Starting phenix.real_space_refine on Mon Aug 25 21:06:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k3o_9910/08_2025/6k3o_9910.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k3o_9910/08_2025/6k3o_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6k3o_9910/08_2025/6k3o_9910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k3o_9910/08_2025/6k3o_9910.map" model { file = "/net/cci-nas-00/data/ceres_data/6k3o_9910/08_2025/6k3o_9910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k3o_9910/08_2025/6k3o_9910.cif" } 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-2.0-5787/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: 7.60, per 1000 atoms: 0.24 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: 3.25 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.76 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: 5.28 Time building geometry restraints manager: 4.04 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.020 Find NCS groups from input model: 0.870 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.920 ------------------------------------------------------------------------------- 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 aren 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 : 1.265 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: 0.8650 (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: U 132 ASP cc_start: 0.8872 (t0) cc_final: 0.8629 (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: 0.1792 time to fit residues: 166.2492 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 : 1.008 ------------------------------------------------------------------------------- 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: 1.9990 chunk 298 optimal weight: 10.0000 overall best weight: 3.2588 ------------------------------------------------------------------------------- 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 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 I 130 HIS 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 U 24 GLN W 24 GLN X 24 GLN X 118 ASN X 156 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.146815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133350 restraints weight = 47770.117| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.59 r_work: 0.3646 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.375 32104 Z= 0.219 Angle : 0.684 24.851 43500 Z= 0.324 Chirality : 0.035 0.133 4829 Planarity : 0.003 0.036 5615 Dihedral : 6.383 89.719 4222 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.66 % Allowed : 12.05 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.13), residues: 3742 helix: 2.46 (0.09), residues: 2898 sheet: None (None), residues: 0 loop : -3.40 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 53 TYR 0.012 0.001 TYR I 25 PHE 0.019 0.002 PHE G 26 TRP 0.013 0.002 TRP S 37 HIS 0.004 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00475 (32072) covalent geometry : angle 0.68398 (43500) hydrogen bonds : bond 0.10850 ( 2494) hydrogen bonds : angle 4.04009 ( 7482) Misc. bond : bond 0.07264 ( 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 647 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 592 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7601 (mm-30) REVERT: B 18 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7793 (mm-30) REVERT: B 130 HIS cc_start: 0.7505 (t-170) cc_final: 0.7204 (m170) REVERT: C 18 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7833 (mm-30) REVERT: C 132 ASP cc_start: 0.8967 (t0) cc_final: 0.8675 (t0) REVERT: D 18 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7594 (mm-30) REVERT: F 18 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7756 (mm-30) REVERT: F 132 ASP cc_start: 0.8926 (t0) cc_final: 0.8664 (t0) REVERT: E 18 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7693 (mm-30) REVERT: E 132 ASP cc_start: 0.8897 (t0) cc_final: 0.8619 (t0) REVERT: G 18 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7516 (mm-30) REVERT: H 18 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7762 (mm-30) REVERT: I 18 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7435 (mm-30) REVERT: J 18 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7419 (mm-30) REVERT: K 18 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7694 (mm-30) REVERT: L 18 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7685 (mm-30) REVERT: L 132 ASP cc_start: 0.9073 (t0) cc_final: 0.8811 (t0) REVERT: L 155 GLU cc_start: 0.8180 (tt0) cc_final: 0.7779 (mt-10) REVERT: M 18 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7723 (mm-30) REVERT: N 18 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7684 (mm-30) REVERT: O 18 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7598 (mm-30) REVERT: P 18 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7751 (mm-30) REVERT: P 132 ASP cc_start: 0.8968 (t0) cc_final: 0.8645 (t0) REVERT: Q 132 ASP cc_start: 0.8996 (t0) cc_final: 0.8699 (t0) REVERT: R 18 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7512 (mm-30) REVERT: S 18 