Starting phenix.real_space_refine on Sun Jul 5 21:14:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6g_33640/07_2026/7y6g_33640_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6g_33640/07_2026/7y6g_33640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y6g_33640/07_2026/7y6g_33640_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6g_33640/07_2026/7y6g_33640_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y6g_33640/07_2026/7y6g_33640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6g_33640/07_2026/7y6g_33640.map" } resolution = 3.6 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 59 7.16 5 S 96 5.16 5 C 19886 2.51 5 N 5356 2.21 5 O 6030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 233 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31427 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1280 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "P" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Chain breaks: 2 Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Chain breaks: 2 Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {' FE': 1, 'FE2': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 1, 'FE2': 1} Chain breaks: 2 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Chain breaks: 2 Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Chain breaks: 2 Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {'FE2': 1} Chain breaks: 1 Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 1, 'FE2': 1} Chain breaks: 2 Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Chain breaks: 2 Chain: "S" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "T" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {' FE': 1, 'FE2': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Chain breaks: 2 Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 1, 'FE2': 1} Chain breaks: 2 Chain: "W" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 1, 'FE2': 1} Chain breaks: 2 Time building chain proxies: 5.60, per 1000 atoms: 0.18 Number of scatterers: 31427 At special positions: 0 Unit cell: (131.274, 131.274, 131.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 59 26.01 S 96 16.00 O 6030 8.00 N 5356 7.00 C 19886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=31, symmetry=0 Number of additional bonds: simple=31, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7256 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 83.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 Processing helix chain 'A' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 110 removed outlier: 3.534A pdb=" N MET A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 145 removed outlier: 3.876A pdb=" N ALA A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'B' and resid 4 through 36 Processing helix chain 'B' and resid 37 through 65 removed outlier: 3.614A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 110 Processing helix chain 'B' and resid 113 through 145 removed outlier: 3.888A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'C' and resid 4 through 35 Processing helix chain 'C' and resid 37 through 65 removed outlier: 3.500A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 110 Processing helix chain 'C' and resid 113 through 145 removed outlier: 3.900A pdb=" N ALA C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'D' and resid 4 through 36 Processing helix chain 'D' and resid 37 through 65 removed outlier: 3.568A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 110 Processing helix chain 'D' and resid 113 through 145 removed outlier: 3.910A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'E' and resid 4 through 35 Processing helix chain 'E' and resid 37 through 65 removed outlier: 3.515A pdb=" N LEU E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 110 Processing helix chain 'E' and resid 113 through 145 removed outlier: 3.872A pdb=" N ALA E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'F' and resid 4 through 36 removed outlier: 3.511A pdb=" N GLY F 36 " --> pdb=" O GLN F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 65 removed outlier: 3.520A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 