0) REVERT: P 52 MET cc_start: 0.8991 (mtt) cc_final: 0.8768 (mtt) REVERT: P 132 ASP cc_start: 0.9008 (t0) cc_final: 0.8690 (t0) REVERT: P 139 ASP cc_start: 0.8331 (t0) cc_final: 0.8119 (t0) REVERT: Q 132 ASP cc_start: 0.9038 (t0) cc_final: 0.8738 (t0) REVERT: Q 139 ASP cc_start: 0.8380 (t0) cc_final: 0.8093 (t0) REVERT: R 18 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7710 (mm-30) REVERT: T 132 ASP cc_start: 0.9032 (t0) cc_final: 0.8744 (t0) REVERT: T 139 ASP cc_start: 0.8261 (t0) cc_final: 0.8056 (t0) REVERT: U 130 HIS cc_start: 0.7607 (t-170) cc_final: 0.7290 (m170) REVERT: U 132 ASP cc_start: 0.8995 (t0) cc_final: 0.8673 (t0) REVERT: V 128 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8213 (mm-30) REVERT: V 139 ASP cc_start: 0.8303 (t0) cc_final: 0.8076 (t0) REVERT: W 18 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7781 (mm-30) REVERT: W 128 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8331 (tp30) REVERT: W 130 HIS cc_start: 0.7561 (t-170) cc_final: 0.7254 (m170) REVERT: X 18 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7491 (mm-30) outliers start: 134 outliers final: 116 residues processed: 607 average time/residue: 0.1933 time to fit residues: 192.7640 Evaluate side-chains 643 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 524 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 151 SER Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 151 SER Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain V residue 128 GLU Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 128 GLU Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 128 GLU Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 141 ILE Chi-restraints excluded: chain X residue 151 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 165 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 281 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 HIS N 130 HIS P 130 HIS Q 130 HIS S 130 HIS T 130 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.146734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.133414 restraints weight = 47309.840| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.55 r_work: 0.3622 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.306 32104 Z= 0.202 Angle : 0.606 24.195 43500 Z= 0.301 Chirality : 0.033 0.131 4829 Planarity : 0.003 0.021 5615 Dihedral : 6.781 89.464 4222 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.31 % Allowed : 15.96 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.45 (0.13), residues: 3742 helix: 3.43 (0.08), residues: 2889 sheet: None (None), residues: 0 loop : -2.19 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 53 TYR 0.009 0.001 TYR U 25 PHE 0.016 0.001 PHE G 26 TRP 0.004 0.001 TRP V 37 HIS 0.003 0.000 HIS G 130 Details of bonding type rmsd covalent geometry : bond 0.00410 (32072) covalent geometry : angle 0.60617 (43500) hydrogen bonds : bond 0.11293 ( 2494) hydrogen bonds : angle 3.94096 ( 7482) Misc. bond : bond 0.06175 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 543 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8247 (t0) cc_final: 0.8027 (t0) REVERT: B 65 LEU cc_start: 0.8408 (mt) cc_final: 0.8179 (tp) REVERT: B 130 HIS cc_start: 0.7629 (t-170) cc_final: 0.7299 (m170) REVERT: C 65 LEU cc_start: 0.8388 (mt) cc_final: 0.8098 (tp) REVERT: C 132 ASP cc_start: 0.9005 (t0) cc_final: 0.8705 (t0) REVERT: D 18 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7814 (mm-30) REVERT: F 132 ASP cc_start: 0.9003 (t0) cc_final: 0.8683 (t0) REVERT: E 132 ASP cc_start: 0.8968 (t0) cc_final: 0.8690 (t0) REVERT: G 18 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7808 (mm-30) REVERT: G 65 LEU cc_start: 0.8379 (mt) cc_final: 0.8137 (tp) REVERT: H 18 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7900 (mm-30) REVERT: H 65 LEU cc_start: 0.8410 (mt) cc_final: 0.8136 (tp) REVERT: I 18 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7723 (mm-30) REVERT: J 18 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7703 (mm-30) REVERT: K 65 LEU cc_start: 0.8453 (mt) cc_final: 0.8177 (tp) REVERT: K 128 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8261 (tp30) REVERT: L 65 LEU cc_start: 0.8304 (mt) cc_final: 0.8035 (tp) REVERT: L 130 HIS cc_start: 0.7509 (t70) cc_final: 0.7158 (m170) REVERT: L 132 ASP cc_start: 0.9090 (t0) cc_final: 0.8816 (t0) REVERT: L 139 ASP cc_start: 0.8259 (t0) cc_final: 0.8029 (t0) REVERT: M 128 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8253 (tp30) REVERT: O 31 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8163 (tt) REVERT: P 65 LEU cc_start: 0.8385 (mt) cc_final: 0.8133 (tp) REVERT: P 132 ASP cc_start: 0.9007 (t0) cc_final: 0.8693 (t0) REVERT: P 139 ASP cc_start: 0.8275 (t0) cc_final: 0.8048 (t0) REVERT: Q 132 ASP cc_start: 