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7717 (mm-30) REVERT: T 18 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7706 (mm-30) REVERT: U 18 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7758 (mm-30) REVERT: U 132 ASP cc_start: 0.8911 (t0) cc_final: 0.8608 (t0) REVERT: V 18 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7480 (mm-30) REVERT: W 18 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7536 (mm-30) REVERT: W 130 HIS cc_start: 0.7552 (t-170) cc_final: 0.7265 (m170) REVERT: X 18 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7433 (mm-30) REVERT: X 155 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8063 (mm-30) outliers start: 55 outliers final: 52 residues processed: 611 average time/residue: 0.1744 time to fit residues: 174.6419 Evaluate side-chains 599 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 547 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 57 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 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 H residue 141 ILE 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 K residue 141 ILE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain L residue 57 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 136 THR Chi-restraints excluded: chain N residue 141 ILE 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 136 THR Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 136 THR 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 S residue 136 THR Chi-restraints excluded: chain T residue 57 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 136 THR Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain W residue 57 VAL Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 141 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 158 optimal weight: 0.4980 chunk 204 optimal weight: 8.9990 chunk 348 optimal weight: 0.0370 chunk 331 optimal weight: 0.9990 chunk 286 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 171 optimal weight: 0.0050 overall best weight: 0.5074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 HIS E 130 HIS G 130 HIS ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN N 130 HIS O 130 HIS ** P 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4151 r_free = 0.4151 target = 0.164570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.150931 restraints weight = 47116.580| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.57 r_work: 0.3847 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.424 32104 Z= 0.155 Angle : 0.579 19.578 43500 Z= 0.281 Chirality : 0.033 0.145 4829 Planarity : 0.003 0.054 5615 Dihedral : 6.927 89.336 4222 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.39 % Allowed : 14.79 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.54 (0.14), residues: 3742 helix: 3.58 (0.08), residues: 2889 sheet: None (None), residues: 0 loop : -2.51 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG L 53 TYR 0.012 0.001 TYR I 25 PHE 0.017 0.001 PHE A 26 TRP 0.007 0.001 TRP S 37 HIS 0.004 0.001 HIS G 130 Details of bonding type rmsd covalent geometry : bond 0.00285 (32072) covalent geometry : angle 0.57924 (43500) hydrogen bonds : bond 0.07299 ( 2494) hydrogen bonds : angle 3.42366 ( 7482) Misc. bond : bond 0.08747 ( 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 582 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 569 time to evaluate : 1.221 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: C 132 ASP cc_start: 0.8867 (t0) cc_final: 0.8606 (t0) REVERT: F 132 ASP cc_start: 0.8866 (t0) cc_final: 0.8603 (t0) REVERT: F 155 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8066 (mm-30) REVERT: E 132 ASP cc_start: 0.8808 (t0) cc_final: 0.8542 (t0) REVERT: J 18 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7780 (mm-30) REVERT: L 130 HIS cc_start: 0.7314 (t70) cc_final: 0.7036 (m170) REVERT: L 132 ASP cc_start: 0.9011 (t0) cc_final: 0.8792 (t0) REVERT: L 155 GLU cc_start: 0.7942 (tt0) cc_final: 0.7564 (mt-10) REVERT: P 132 ASP cc_start: 0.8873 (t0) cc_final: 0.8602 (t0) REVERT: Q 132 ASP cc_start: 0.8902 (t0) cc_final: 0.8634 (t0) REVERT: U 132 ASP cc_start: 0.8823 (t0) cc_final: 0.8540 (t0) REVERT: X 18 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7714 (mm-30) REVERT: X 155 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8134 (mm-30) outliers start: 13 outliers final: 5 residues processed: 574 average time/residue: 0.1622 time to fit residues: 154.8863 Evaluate side-chains 511 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 506 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain Q residue 2 GLN Chi-restraints excluded: chain R residue 155 GLU Chi-restraints excluded: chain W 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: 1.9990 chunk 1 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 342 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** P 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS ** S 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 130 HIS U 