110 removed outlier: 3.572A pdb=" N MET F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 145 removed outlier: 3.869A pdb=" N ALA F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 151 Processing helix chain 'G' and resid 4 through 35 Processing helix chain 'G' and resid 37 through 65 removed outlier: 3.526A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 110 Processing helix chain 'G' and resid 113 through 145 removed outlier: 3.876A pdb=" N ALA G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'H' and resid 4 through 35 Processing helix chain 'H' and resid 37 through 65 removed outlier: 3.508A pdb=" N LEU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 110 Processing helix chain 'H' and resid 113 through 145 removed outlier: 3.906A pdb=" N ALA H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 151 Processing helix chain 'I' and resid 4 through 35 Processing helix chain 'I' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 110 Processing helix chain 'I' and resid 113 through 145 removed outlier: 3.885A pdb=" N ALA I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 151 Processing helix chain 'J' and resid 4 through 36 removed outlier: 3.539A pdb=" N GLY J 36 " --> pdb=" O GLN J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 65 removed outlier: 3.507A pdb=" N ALA J 41 " --> pdb=" O TRP J 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 65 " --> pdb=" O ARG J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 110 Processing helix chain 'J' and resid 113 through 145 removed outlier: 3.872A pdb=" N ALA J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 151 Processing helix chain 'K' and resid 4 through 35 Processing helix chain 'K' and resid 37 through 65 removed outlier: 3.616A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing helix chain 'K' and resid 113 through 145 removed outlier: 3.887A pdb=" N ALA K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'L' and resid 4 through 35 removed outlier: 3.510A pdb=" N LYS L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 65 removed outlier: 3.626A pdb=" N ALA L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 111 Processing helix chain 'L' and resid 113 through 145 removed outlier: 3.791A pdb=" N ALA L 117 " --> pdb=" O ASP L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'M' and resid 4 through 35 removed outlier: 3.503A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 65 Processing helix chain 'M' and resid 82 through 111 removed outlier: 3.506A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 145 removed outlier: 3.708A pdb=" N ALA M 117 " --> pdb=" O ASP M 113 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP M 126 " --> pdb=" O ALA M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 151 Processing helix chain 'N' and resid 4 through 36 Processing helix chain 'N' and resid 37 through 65 Processing helix chain 'N' and resid 82 through 110 Processing helix chain 'N' and resid 113 through 145 removed outlier: 3.874A pdb=" N ALA N 117 " --> pdb=" O ASP N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 151 Processing helix chain 'O' and resid 4 through 35 Processing helix chain 'O' and resid 37 through 65 Processing helix chain 'O' and resid 82 through 111 removed outlier: 3.539A pdb=" N LYS O 111 " --> pdb=" O VAL O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 145 removed outlier: 3.823A pdb=" N ALA O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 151 Processing helix chain 'P' and resid 4 through 36 Processing helix chain 'P' and resid 37 through 65 removed outlier: 3.611A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU P 65 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 110 Processing helix chain 'P' and resid 113 through 145 removed outlier: 3.899A pdb=" N ALA P 117 " --> pdb=" O ASP P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 151 Processing helix chain 'Q' and resid 4 through 35 Processing helix chain 'Q' and resid 37 through 65 removed outlier: 3.522A pdb=" N ALA Q 41 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 110 Processing helix chain 'Q' and resid 113 through 145 removed outlier: 