0.9014 (t0) cc_final: 0.8732 (t0) REVERT: Q 139 ASP cc_start: 0.8271 (t0) cc_final: 0.8010 (t0) REVERT: R 18 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7763 (mm-30) REVERT: T 132 ASP cc_start: 0.9021 (t0) cc_final: 0.8749 (t0) REVERT: U 130 HIS cc_start: 0.7511 (t-170) cc_final: 0.7168 (m170) REVERT: U 132 ASP cc_start: 0.8973 (t0) cc_final: 0.8678 (t0) REVERT: V 128 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8188 (mm-30) REVERT: W 130 HIS cc_start: 0.7517 (t-170) cc_final: 0.7243 (m170) REVERT: X 52 MET cc_start: 0.7340 (mtp) cc_final: 0.7030 (mtp) REVERT: X 155 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8058 (mm-30) outliers start: 143 outliers final: 110 residues processed: 616 average time/residue: 0.1901 time to fit residues: 192.6151 Evaluate side-chains 638 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 524 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 128 GLU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 107 VAL Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 151 SER Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 2 GLN Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 151 SER Chi-restraints excluded: chain R residue 155 GLU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 128 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 116 SER Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain V residue 128 GLU Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 128 GLU Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 141 ILE Chi-restraints excluded: chain X residue 151 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 352 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 326 optimal weight: 8.9990 chunk 337 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 168 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS P 130 HIS Q 130 HIS S 130 HIS ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.149760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136403 restraints weight = 47052.663| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.55 r_work: 0.3656 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.282 32104 Z= 0.191 Angle : 0.598 18.923 43500 Z= 0.295 Chirality : 0.033 0.153 4829 Planarity : 0.003 0.056 5615 Dihedral : 6.778 84.734 4222 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.97 % Allowed : 15.66 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.75 (0.13), residues: 3742 helix: 3.61 (0.08), residues: 2895 sheet: None (None), residues: 0 loop : -1.97 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG L 53 TYR 0.020 0.001 TYR B 25 PHE 0.015 0.001 PHE G 26 TRP 0.004 0.001 TRP I 37 HIS 0.003 0.000 HIS M 130 Details of bonding type rmsd covalent geometry : bond 0.00382 (32072) covalent geometry : angle 0.59788 (43500) hydrogen bonds : bond 0.10596 ( 2494) hydrogen bonds : angle 3.82995 ( 7482) Misc. bond : bond 0.05794 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 525 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8043 (tt) REVERT: B 65 LEU cc_start: 0.8326 (mt) cc_final: 0.8107 (tp) REVERT: B 130 HIS cc_start: 0.7586 (t-170) cc_final: 0.7276 (m170) REVERT: C 31 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8130 (tt) REVERT: C 65 LEU cc_start: 0.8296 (mt) cc_final: 0.8051 (tp) REVERT: C 132 ASP cc_start: 0.8990 (t0) cc_final: 0.8713 (t0) REVERT: D 18 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7829 (mm-30) REVERT: D 31 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8124 (tt) REVERT: F 132 ASP cc_start: 0.8981 (t0) cc_final: 0.8673 (t0) REVERT: E 31 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8090 (tt) REVERT: E 52 MET cc_start: 0.8774 (mtm) cc_final: 0.8553 (mtt) REVERT: E 132 ASP cc_start: 0.8940 (t0) cc_final: 0.8682 (t0) REVERT: G 18 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7832 (mm-30) REVERT: G 31 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8059 (tt) REVERT: G 65 LEU cc_start: 0.8324 (mt) cc_final: 0.8079 (tp) REVERT: H 18 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7879 (mm-30) REVERT: H 31 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8102 (tt) REVERT: H 65 LEU cc_start: 0.8352 (mt) cc_final: 0.8091 (tp) REVERT: I 18 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7724 (mm-30) REVERT: I 31 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8128 (tt) REVERT: J 18 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7691 (mm-30) REVERT: J 31 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8114 (tt) REVERT: K 31 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8163 (tt) REVERT: K 65 LEU cc_start: 0.8316 (mt) cc_final: 0.8082 (tp) REVERT: L 31 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8137 (tt) REVERT: L 130 HIS cc_start: 0.7448 (t70) cc_final: 