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.155037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.140169 restraints weight = 45645.084| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.65 r_work: 0.3706 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.332 32104 Z= 0.155 Angle : 0.568 18.401 43500 Z= 0.270 Chirality : 0.032 0.154 4829 Planarity : 0.002 0.025 5615 Dihedral : 6.734 88.596 4222 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.39 % Allowed : 16.20 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.85 (0.14), residues: 3742 helix: 3.78 (0.08), residues: 2889 sheet: None (None), residues: 0 loop : -2.32 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 53 TYR 0.025 0.001 TYR V 25 PHE 0.018 0.001 PHE G 26 TRP 0.007 0.001 TRP T 37 HIS 0.003 0.000 HIS G 130 Details of bonding type rmsd covalent geometry : bond 0.00314 (32072) covalent geometry : angle 0.56750 (43500) hydrogen bonds : bond 0.08009 ( 2494) hydrogen bonds : angle 3.43909 ( 7482) Misc. bond : bond 0.06680 ( 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 594 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 548 time to evaluate : 1.332 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: C 132 ASP cc_start: 0.8873 (t0) cc_final: 0.8598 (t0) REVERT: F 132 ASP cc_start: 0.8909 (t0) cc_final: 0.8627 (t0) REVERT: E 132 ASP cc_start: 0.8838 (t0) cc_final: 0.8541 (t0) REVERT: G 18 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7933 (mm-30) REVERT: J 18 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7805 (mm-30) REVERT: K 65 LEU cc_start: 0.8247 (mt) cc_final: 0.8002 (tp) REVERT: L 130 HIS cc_start: 0.7335 (t70) cc_final: 0.7017 (m170) REVERT: L 132 ASP cc_start: 0.8926 (t0) cc_final: 0.8668 (t0) REVERT: L 155 GLU cc_start: 0.8309 (tt0) cc_final: 0.7897 (mt-10) REVERT: P 132 ASP cc_start: 0.8884 (t0) cc_final: 0.8611 (t0) REVERT: Q 132 ASP cc_start: 0.8919 (t0) cc_final: 0.8667 (t0) REVERT: U 130 HIS cc_start: 0.7489 (t-170) cc_final: 0.7255 (m170) REVERT: U 132 ASP cc_start: 0.8862 (t0) cc_final: 0.8595 (t0) REVERT: X 18 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7827 (mm-30) REVERT: X 155 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8201 (mm-30) outliers start: 46 outliers final: 42 residues processed: 560 average time/residue: 0.1794 time to fit residues: 164.1549 Evaluate side-chains 556 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 514 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 136 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 141 ILE 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 136 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 136 THR 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 53 ARG Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 136 THR Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain Q residue 2 GLN Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 155 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 141 ILE 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: 0.9990 chunk 61 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** P 156 GLN Q 130 HIS ** S 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.159469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.146330 restraints weight = 46730.784| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.43 r_work: 0.3848 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.335 32104 Z= 0.156 Angle : 0.603 22.477 43500 Z= 0.277 Chirality : 0.033 0.188 4829 Planarity : 0.002 0.017 5615 Dihedral : 6.759 88.752 4222 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.02 % Allowed : 16.57 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.98 (0.14), residues: 3742 helix: 3.85 (0.08), residues: 2897 sheet: None (None), residues: 0 loop : -2.23 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 45 TYR 0.012 0.001 TYR W 25 PHE 0.015 0.001 PHE G 26 TRP 0.012 0.001 TRP O 37 HIS 0.003 0.000 HIS P 130 Details of bonding type rmsd covalent geometry : bond 0.00316 (32072) covalent geometry : angle 0.60286 (43500) hydrogen bonds : bond 0.08165 ( 2494) hydrogen bonds : angle 3.45128 ( 7482) Misc. bond : bond 0.06889 ( 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 610 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 543 time to evaluate : 0.962 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: C 132 ASP cc_start: 0.8932 (t0) cc_final: 0.8633 (t0) REVERT: F 132 ASP cc_start: 0.8959 (t0) cc_final: 0.8702 (t0) REVERT: E 132 ASP cc_start: 0.8847 (t0) cc_final: 0.8550 (t0) REVERT: J 18 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7824 (mm-30) REVERT: L 130 HIS cc_start: 0.7491 (t70) cc_final: 0.7184 (m170) REVERT: L 132 ASP cc_start: 0.8941 (t0) cc_final: 0.8671 (t0) REVERT: L 155 GLU cc_start: 0.7791 (tt0) cc_final: 0.7400 (mt-10) REVERT: P 132 ASP cc_start: 0.8927 (t0) cc_final: 0.8630 (t0) REVERT: Q 132 ASP cc_start: 0.8957 (t0) cc_final: 0.8704 (t0) REVERT: U 130 HIS cc_start: 0.7628 (t-170) cc_final: 0.7357 (m170) REVERT: U 132 ASP cc_start: 0.8908 (t0) cc_final: 0.8643 (t0) REVERT: X 18 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7830 (mm-30) REVERT: X 155 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8099 (mm-30) outliers start: 67 outliers final: 60 residues processed: 566 average time/residue: 0.1867 time to fit residues: 173.3506 Evaluate side-chains 571 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 511 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 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 136 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 141 ILE 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 I residue 136 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain L residue 53 ARG Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 141 ILE 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 P residue 136 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 151 SER Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 2 GLN 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 136 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 155 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 141 ILE 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: 3.9990 chunk 37 optimal weight: 6.9990 chunk 352 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 326 optimal weight: 8.9990 chunk 337 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 E 130 HIS G 130 HIS H 130 HIS K 130 HIS K 156 GLN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.140777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.127207 restraints weight = 47328.754| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.61 r_work: 0.3566 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.290 32104 Z= 0.269 Angle : 0.719 22.040 43500 Z= 0.352 Chirality : 0.037 0.160 4829 Planarity : 0.003 0.035 5615 Dihedral : 6.746 88.763 4222 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.24 % Allowed : 15.12 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.24 (0.13), residues: 3742 helix: 3.24 (0.08), residues: 2889 sheet: None (None), residues: 0 loop : -2.08 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 53 TYR 0.018 0.002 TYR U 25 PHE 0.021 0.002 PHE N 26 TRP 0.006 0.002 TRP B 37 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00610 (32072) covalent geometry : angle 0.71857 (43500) hydrogen bonds : bond 0.13144 ( 2494) hydrogen bonds : angle 4.15619 ( 7482) Misc. bond : bond 0.06296 ( 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 712 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 538 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8378 (t0) cc_final: 0.8171 (t0) REVERT: C 132 ASP cc_start: 0.9055 (t0) cc_final: 0.8776 (t0) REVERT: C 139 ASP cc_start: 0.8345 (t0) cc_final: 0.8123 (t0) REVERT: D 139 ASP cc_start: 0.8299 (t0) cc_final: 0.8072 (t0) REVERT: F 132 ASP cc_start: 0.9022 (t0) cc_final: 0.8710 (t0) REVERT: F 139 ASP cc_start: 0.8287 (t0) cc_final: 0.8056 (t0) REVERT: E 132 ASP cc_start: 0.9009 (t0) cc_final: 0.8737 (t0) REVERT: J 18 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7592 (mm-30) REVERT: J 139 ASP cc_start: 0.8379 (t0) cc_final: 0.8173 (t0) REVERT: K 128 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8200 (tp30) REVERT: L 130 HIS cc_start: 0.7488 (t70) cc_final: 0.7121 (m170) REVERT: L 132 ASP cc_start: 0.9063 (t0) cc_final: 0.8736 (t0) REVERT: L 139 ASP cc_start: 0.8387 (t0) cc_final: 0.8124 (t0) REVERT: N 139 ASP cc_start: 0.8382 (t0) cc_final: 0.8144 (t0) REVERT: O 31 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8220 (tt) REVERT: P 2 GLN cc_start: 0.7929 (mt0) cc_final: 0.7614 (mt0) REVERT: P 132 ASP cc_start: 0.9032 (t0) cc_final: 0.8736 (t0) REVERT: Q 132 ASP cc_start: 0.9078 (t0) cc_final: 0.8810 (t0) REVERT: Q 139 ASP cc_start: 0.8371 (t0) cc_final: 0.8150 (t0) REVERT: R 139 ASP cc_start: 0.8206 (t0) cc_final: 0.7979 (t0) REVERT: R 155 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8518 (mm-30) REVERT: T 139 ASP cc_start: 0.8322 (t0) cc_final: 0.8119 (t0) REVERT: U 132 ASP cc_start: 0.8989 (t0) cc_final: 0.8700 (t0) REVERT: V 139 ASP cc_start: 0.8356 (t0) cc_final: 0.8143 (t0) REVERT: W 139 ASP cc_start: 0.8206 (t0) cc_final: 0.7986 (t0) REVERT: X 18 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7607 (mm-30) outliers start: 174 outliers final: 122 residues processed: 618 average time/residue: 0.1831 time to fit residues: 183.9567 Evaluate side-chains 614 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 489 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 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 108 MET Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 107 VAL 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 108 MET Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 MET 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 108 MET 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 108 MET 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 107 VAL 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 I residue 57 VAL Chi-restraints excluded: chain I residue 107 VAL 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 