3.902A pdb=" N ALA Q 117 " --> pdb=" O ASP Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 151 Processing helix chain 'R' and resid 4 through 36 Processing helix chain 'R' and resid 37 through 65 removed outlier: 3.572A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 110 removed outlier: 3.544A pdb=" N MET R 86 " --> pdb=" O SER R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 145 removed outlier: 3.873A pdb=" N ALA R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 151 Processing helix chain 'S' and resid 4 through 36 removed outlier: 3.508A pdb=" N GLY S 36 " --> pdb=" O GLN S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 65 removed outlier: 3.519A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 110 removed outlier: 3.569A pdb=" N MET S 86 " --> pdb=" O SER S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 145 removed outlier: 3.860A pdb=" N ALA S 117 " --> pdb=" O ASP S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 151 Processing helix chain 'T' and resid 4 through 35 Processing helix chain 'T' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU T 65 " --> pdb=" O ARG T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 110 removed outlier: 3.549A pdb=" N MET T 86 " --> pdb=" O SER T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 113 through 145 removed outlier: 3.905A pdb=" N ALA T 117 " --> pdb=" O ASP T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 151 Processing helix chain 'U' and resid 4 through 35 removed outlier: 3.542A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 65 removed outlier: 3.608A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU U 65 " --> pdb=" O ARG U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 110 Processing helix chain 'U' and resid 113 through 145 removed outlier: 3.903A pdb=" N ALA U 117 " --> pdb=" O ASP U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 151 Processing helix chain 'V' and resid 4 through 35 removed outlier: 3.541A pdb=" N ILE V 8 " --> pdb=" O ASP V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 65 Processing helix chain 'V' and resid 82 through 111 Processing helix chain 'V' and resid 113 through 145 removed outlier: 3.711A pdb=" N ALA V 117 " --> pdb=" O ASP V 113 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 145 through 151 Processing helix chain 'W' and resid 4 through 36 removed outlier: 3.601A pdb=" N GLY W 36 " --> pdb=" O GLN W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 65 removed outlier: 3.682A pdb=" N ALA W 41 " --> pdb=" O TRP W 37 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS W 42 " --> pdb=" O THR W 38 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 110 removed outlier: 3.553A pdb=" N MET W 86 " --> pdb=" O SER W 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 145 removed outlier: 3.867A pdb=" N ALA W 117 " --> pdb=" O ASP W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 151 Processing helix chain 'X' and resid 4 through 35 Processing helix chain 'X' and resid 37 through 65 removed outlier: 3.570A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 110 removed outlier: 3.574A pdb=" N MET X 86 " --> pdb=" O SER X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 145 removed outlier: 3.879A pdb=" N ALA X 117 " --> pdb=" O ASP X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 151 2579 hydrogen bonds defined for protein. 7737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.41: 13351 1.41 - 1.59: 18377 1.59 - 1.78: 6 1.78 - 1.96: 186 1.96 - 2.14: 48 Bond restraints: 31968 Sorted by residual: bond pdb=" C GLN W 14 " pdb=" N LEU W 15 " ideal model delta sigma weight residual 1.335 1.407 -0.072 1.31e-02 5.83e+03 3.01e+01 bond pdb=" C GLU W 13 " pdb=" N GLN W 14 " ideal model delta sigma weight residual 1.335 1.405 -0.070 1.31e-02 5.83e+03 2.89e+01 bond pdb=" CB MET Q 52 " pdb=" CG MET Q 52 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.79e+00 bond pdb=" CGA HEM C 203 " pdb=" O2A HEM C 203 " ideal model delta sigma weight residual 1.258 1.288 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" NB HEM S 203 " pdb="FE HEM S 203 " ideal model delta sigma weight residual 