0.7111 (m170) REVERT: L 132 ASP cc_start: 0.8966 (t0) cc_final: 0.8685 (t0) REVERT: M 31 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8083 (tt) REVERT: M 128 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8313 (tp30) REVERT: O 31 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8167 (tt) REVERT: P 31 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8087 (tt) REVERT: P 65 LEU cc_start: 0.8290 (mt) cc_final: 0.8058 (tp) REVERT: P 132 ASP cc_start: 0.8981 (t0) cc_final: 0.8685 (t0) REVERT: Q 31 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8133 (tt) REVERT: Q 132 ASP cc_start: 0.8993 (t0) cc_final: 0.8722 (t0) REVERT: R 18 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7768 (mm-30) REVERT: R 31 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8152 (tt) REVERT: S 31 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8113 (tt) REVERT: T 31 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8106 (tt) REVERT: T 65 LEU cc_start: 0.8354 (mt) cc_final: 0.8110 (tp) REVERT: T 132 ASP cc_start: 0.8980 (t0) cc_final: 0.8713 (t0) REVERT: U 130 HIS cc_start: 0.7505 (t-170) cc_final: 0.7141 (m170) REVERT: U 132 ASP cc_start: 0.8942 (t0) cc_final: 0.8670 (t0) REVERT: V 31 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8117 (tt) REVERT: W 31 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8109 (tt) REVERT: W 130 HIS cc_start: 0.7477 (t-170) cc_final: 0.7222 (m170) REVERT: X 155 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8034 (mm-30) outliers start: 165 outliers final: 116 residues processed: 621 average time/residue: 0.1931 time to fit residues: 197.1251 Evaluate side-chains 647 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 511 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 128 GLU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 151 SER Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 116 SER Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 2 GLN Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 128 GLU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 128 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 116 SER Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 157 THR Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 31 LEU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain W residue 155 GLU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 128 GLU Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 141 ILE Chi-restraints excluded: chain X residue 151 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 349 optimal weight: 0.8980 chunk 289 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 278 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 334 optimal weight: 0.8980 chunk 335 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS O 130 HIS ** P 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS S 130 HIS ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.157273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.143611 restraints weight = 46985.114| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.61 r_work: 0.3765 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.303 32104 Z= 0.156 Angle : 0.554 16.516 43500 Z= 0.277 Chirality : 0.032 0.158 4829 Planarity : 0.003 0.036 5615 Dihedral : 6.891 88.862 4222 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.80 % Allowed : 18.01 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.16 (0.13), residues: 3742 helix: 3.93 (0.08), residues: 2903 sheet: None (None), residues: 0 loop : -1.99 (0.23), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 53 TYR 0.012 0.001 TYR F 25 PHE 0.016 0.001 PHE G 26 TRP 0.005 0.001 TRP G 37 HIS 0.005 0.001 HIS X 54 Details of bonding type rmsd covalent geometry : bond 0.00294 (32072) covalent geometry : angle 0.55405 (43500) hydrogen bonds : bond 0.08406 ( 2494) hydrogen bonds : angle 3.50984 ( 7482) Misc. bond : bond 0.06251 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 550 time to evaluate : 1.297 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: B 31 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8076 (tt) REVERT: B 130 HIS cc_start: 0.7434 (t-170) cc_final: 0.7125 (m170) REVERT: C 2 GLN cc_start: 0.8728 (mt0) cc_final: 0.8478 (mt0) REVERT: C 132 ASP cc_start: 0.8946 (t0) cc_final: 0.8692 (t0) REVERT: F 31 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8090 (tt) REVERT: F 132 ASP cc_start: 0.8922 (t0) cc_final: 0.8662 (t0) REVERT: E 132 ASP cc_start: 0.8863 (t0) cc_final: 0.8577 (t0) REVERT: G 18 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7890 (mm-30) REVERT: I 18 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7835 (mm-30) REVERT: J 18 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7768 (mm-30) REVERT: K 52 MET