57 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain J residue 108 MET 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 128 GLU Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain L residue 53 ARG Chi-restraints excluded: chain L residue 54 HIS Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 107 VAL 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 57 VAL Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 108 MET 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 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 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 107 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 151 SER 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 107 VAL 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 107 VAL Chi-restraints excluded: chain R residue 108 MET 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 107 VAL Chi-restraints excluded: chain S residue 108 MET 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 107 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 108 MET 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 57 VAL Chi-restraints excluded: chain V residue 107 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 107 VAL Chi-restraints excluded: chain W residue 136 THR Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 155 GLU Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 108 MET 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: 0.9990 chunk 289 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 334 optimal weight: 0.9990 chunk 335 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 310 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** H 130 HIS K 130 HIS M 130 HIS ** N 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.157631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.143807 restraints weight = 47095.550| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.58 r_work: 0.3752 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.362 32104 Z= 0.170 Angle : 0.627 26.270 43500 Z= 0.301 Chirality : 0.033 0.203 4829 Planarity : 0.003 0.022 5615 Dihedral : 6.790 88.507 4222 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.23 % Allowed : 18.46 % Favored : 79.31 % 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 aren not related in a simple way. whole: 4.12 (0.13), residues: 3742 helix: 3.86 (0.08), residues: 2912 sheet: None (None), residues: 0 loop : -1.92 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 61 TYR 0.013 0.001 TYR B 25 PHE 0.016 0.001 PHE K 26 TRP 0.008 0.001 TRP O 37 HIS 0.003 0.001 HIS K 130 Details of bonding type rmsd covalent geometry : bond 0.00331 (32072) covalent geometry : angle 0.62743 (43500) hydrogen bonds : bond 0.08969 ( 2494) hydrogen bonds : angle 3.59281 ( 7482) Misc. bond : bond 0.07250 ( 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 583 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 509 time to evaluate : 1.231 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 31 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.7935 (tt) REVERT: B 2 GLN cc_start: 0.7845 (mt0) cc_final: 0.7527 (mt0) REVERT: C 132 ASP cc_start: 0.8962 (t0) cc_final: 0.8701 (t0) REVERT: F 132 ASP cc_start: 0.8967 (t0) cc_final: 0.8692 (t0) REVERT: E 132 ASP cc_start: 0.8863 (t0) cc_final: 0.8579 (t0) REVERT: H 2 GLN cc_start: 0.7864 (mt0) cc_final: 0.7656 (mt0) REVERT: I 1 MET cc_start: 0.5929 (ttp) cc_final: 0.5709 (ttm) REVERT: L 130 HIS cc_start: 0.7360 (t70) cc_final: 0.7138 (m170) REVERT: L 132 ASP cc_start: 0.8986 (t0) cc_final: 0.8699 (t0) REVERT: L 155 GLU cc_start: 0.8139 (tt0) cc_final: 0.7682 (mt-10) REVERT: P 2 GLN cc_start: 0.7807 (mt0) cc_final: 0.7519 (mt0) REVERT: P 52 MET cc_start: 0.8884 (mtt) cc_final: 0.8621 (mtt) REVERT: P 132 ASP cc_start: 0.8936 (t0) cc_final: 0.8667 (t0) REVERT: Q 132 ASP cc_start: 0.8956 (t0) cc_final: 0.8748 (t0) REVERT: U 130 HIS cc_start: 0.7526 (t-170) cc_final: 0.7169 (m170) REVERT: U 132 ASP cc_start: 0.8902 (t0) cc_final: 0.8631 (t0) REVERT: V 2 GLN cc_start: 0.8718 (mt0) cc_final: 0.8501 (mt0) outliers start: 74 outliers final: 52 residues processed: 556 average time/residue: 0.1762 time to fit residues: 160.9582 Evaluate side-chains 524 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 471 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU 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 108 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 136 THR 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 F residue 57 VAL Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 108 MET 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 108 MET Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain L residue 53 ARG Chi-restraints excluded: chain L residue 54 HIS Chi-restraints excluded: chain M 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 141 ILE Chi-restraints excluded: chain O residue 151 SER Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 151 SER Chi-restraints excluded: chain Q residue 108 