2.080 1.975 0.105 7.00e-02 2.04e+02 2.25e+00 ... (remaining 31963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.37: 43332 6.37 - 12.74: 15 12.74 - 19.12: 2 19.12 - 25.49: 2 25.49 - 31.86: 3 Bond angle restraints: 43354 Sorted by residual: angle pdb=" CB MET C 52 " pdb=" CG MET C 52 " pdb=" SD MET C 52 " ideal model delta sigma weight residual 112.70 83.42 29.28 3.00e+00 1.11e-01 9.52e+01 angle pdb=" CB MET X 52 " pdb=" CG MET X 52 " pdb=" SD MET X 52 " ideal model delta sigma weight residual 112.70 93.08 19.62 3.00e+00 1.11e-01 4.28e+01 angle pdb=" CB MET S 52 " pdb=" CG MET S 52 " pdb=" SD MET S 52 " ideal model delta sigma weight residual 112.70 93.25 19.45 3.00e+00 1.11e-01 4.20e+01 angle pdb=" O GLN W 14 " pdb=" C GLN W 14 " pdb=" N LEU W 15 " ideal model delta sigma weight residual 122.12 115.48 6.64 1.06e+00 8.90e-01 3.92e+01 angle pdb=" CB MET N 52 " pdb=" CG MET N 52 " pdb=" SD MET N 52 " ideal model delta sigma weight residual 112.70 95.16 17.54 3.00e+00 1.11e-01 3.42e+01 ... (remaining 43349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 16867 17.68 - 35.35: 1827 35.35 - 53.03: 296 53.03 - 70.70: 99 70.70 - 88.38: 29 Dihedral angle restraints: 19118 sinusoidal: 7994 harmonic: 11124 Sorted by residual: dihedral pdb=" C2B HEM S 203 " pdb=" C3B HEM S 203 " pdb=" CAB HEM S 203 " pdb=" CBB HEM S 203 " ideal model delta sinusoidal sigma weight residual 0.00 32.74 -32.74 2 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CA GLU Q 51 " pdb=" C GLU Q 51 " pdb=" N MET Q 52 " pdb=" CA MET Q 52 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" C2B HEM K 203 " pdb=" C3B HEM K 203 " pdb=" CAB HEM K 203 " pdb=" CBB HEM K 203 " ideal model delta sinusoidal sigma weight residual 0.00 -30.74 30.74 2 1.00e+01 1.00e-02 1.25e+01 ... (remaining 19115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3785 0.034 - 0.069: 722 0.069 - 0.103: 269 0.103 - 0.137: 28 0.137 - 0.172: 2 Chirality restraints: 4806 Sorted by residual: chirality pdb=" CA MET Q 52 " pdb=" N MET Q 52 " pdb=" C MET Q 52 " pdb=" CB MET Q 52 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA PHE F 49 " pdb=" N PHE F 49 " pdb=" C PHE F 49 " pdb=" CB PHE F 49 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA MET C 52 " pdb=" N MET C 52 " pdb=" C MET C 52 " pdb=" CB MET C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 4803 not shown) Planarity restraints: 5596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 45 " -0.450 9.50e-02 1.11e+02 2.02e-01 2.63e+01 pdb=" NE ARG R 45 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG R 45 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG R 45 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG R 45 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 49 " 0.016 2.00e-02 2.50e+03 2.93e-02 1.50e+01 pdb=" CG PHE F 49 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE F 49 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE F 49 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE F 49 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE F 49 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 49 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM C 203 " 0.011 2.00e-02 2.50e+03 2.11e-02 1.00e+01 pdb=" C2A HEM C 203 " 0.028 2.00e-02 2.50e+03 pdb=" C3A HEM C 203 " 0.010 2.00e-02 2.50e+03 pdb=" C4A HEM C 203 " 0.004 2.00e-02 2.50e+03 pdb=" CAA HEM C 203 " -0.032 2.00e-02 2.50e+03 pdb=" CHA HEM C 203 " 0.017 2.00e-02 2.50e+03 pdb=" CHB HEM C 203 " 0.003 2.00e-02 2.50e+03 pdb=" CMA HEM C 203 " 0.001 2.00e-02 2.50e+03 pdb=" NA HEM C 203 " -0.041 2.00e-02 2.50e+03 ... (remaining 5593 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 74 2.43 - 3.04: 19740 3.04 - 3.66: 43843 3.66 - 4.28: 68450 4.28 - 4.90: 115959 Nonbonded interactions: 248066 Sorted by model distance: nonbonded pdb=" OE2 GLU H 94 " pdb="FE FE H 202 " model vdw 1.807 3.000 nonbonded pdb=" OE1 GLU G 127 " pdb="FE FE G 202 " model vdw 1.953 3.000 nonbonded pdb=" OE1 GLU T 127 " pdb="FE FE2 T 203 " model vdw 1.972 3.000 nonbonded pdb=" OE1 GLU F 127 " pdb="FE FE2 F 202 " model vdw 1.974 3.000 nonbonded pdb=" OE1 GLU R 127 " pdb="FE FE R 202 " model vdw 2.031 