cc_start: 0.8894 (mtt) cc_final: 0.8650 (mtm) REVERT: K 81 GLN cc_start: 0.8468 (mt0) cc_final: 0.8145 (mp10) REVERT: K 128 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8266 (tp30) REVERT: L 130 HIS cc_start: 0.7336 (t70) cc_final: 0.7101 (m170) REVERT: L 132 ASP cc_start: 0.8937 (t0) cc_final: 0.8661 (t0) REVERT: L 155 GLU cc_start: 0.8115 (tt0) cc_final: 0.7662 (mt-10) REVERT: P 132 ASP cc_start: 0.8954 (t0) cc_final: 0.8697 (t0) REVERT: Q 132 ASP cc_start: 0.8963 (t0) cc_final: 0.8725 (t0) REVERT: R 18 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7872 (mm-30) REVERT: U 31 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8099 (tt) REVERT: U 130 HIS cc_start: 0.7434 (t-170) cc_final: 0.7203 (m170) REVERT: U 132 ASP cc_start: 0.8875 (t0) cc_final: 0.8601 (t0) REVERT: W 130 HIS cc_start: 0.7378 (t-170) cc_final: 0.7109 (m170) REVERT: X 31 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8064 (tt) REVERT: X 155 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8069 (mm-30) outliers start: 93 outliers final: 48 residues processed: 615 average time/residue: 0.1924 time to fit residues: 195.3371 Evaluate side-chains 581 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 528 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain Q residue 2 GLN Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 128 GLU Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 31 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 108 MET Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain W residue 128 GLU Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 31 LEU Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 45 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 320 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 357 optimal weight: 0.9990 chunk 349 optimal weight: 0.9980 chunk 355 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 146 optimal weight: 0.0170 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS C 130 HIS ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS P 130 HIS Q 130 HIS S 130 HIS ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 54 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.158167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.144474 restraints weight = 46938.292| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.57 r_work: 0.3758 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.273 32104 Z= 0.164 Angle : 0.584 20.908 43500 Z= 0.286 Chirality : 0.032 0.161 4829 Planarity : 0.003 0.020 5615 Dihedral : 6.810 89.171 4222 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.95 % Allowed : 18.40 % Favored : 78.64 % 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 are not related in a simple way. whole: 4.13 (0.13), residues: 3742 helix: 3.89 (0.08), residues: 2910 sheet: None (None), residues: 0 loop : -1.98 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 53 TYR 0.015 0.001 TYR B 25 PHE 0.015 0.001 PHE G 26 TRP 0.005 0.001 TRP L 37 HIS 0.003 0.000 HIS M 130 Details of bonding type rmsd covalent geometry : bond 0.00330 (32072) covalent geometry : angle 0.58432 (43500) hydrogen bonds : bond 0.08530 ( 2494) hydrogen bonds : angle 3.54011 ( 7482) Misc. bond : bond 0.05798 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 531 time to evaluate : 1.216 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: B 31 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8049 (tt) REVERT: B 81 GLN cc_start: 0.8490 (mt0) cc_final: 0.8100 (mp10) REVERT: C 31 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8054 (tt) REVERT: C 132 ASP cc_start: 0.8964 (t0) cc_final: 0.8688 (t0) REVERT: D 31 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8093 (tt) REVERT: F 31 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8085 (tt) REVERT: F 132 ASP cc_start: 0.8917 (t0) cc_final: 0.8657 (t0) REVERT: E 31 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8001 (tt) REVERT: E 132 ASP cc_start: 0.8864 (t0) cc_final: 0.8581 (t0) REVERT: G 18 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7864 (mm-30) REVERT: H 31 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8022 (tt) REVERT: I 18 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7829 (mm-30) REVERT: J 18 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7779 (mm-30) REVERT: J 31 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8077 (tt) REVERT: K 81 GLN cc_start: 0.8446 (mt0) cc_final: 0.8077 (mp10) REVERT: K 128 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8208 (tp30) REVERT: L 31 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8057 (tt) REVERT: L 130 HIS cc_start: 0.7300 (t70) cc_final: 0.7054 (m170) REVERT: L 132 ASP cc_start: 0.8916 (t0) cc_final: 0.8649 (t0) REVERT: L 155 GLU cc_start: 0.8165 (tt0) cc_final: 