MET Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 151 SER Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain V residue 108 MET Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 108 MET 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: 6.9990 chunk 320 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 chunk 357 optimal weight: 1.9990 chunk 349 optimal weight: 6.9990 chunk 355 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** P 130 HIS Q 130 HIS S 130 HIS T 130 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.147947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134376 restraints weight = 47333.169| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.57 r_work: 0.3625 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.259 32104 Z= 0.235 Angle : 0.697 23.658 43500 Z= 0.333 Chirality : 0.035 0.162 4829 Planarity : 0.003 0.020 5615 Dihedral : 6.699 89.107 4222 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.16 % Allowed : 17.71 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.78 (0.13), residues: 3742 helix: 3.56 (0.08), residues: 2913 sheet: None (None), residues: 0 loop : -1.81 (0.24), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 53 TYR 0.020 0.001 TYR U 25 PHE 0.018 0.001 PHE N 26 TRP 0.004 0.001 TRP G 37 HIS 0.005 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00537 (32072) covalent geometry : angle 0.69692 (43500) hydrogen bonds : bond 0.11352 ( 2494) hydrogen bonds : angle 3.91921 ( 7482) Misc. bond : bond 0.05512 ( 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 604 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 499 time to evaluate : 1.169 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 31 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8067 (tt) REVERT: C 132 ASP cc_start: 0.9006 (t0) cc_final: 0.8770 (t0) REVERT: D 31 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8123 (tt) REVERT: F 132 ASP cc_start: 0.9006 (t0) cc_final: 0.8703 (t0) REVERT: E 132 ASP cc_start: 0.8947 (t0) cc_final: 0.8731 (t0) REVERT: G 31 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8148 (tt) REVERT: H 31 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8149 (tt) REVERT: I 31 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8144 (tt) REVERT: L 31 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8141 (tt) REVERT: L 130 HIS cc_start: 0.7465 (t70) cc_final: 0.7163 (m170) REVERT: L 132 ASP cc_start: 0.9018 (t0) cc_final: 0.8711 (t0) REVERT: M 31 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8133 (tt) REVERT: P 132 ASP cc_start: 0.8988 (t0) cc_final: 0.8720 (t0) REVERT: Q 132 ASP cc_start: 0.8992 (t0) cc_final: 0.8749 (t0) REVERT: T 31 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8116 (tt) REVERT: U 130 HIS cc_start: 0.7510 (t-170) cc_final: 0.7148 (m170) REVERT: U 132 ASP cc_start: 0.8955 (t0) cc_final: 0.8703 (t0) outliers start: 105 outliers final: 86 residues processed: 559 average time/residue: 0.1794 time to fit residues: 163.0174 Evaluate side-chains 578 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 484 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 MET 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 108 MET Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 116 SER 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 155 GLU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 116 SER 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 141 ILE Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 53 ARG Chi-restraints excluded: chain L residue 108 MET Chi-restraints excluded: chain L residue 116 SER 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 108 MET Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 151 SER 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 151 SER Chi-restraints excluded: chain Q residue 2 GLN Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 108 MET Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 116 SER 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 108 MET Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 107 VAL 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 151 SER 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 108 MET Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 108 MET 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 108 MET 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: 0.9990 chunk 171 optimal weight: 0.6980 chunk 324 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 344 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 316 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 HIS ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 HIS ** K 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4102 r_free = 0.4102 target = 0.160581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.146652 restraints weight = 46725.513| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.58 r_work: 0.3786 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.316 32104 Z= 0.163 Angle : 0.625 24.738 43500 Z= 0.298 Chirality : 0.032 0.160 4829 Planarity : 0.003 0.021 