3.000 ... (remaining 248061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 156) selection = (chain 'B' and resid 1 through 156) selection = (chain 'C' and resid 1 through 156) selection = (chain 'D' and resid 1 through 156) selection = (chain 'E' and resid 1 through 156) selection = (chain 'F' and resid 1 through 156) selection = (chain 'G' and resid 1 through 156) selection = (chain 'H' and resid 1 through 156) selection = (chain 'I' and resid 1 through 156) selection = (chain 'J' and resid 1 through 156) selection = (chain 'K' and resid 1 through 156) selection = (chain 'L' and resid 1 through 156) selection = (chain 'M' and resid 1 through 156) selection = (chain 'N' and resid 1 through 156) selection = (chain 'O' and resid 1 through 156) selection = (chain 'P' and resid 1 through 156) selection = (chain 'Q' and resid 1 through 156) selection = (chain 'R' and resid 1 through 156) selection = (chain 'S' and resid 1 through 156) selection = (chain 'T' and resid 1 through 156) selection = (chain 'U' and resid 1 through 156) selection = (chain 'V' and resid 1 through 156) selection = (chain 'W' and resid 1 through 156) selection = (chain 'X' and resid 1 through 156) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 25.340 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.666 31999 Z= 0.211 Angle : 0.618 31.860 43354 Z= 0.323 Chirality : 0.033 0.172 4806 Planarity : 0.004 0.202 5596 Dihedral : 15.053 88.377 11862 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.11 (0.13), residues: 3724 helix: 3.83 (0.08), residues: 2999 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG R 45 TYR 0.047 0.001 TYR T 71 PHE 0.062 0.003 PHE F 49 TRP 0.013 0.001 TRP H 37 HIS 0.003 0.001 HIS U 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.18 (31968) covalent geometry : angle 0.61805 / 0.32 (43354) hydrogen bonds : bond 0.13535 / 9.25 ( 2579) hydrogen bonds : angle 4.25600 / 3.16 ( 7737) Misc. bond : bond 0.25639 / 16.01 ( 31) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.1915 time to fit residues: 143.5468 Evaluate side-chains 208 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.0570 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 overall best weight: 7.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 112 HIS M 137 GLN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 112 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 = 0.2887 r_free = 0.2887 target = 0.033992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.027402 restraints weight = 210619.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.028435 restraints weight = 131398.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.029221 restraints weight = 93097.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.029822 restraints weight = 70536.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.030281 restraints weight = 55720.481| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.337 31999 Z= 0.187 Angle : 0.662 15.684 43354 Z= 0.316 Chirality : 0.033 0.129 4806 Planarity : 0.003 0.080 5596 Dihedral : 6.794 78.872 4204 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.78 % Allowed : 8.00 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.34 (0.13), residues: 3724 helix: 3.86 (0.08), residues: 3062 sheet: None (None), residues: 0 loop : -2.54 (0.20), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 100 TYR 0.030 0.001 TYR T 71 PHE 0.032 0.002 PHE F 49 TRP 0.010 0.001 TRP H 37 HIS 0.004 0.001 HIS J 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (31968) covalent geometry : angle 0.66232 / 0.32 (43354) hydrogen bonds : bond 0.07488 / 5.07 ( 2579) hydrogen bonds : angle 3.99131 / 2.97 ( 7737) Misc. bond : bond 0.09274 / 4.97 ( 31) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 257 time to evaluate : 1.447 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: H 52 MET cc_start: 0.7301 (mtm) cc_final: 0.6723 (mtm) REVERT: I 52 MET cc_start: 0.6092 (mtm) cc_final: 0.5877 (mtm) REVERT: J 53 ARG cc_start: 0.8979 (mtt90) cc_final: 0.8611 (mtm-85) REVERT: K 52 MET cc_start: 0.7723 (mtm) cc_final: 0.7357 (mtp) REVERT: L 52 MET cc_start: 0.7444 (mtm) cc_final: 