0.7692 (mt-10) REVERT: P 31 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8036 (tt) REVERT: P 132 ASP cc_start: 0.8940 (t0) cc_final: 0.8682 (t0) REVERT: Q 31 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8048 (tt) REVERT: Q 132 ASP cc_start: 0.8946 (t0) cc_final: 0.8716 (t0) REVERT: R 18 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7857 (mm-30) REVERT: R 31 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8082 (tt) REVERT: S 31 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8015 (tt) REVERT: U 31 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8071 (tt) REVERT: U 130 HIS cc_start: 0.7480 (t-170) cc_final: 0.7172 (m170) REVERT: U 132 ASP cc_start: 0.8886 (t0) cc_final: 0.8611 (t0) REVERT: V 31 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8029 (tt) REVERT: W 130 HIS cc_start: 0.7442 (t-170) cc_final: 0.7097 (m170) REVERT: X 31 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8059 (tt) REVERT: X 155 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8021 (mm-30) outliers start: 98 outliers final: 68 residues processed: 595 average time/residue: 0.1931 time to fit residues: 189.3671 Evaluate side-chains 607 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 523 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 108 MET Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 108 MET Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 2 GLN Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 108 MET Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 128 GLU Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 155 GLU Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 108 MET Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 157 THR Chi-restraints excluded: chain U residue 31 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 108 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 31 LEU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 108 MET Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain W residue 128 GLU Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain W residue 155 GLU Chi-restraints excluded: chain X residue 31 LEU Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 38 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 324 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 344 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 316 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS C 130 HIS ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 130 HIS P 130 HIS Q 130 HIS S 130 HIS ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 130 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.155504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.142087 restraints weight = 46964.659| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.56 r_work: 0.3728 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.272 32104 Z= 0.174 Angle : 0.583 16.782 43500 Z= 0.283 Chirality : 0.033 0.164 4829 Planarity : 0.003 0.019 5615 Dihedral : 6.774 88.768 4222 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.43 % Allowed : 18.25 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.10 (0.13), residues: 3742 helix: 3.86 (0.08), residues: 2910 sheet: None (None), residues: 0 loop : -1.98 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 53 TYR 0.017 0.001 TYR R 25 PHE 0.013 0.001 PHE A 26 TRP 0.004 0.001 TRP F 37 HIS 0.003 0.000 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00358 (32072) covalent geometry : angle 0.58317 (43500) hydrogen bonds : bond 0.09125 ( 2494) hydrogen bonds : angle 3.59693 ( 7482) Misc. bond : bond 0.06516 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 500 time to evaluate : 1.262 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: B 31 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8088 (tt) REVERT: C 2 GLN cc_start: 0.8633 (mt0) cc_final: 0.8354 (mt0) REVERT: C 31 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8080 (tt) REVERT: C 132 ASP cc_start: 0.8960 (t0) cc_final: 0.8713 (t0) REVERT: D 31 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8104 (tt) REVERT: F 31 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8112 (tt) REVERT: F 132 ASP cc_start: 0.8964 (t0) cc_final: 0.8676 (t0) REVERT: E 31 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8078 (tt) REVERT: E 132 ASP cc_start: 0.8908 (t0) cc_final: 0.8627 (t0) REVERT: G 18 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7829 (mm-30) REVERT: H 31 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8091 (tt) REVERT: I 18 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7790 (mm-30) REVERT: J 31 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8091 (tt) REVERT: K 31 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8158 (tt) REVERT: K 81 GLN