5615 Dihedral : 6.742 88.218 4222 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.35 % Allowed : 18.67 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.33 (0.14), residues: 3742 helix: 3.99 (0.08), residues: 2919 sheet: None (None), residues: 0 loop : -1.80 (0.24), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 53 TYR 0.013 0.001 TYR R 25 PHE 0.016 0.001 PHE K 26 TRP 0.006 0.001 TRP O 37 HIS 0.005 0.001 HIS J 54 Details of bonding type rmsd covalent geometry : bond 0.00322 (32072) covalent geometry : angle 0.62499 (43500) hydrogen bonds : bond 0.08142 ( 2494) hydrogen bonds : angle 3.48352 ( 7482) Misc. bond : bond 0.06831 ( 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 597 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 519 time to evaluate : 1.279 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 66 ASP cc_start: 0.8005 (t70) cc_final: 0.7548 (p0) REVERT: C 66 ASP cc_start: 0.7904 (t70) cc_final: 0.7587 (p0) REVERT: C 132 ASP cc_start: 0.8916 (t0) cc_final: 0.8645 (t0) REVERT: F 132 ASP cc_start: 0.8962 (t0) cc_final: 0.8709 (t0) REVERT: E 132 ASP cc_start: 0.8837 (t0) cc_final: 0.8590 (t0) REVERT: G 66 ASP cc_start: 0.7927 (t70) cc_final: 0.7173 (p0) REVERT: H 66 ASP cc_start: 0.7950 (t70) cc_final: 0.7593 (p0) REVERT: I 2 GLN cc_start: 0.8068 (mt0) cc_final: 0.7542 (mm-40) REVERT: I 25 TYR cc_start: 0.8608 (m-80) cc_final: 0.8187 (m-10) REVERT: K 31 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8045 (tt) REVERT: L 66 ASP cc_start: 0.7986 (t70) cc_final: 0.7758 (p0) REVERT: L 130 HIS cc_start: 0.7438 (t70) cc_final: 0.7088 (m170) REVERT: L 132 ASP cc_start: 0.8976 (t0) cc_final: 0.8692 (t0) REVERT: L 155 GLU cc_start: 0.8155 (tt0) cc_final: 0.7675 (mt-10) REVERT: P 31 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.7948 (tt) REVERT: P 66 ASP cc_start: 0.7978 (t70) cc_final: 0.7604 (p0) REVERT: P 132 ASP cc_start: 0.8897 (t0) cc_final: 0.8610 (t0) REVERT: Q 132 ASP cc_start: 0.8941 (t0) cc_final: 0.8705 (t0) REVERT: S 31 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.7961 (tt) REVERT: T 31 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.7972 (tt) REVERT: U 132 ASP cc_start: 0.8855 (t0) cc_final: 0.8579 (t0) REVERT: V 2 GLN cc_start: 0.8705 (mt0) cc_final: 0.8452 (mt0) outliers start: 78 outliers final: 60 residues processed: 551 average time/residue: 0.1763 time to fit residues: 160.6641 Evaluate side-chains 564 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 500 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 108 MET Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain D residue 108 MET 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 108 MET Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 108 MET 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 108 MET Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain L residue 53 ARG Chi-restraints excluded: chain L residue 54 HIS Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain M residue 108 MET 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 141 ILE Chi-restraints excluded: chain O residue 151 SER Chi-restraints excluded: chain P residue 31 LEU 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 151 SER Chi-restraints excluded: chain Q residue 108 MET Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 108 MET Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain U residue 108 MET Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 108 MET Chi-restraints excluded: chain V residue 141 ILE 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 108 MET 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: 6.9990 chunk 74 optimal weight: 5.9990 chunk 270 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 262 optimal weight: 0.0470 chunk 205 optimal weight: 8.9990 chunk 320 optimal weight: 1.9990 chunk 305 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 356 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 HIS ** N 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.152321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.138639 restraints weight = 47245.886| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.58 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: 0.7890 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.278 32104 Z= 0.200 Angle : 0.690 29.143 43500 Z= 0.322 Chirality : 0.034 0.173 4829 Planarity : 0.003 0.020 5615 Dihedral : 6.552 89.395 4222 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.62 % Allowed : 18.46 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.06 (0.13), residues: 3742 helix: 3.74 (0.08), residues: 2919 sheet: None (None), residues: 0 loop : -1.65 (0.24), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 53 TYR 0.016 0.001 TYR R 25 PHE 0.016 0.001 PHE N 26 TRP 0.006 0.001 TRP F 37 HIS 0.004 0.001 HIS F 130 Details of bonding type rmsd covalent geometry : bond 0.00439 (32072) covalent geometry : angle 0.69002 (43500) hydrogen bonds : bond 0.10069 ( 2494) hydrogen bonds : angle 3.72219 ( 7482) Misc. bond : bond 0.06398 ( 