0.7208 (mtm) REVERT: M 53 ARG cc_start: 0.8969 (mtt90) cc_final: 0.8761 (mtm-85) REVERT: M 86 MET cc_start: 0.9476 (mtt) cc_final: 0.9230 (mtt) REVERT: V 1 MET cc_start: 0.7710 (tpt) cc_final: 0.7476 (tpp) REVERT: W 52 MET cc_start: 0.6652 (mtm) cc_final: 0.6397 (mtm) REVERT: X 86 MET cc_start: 0.9437 (mtt) cc_final: 0.9236 (mtt) outliers start: 26 outliers final: 15 residues processed: 261 average time/residue: 0.1769 time to fit residues: 79.6504 Evaluate side-chains 202 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain W residue 98 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 30.0000 chunk 162 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 266 optimal weight: 0.0570 chunk 93 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 242 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 164 optimal weight: 6.9990 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.034888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.028234 restraints weight = 217030.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.029298 restraints weight = 136576.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.030137 restraints weight = 96141.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.030793 restraints weight = 72280.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.031271 restraints weight = 56940.176| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.348 31999 Z= 0.150 Angle : 0.604 14.195 43354 Z= 0.279 Chirality : 0.032 0.120 4806 Planarity : 0.002 0.054 5596 Dihedral : 6.938 83.924 4204 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.48 % Allowed : 10.08 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.55 (0.13), residues: 3724 helix: 3.97 (0.08), residues: 3067 sheet: None (None), residues: 0 loop : -2.38 (0.20), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 53 TYR 0.038 0.001 TYR T 71 PHE 0.021 0.002 PHE F 49 TRP 0.007 0.001 TRP H 37 HIS 0.004 0.001 HIS L 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (31968) covalent geometry : angle 0.60355 / 0.28 (43354) hydrogen bonds : bond 0.06284 / 4.26 ( 2579) hydrogen bonds : angle 3.72409 / 2.77 ( 7737) Misc. bond : bond 0.08338 / 4.49 ( 31) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.857 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 59 THR cc_start: 0.9363 (m) cc_final: 0.9090 (p) REVERT: A 86 MET cc_start: 0.9366 (mtt) cc_final: 0.8832 (mpp) REVERT: C 59 THR cc_start: 0.9289 (m) cc_final: 0.9029 (p) REVERT: D 86 MET cc_start: 0.9403 (mtt) cc_final: 0.9177 (mtt) REVERT: E 53 ARG cc_start: 0.8991 (mtt90) cc_final: 0.8581 (mtm-85) REVERT: F 59 THR cc_start: 0.9385 (m) cc_final: 0.9111 (p) REVERT: F 86 MET cc_start: 0.9368 (mtt) cc_final: 0.8835 (mpp) REVERT: G 52 MET cc_start: 0.7831 (ttm) cc_final: 0.7624 (ttp) REVERT: G 59 THR cc_start: 0.9399 (m) cc_final: 0.9121 (p) REVERT: H 52 MET cc_start: 0.7482 (mtm) cc_final: 0.7026 (mtm) REVERT: I 59 THR cc_start: 0.9379 (m) cc_final: 0.9118 (p) REVERT: J 53 ARG cc_start: 0.8982 (mtt90) cc_final: 0.8656 (mtm-85) REVERT: J 86 MET cc_start: 0.9400 (mtt) cc_final: 0.9189 (mtt) REVERT: K 52 MET cc_start: 0.7829 (mtm) cc_final: 0.7474 (mtp) REVERT: K 59 THR cc_start: 0.9381 (m) cc_final: 0.9122 (p) REVERT: M 53 ARG cc_start: 0.8899 (mtt90) cc_final: 0.8565 (mtm-85) REVERT: N 86 MET cc_start: 0.9404 (mtt) cc_final: 0.9185 (mtt) REVERT: O 59 THR cc_start: 0.9370 (m) cc_final: 0.9100 (p) REVERT: R 86 MET cc_start: 0.9356 (mtt) cc_final: 0.8823 (mpp) REVERT: S 86 MET cc_start: 0.9365 (mtt) cc_final: 0.8831 (mpp) REVERT: T 86 MET cc_start: 0.9374 (mtt) cc_final: 0.8822 (mpp) REVERT: V 86 MET cc_start: 0.9396 (mtt) cc_final: 0.9195 (mtt) REVERT: W 86 MET cc_start: 0.9363 (mtt) cc_final: 0.8818 (mpp) outliers start: 16 outliers final: 4 residues processed: 212 average time/residue: 0.1563 time to fit residues: 57.7929 Evaluate side-chains 183 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 179 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain T residue 98 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 272 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 325 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 175 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 264 optimal weight: 20.0000 chunk 278 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 336 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.034151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.027626 restraints weight = 216206.