cc_start: 0.8426 (mt0) cc_final: 0.8060 (mp10) REVERT: K 128 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8203 (tp30) REVERT: L 31 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8086 (tt) REVERT: L 130 HIS cc_start: 0.7365 (t70) cc_final: 0.7096 (m170) REVERT: L 132 ASP cc_start: 0.8944 (t0) cc_final: 0.8672 (t0) REVERT: L 155 GLU cc_start: 0.8162 (tt0) cc_final: 0.7724 (mt-10) REVERT: M 128 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8206 (tp30) REVERT: P 31 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8092 (tt) REVERT: P 132 ASP cc_start: 0.8962 (t0) cc_final: 0.8708 (t0) REVERT: Q 31 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8057 (tt) REVERT: Q 132 ASP cc_start: 0.8974 (t0) cc_final: 0.8739 (t0) REVERT: R 18 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7807 (mm-30) REVERT: R 31 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8109 (tt) REVERT: S 31 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8065 (tt) REVERT: U 31 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8115 (tt) REVERT: U 130 HIS cc_start: 0.7393 (t70) cc_final: 0.7158 (m170) REVERT: U 132 ASP cc_start: 0.8898 (t0) cc_final: 0.8635 (t0) REVERT: V 31 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8060 (tt) REVERT: X 31 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8098 (tt) outliers start: 114 outliers final: 91 residues processed: 572 average time/residue: 0.1979 time to fit residues: 183.9192 Evaluate side-chains 593 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 484 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 108 MET Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 128 GLU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 108 MET Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain P residue 156 GLN Chi-restraints excluded: chain Q residue 2 GLN Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 108 MET Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 128 GLU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 155 GLU Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 108 MET Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 157 THR Chi-restraints excluded: chain U residue 31 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 108 MET Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 31 LEU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 108 MET Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain W residue 128 GLU Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain W residue 155 GLU Chi-restraints excluded: chain X residue 31 LEU Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 108 MET Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 128 GLU Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 2 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 270 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 262 optimal weight: 7.9990 chunk 205 optimal weight: 7.9990 chunk 320 optimal weight: 3.9990 chunk 305 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 356 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS C 130 HIS D 130 HIS E 130 HIS G 130 HIS H 130 HIS ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 HIS N 130 HIS P 130 HIS Q 130 HIS S 130 HIS T 130 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.142012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.128460 restraints weight = 47301.399| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.60 r_work: 0.3564 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.263 32104 Z= 0.263 Angle : 0.716 22.284 43500 Z= 0.352 Chirality : 0.037 0.165 4829 Planarity : 0.003 0.049 5615 Dihedral : 6.893 89.074 4222 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.80 % Allowed : 17.89 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.44 (0.13), residues: 3742 helix: 3.30 (0.08), residues: 2918 sheet: None (None), residues: 0 loop : -1.85 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 53 TYR 0.023 0.002 TYR W 25 PHE 0.021 0.002 PHE N 26 TRP 0.008 0.002 TRP X 37 HIS 0.008 0.001 HIS U 130 Details of bonding type rmsd covalent geometry : bond 0.00595 (32072) covalent geometry : angle 0.71610 (43500) hydrogen bonds : bond 0.12814 ( 2494) hydrogen bonds : angle 4.16582 ( 7482) Misc. bond : bond 0.05943 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 522 time to evaluate : 1.164 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: B 31 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8149 (tt) REVERT: C 2 GLN cc_start: 0.8553 (mt0) cc_final: 0.8326 (mt0) REVERT: C 31 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8210 (tt) REVERT: C 132 ASP cc_start: 0.9038 (t0) cc_final: 0.8761 (t0) REVERT: D 31 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8196 (tt) REVERT: F 31 