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 564 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 477 time to evaluate : 1.121 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 31 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8012 (tt) REVERT: B 31 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8040 (tt) REVERT: C 132 ASP cc_start: 0.8963 (t0) cc_final: 0.8689 (t0) REVERT: F 132 ASP cc_start: 0.8973 (t0) cc_final: 0.8677 (t0) REVERT: E 31 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8038 (tt) REVERT: E 132 ASP cc_start: 0.8901 (t0) cc_final: 0.8658 (t0) REVERT: G 2 GLN cc_start: 0.7396 (mm-40) cc_final: 0.7187 (mm-40) REVERT: I 25 TYR cc_start: 0.8641 (m-80) cc_final: 0.8232 (m-10) REVERT: K 31 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8145 (tt) REVERT: L 130 HIS cc_start: 0.7554 (t70) cc_final: 0.7147 (m170) REVERT: L 132 ASP cc_start: 0.9001 (t0) cc_final: 0.8698 (t0) REVERT: N 1 MET cc_start: 0.6020 (ttm) cc_final: 0.5815 (ttm) REVERT: P 31 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8120 (tt) REVERT: P 132 ASP cc_start: 0.8954 (t0) cc_final: 0.8684 (t0) REVERT: Q 31 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8082 (tt) REVERT: Q 132 ASP cc_start: 0.8942 (t0) cc_final: 0.8722 (t0) REVERT: S 31 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8035 (tt) REVERT: T 31 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8094 (tt) REVERT: U 132 ASP cc_start: 0.8931 (t0) cc_final: 0.8674 (t0) REVERT: V 25 TYR cc_start: 0.8644 (m-80) cc_final: 0.8174 (m-10) REVERT: W 31 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8034 (tt) outliers start: 87 outliers final: 70 residues processed: 528 average time/residue: 0.1975 time to fit residues: 168.7873 Evaluate side-chains 547 residues out of total 3358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 468 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU 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 108 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 136 THR 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 F residue 108 MET Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 108 MET 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 141 ILE 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 141 ILE Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 108 MET 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 141 ILE Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain L residue 2 GLN Chi-restraints excluded: chain L residue 53 ARG Chi-restraints excluded: chain L residue 54 HIS Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain M residue 108 MET Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 141 ILE 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 141 ILE Chi-restraints excluded: chain O residue 151 SER Chi-restraints excluded: chain P residue 31 LEU 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 151 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 108 MET Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 108 MET 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 108 MET Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 108 MET 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 151 SER Chi-restraints excluded: chain U residue 108 MET Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain V residue 108 MET Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 31 LEU 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 108 MET 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: 8.9990 chunk 203 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 269 optimal weight: 0.0570 chunk 112 optimal weight: 1.9990 chunk 281 optimal weight: 3.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 HIS ** 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 ** 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 ** 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 = 0.4068 r_free = 0.4068 target = 0.162372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.145238 restraints weight = 48487.245| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.77 r_work: 0.3794 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.319 32104 Z= 0.157 Angle : 0.635 24.314 43500 Z= 0.295 Chirality : 0.032 0.185 4829 Planarity : 0.003 0.023 5615 Dihedral : 6.561 85.715 4222 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.08 % Allowed : 19.25 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.44 (0.14), residues: 3742 helix: 4.05 (0.08), residues: 2919 sheet: None (None), residues: 0 loop : -1.69 (0.24), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 53 TYR 0.014 0.001 TYR B 25 PHE 0.015 0.001 PHE K 26 TRP 0.006 0.001 TRP O 37 HIS 0.008 0.001 HIS J 54 Details of bonding type rmsd covalent geometry : bond 0.00316 (32072) covalent geometry : angle 0.63483 (43500) hydrogen bonds : bond 0.07782 ( 2494) hydrogen bonds : angle 3.41276 ( 7482) Misc. bond : bond 0.07692 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5147.29 seconds wall clock time: 89 minutes 23.25 seconds (5363.25 seconds total)