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.028675 restraints weight = 135274.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.029478 restraints weight = 95319.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.030138 restraints weight = 71530.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.030612 restraints weight = 56232.984| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.348 31999 Z= 0.157 Angle : 0.595 12.880 43354 Z= 0.278 Chirality : 0.032 0.125 4806 Planarity : 0.002 0.040 5596 Dihedral : 6.973 87.369 4204 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.66 % Allowed : 10.32 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.46 (0.13), residues: 3724 helix: 3.86 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -2.16 (0.20), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 45 TYR 0.028 0.001 TYR T 71 PHE 0.018 0.001 PHE N 26 TRP 0.005 0.001 TRP H 37 HIS 0.003 0.001 HIS L 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (31968) covalent geometry : angle 0.59499 / 0.28 (43354) hydrogen bonds : bond 0.06253 / 4.24 ( 2579) hydrogen bonds : angle 3.76694 / 2.80 ( 7737) Misc. bond : bond 0.10144 / 6.81 ( 31) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 1.273 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 59 THR cc_start: 0.9347 (m) cc_final: 0.9060 (p) REVERT: C 59 THR cc_start: 0.9293 (m) cc_final: 0.9026 (p) REVERT: C 108 MET cc_start: 0.8873 (ptm) cc_final: 0.8537 (ppp) REVERT: D 86 MET cc_start: 0.9399 (mtt) cc_final: 0.9183 (mtt) REVERT: E 53 ARG cc_start: 0.8962 (mtt90) cc_final: 0.8557 (mtm-85) REVERT: F 59 THR cc_start: 0.9403 (m) cc_final: 0.9123 (p) REVERT: F 108 MET cc_start: 0.8862 (ptm) cc_final: 0.8517 (ppp) REVERT: G 59 THR cc_start: 0.9396 (m) cc_final: 0.9112 (p) REVERT: H 52 MET cc_start: 0.7447 (mtm) cc_final: 0.7035 (mtm) REVERT: I 59 THR cc_start: 0.9394 (m) cc_final: 0.9122 (p) REVERT: J 53 ARG cc_start: 0.8932 (mtt90) cc_final: 0.8593 (mtm-85) REVERT: J 86 MET cc_start: 0.9397 (mtt) cc_final: 0.9190 (mtt) REVERT: K 52 MET cc_start: 0.8032 (mtm) cc_final: 0.7726 (mtp) REVERT: K 59 THR cc_start: 0.9404 (m) cc_final: 0.9135 (p) REVERT: L 2 GLN cc_start: 0.8740 (pp30) cc_final: 0.8537 (pp30) REVERT: M 53 ARG cc_start: 0.8924 (mtt90) cc_final: 0.8579 (mtm-85) REVERT: N 86 MET cc_start: 0.9407 (mtt) cc_final: 0.9201 (mtt) REVERT: N 108 MET cc_start: 0.8875 (ptm) cc_final: 0.8511 (ppp) REVERT: O 59 THR cc_start: 0.9377 (m) cc_final: 0.9106 (p) REVERT: O 108 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.9122 (ptm) REVERT: R 108 MET cc_start: 0.8756 (ptm) cc_final: 0.8246 (ppp) REVERT: S 59 THR cc_start: 0.9444 (m) cc_final: 0.9182 (p) REVERT: T 108 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8880 (ppp) REVERT: W 108 MET cc_start: 0.8781 (ptm) cc_final: 0.8463 (ppp) REVERT: X 108 MET cc_start: 0.8820 (ptm) cc_final: 0.8525 (ppp) outliers start: 22 outliers final: 14 residues processed: 197 average time/residue: 0.1674 time to fit residues: 56.5564 Evaluate side-chains 192 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain T residue 108 MET Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain X residue 98 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 84 optimal weight: 10.0000 chunk 343 optimal weight: 20.0000 chunk 251 optimal weight: 20.0000 chunk 243 optimal weight: 8.9990 chunk 233 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 357 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 130 HIS I 130 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS T 130 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.033416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.026945 restraints weight = 221924.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.027997 restraints weight = 138306.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.028784 restraints weight = 97527.