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8209 (tt) REVERT: F 132 ASP cc_start: 0.9027 (t0) cc_final: 0.8719 (t0) REVERT: E 31 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8186 (tt) REVERT: E 132 ASP cc_start: 0.8994 (t0) cc_final: 0.8748 (t0) REVERT: G 18 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7621 (mm-30) REVERT: H 31 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8191 (tt) REVERT: I 18 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7554 (mm-30) REVERT: J 31 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8201 (tt) REVERT: K 31 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8240 (tt) REVERT: K 128 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8226 (tp30) REVERT: L 31 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8215 (tt) REVERT: L 130 HIS cc_start: 0.7348 (t70) cc_final: 0.7008 (m170) REVERT: L 132 ASP cc_start: 0.9039 (t0) cc_final: 0.8722 (t0) REVERT: M 128 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8220 (tp30) REVERT: P 31 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8199 (tt) REVERT: P 132 ASP cc_start: 0.9026 (t0) cc_final: 0.8751 (t0) REVERT: Q 31 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8214 (tt) REVERT: Q 132 ASP cc_start: 0.9014 (t0) cc_final: 0.8743 (t0) REVERT: R 18 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7644 (mm-30) REVERT: R 31 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8201 (tt) REVERT: S 31 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8165 (tt) REVERT: U 31 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8221 (tt) REVERT: U 132 ASP cc_start: 0.8995 (t0) cc_final: 0.8745 (t0) REVERT: V 31 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8175 (tt) REVERT: X 31 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8201 (tt) outliers start: 126 outliers final: 98 residues processed: 593 average time/residue: 0.1977 time to fit residues: 191.0051 Evaluate side-chains 621 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 505 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 108 MET Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 128 GLU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 108 MET Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 2 GLN Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 108 MET Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 128 GLU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 151 SER Chi-restraints excluded: chain R residue 155 GLU Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 116 SER Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 108 MET Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 157 THR Chi-restraints excluded: chain U residue 31 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 108 MET Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 31 LEU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 108 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain W residue 155 GLU Chi-restraints excluded: chain X residue 31 LEU Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 108 MET Chi-restraints excluded: chain X residue 128 GLU Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 252 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 201 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 168 optimal weight: 0.6980 chunk 319 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 HIS F 54 HIS ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 HIS J 54 HIS M 130 HIS ** N 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS S 130 HIS ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 130 HIS V 54 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.158374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.144847 restraints weight = 46709.688| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.55 r_work: 0.3762 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.327 32104 Z= 0.168 Angle : 0.637 23.656 43500 Z= 0.309 Chirality : 0.033 0.147 4829 Planarity : 0.003 0.028 5615 Dihedral : 6.773 84.582 4222 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.99 % Allowed : 19.94 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.14 (0.13), residues: 3742 helix: 3.87 (0.08), residues: 2922 sheet: None (None), residues: 0 loop : -1.97 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 53 TYR 0.013 0.001 TYR F 25 PHE 0.017 0.001 PHE K 26 TRP 0.005 0.001 TRP J 37 HIS 0.005 0.001 HIS O 130 Details of bonding type rmsd covalent geometry : bond 0.00309 (32072) covalent geometry : angle 0.63711 (43500) hydrogen bonds : bond 0.08551 ( 2494) hydrogen bonds : angle 3.58031 ( 7482) Misc. bond : bond 0.07648 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5394.83 seconds wall clock time: 94 minutes 4.45 seconds (5644.45 seconds total)