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.029415 restraints weight = 73743.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.029897 restraints weight = 58338.141| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.344 31999 Z= 0.175 Angle : 0.596 13.948 43354 Z= 0.279 Chirality : 0.032 0.120 4806 Planarity : 0.002 0.038 5596 Dihedral : 6.977 88.412 4204 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.00 % Allowed : 9.96 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.42 (0.13), residues: 3724 helix: 3.81 (0.08), residues: 3067 sheet: None (None), residues: 0 loop : -1.99 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 45 TYR 0.028 0.001 TYR T 71 PHE 0.019 0.001 PHE S 26 TRP 0.004 0.001 TRP W 37 HIS 0.003 0.001 HIS P 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (31968) covalent geometry : angle 0.59584 / 0.28 (43354) hydrogen bonds : bond 0.06467 / 4.38 ( 2579) hydrogen bonds : angle 3.77525 / 2.80 ( 7737) Misc. bond : bond 0.08693 / 5.58 ( 31) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 1.330 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 108 MET cc_start: 0.8693 (ptm) cc_final: 0.8385 (ppp) REVERT: C 59 THR cc_start: 0.9293 (m) cc_final: 0.9024 (p) REVERT: C 108 MET cc_start: 0.8852 (ptm) cc_final: 0.8538 (ppp) REVERT: D 86 MET cc_start: 0.9403 (mtt) cc_final: 0.9194 (mtt) REVERT: D 108 MET cc_start: 0.8707 (ptm) cc_final: 0.8393 (ppp) REVERT: E 53 ARG cc_start: 0.8954 (mtt90) cc_final: 0.8510 (mtm-85) REVERT: E 108 MET cc_start: 0.8766 (ptm) cc_final: 0.8441 (ppp) REVERT: F 59 THR cc_start: 0.9409 (m) cc_final: 0.9128 (p) REVERT: F 108 MET cc_start: 0.8833 (ptm) cc_final: 0.8551 (ppp) REVERT: G 108 MET cc_start: 0.8607 (ptm) cc_final: 0.8327 (ppp) REVERT: H 52 MET cc_start: 0.7568 (mtm) cc_final: 0.7150 (mtm) REVERT: H 108 MET cc_start: 0.9149 (tmm) cc_final: 0.8823 (ppp) REVERT: I 59 THR cc_start: 0.9405 (m) cc_final: 0.9120 (p) REVERT: I 108 MET cc_start: 0.8830 (ptm) cc_final: 0.8309 (ppp) REVERT: J 53 ARG cc_start: 0.8922 (mtt90) cc_final: 0.8599 (mtm-85) REVERT: J 86 MET cc_start: 0.9418 (mtt) cc_final: 0.9209 (mtt) REVERT: J 108 MET cc_start: 0.8888 (ptm) cc_final: 0.8364 (ppp) REVERT: K 52 MET cc_start: 0.7983 (mtm) cc_final: 0.7660 (mtp) REVERT: K 59 THR cc_start: 0.9417 (m) cc_final: 0.9148 (p) REVERT: K 108 MET cc_start: 0.8686 (ptm) cc_final: 0.8401 (ppp) REVERT: L 108 MET cc_start: 0.9012 (ptm) cc_final: 0.8396 (ppp) REVERT: M 53 ARG cc_start: 0.8919 (mtt90) cc_final: 0.8571 (mtm-85) REVERT: M 108 MET cc_start: 0.8982 (ptm) cc_final: 0.8451 (ppp) REVERT: N 86 MET cc_start: 0.9421 (mtt) cc_final: 0.9217 (mtt) REVERT: N 108 MET cc_start: 0.8850 (ptm) cc_final: 0.8558 (ppp) REVERT: O 59 THR cc_start: 0.9385 (m) cc_final: 0.9112 (p) REVERT: O 108 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.8962 (ppp) REVERT: P 108 MET cc_start: 0.8672 (ptm) cc_final: 0.8365 (ppp) REVERT: Q 108 MET cc_start: 0.8751 (ptm) cc_final: 0.8399 (ppp) REVERT: R 108 MET cc_start: 0.8775 (ptm) cc_final: 0.8298 (ppp) REVERT: S 59 THR cc_start: 0.9432 (m) cc_final: 0.9174 (p) REVERT: T 108 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8981 (ptm) REVERT: U 108 MET cc_start: 0.8778 (ptm) cc_final: 0.8415 (ppp) REVERT: W 108 MET cc_start: 0.8772 (ptm) cc_final: 0.8471 (ppp) REVERT: X 86 MET cc_start: 0.9273 (mtm) cc_final: 0.8861 (mpp) REVERT: X 108 MET cc_start: 0.8800 (ptm) cc_final: 0.8536 (ppp) outliers start: 33 outliers final: 21 residues processed: 192 average time/residue: 0.1848 time to fit residues: 60.7384 Evaluate side-chains 191 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain T residue 108 MET Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain X residue 98 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 134 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 290 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 142 optimal weight: 30.0000 chunk 308 optimal weight: 7.9990 chunk 344 optimal weight: 10.0000 chunk 317 optimal weight: 20.0000 chunk 209 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 HIS B 130 HIS C 130 HIS M 156 GLN N 130 HIS O 130 HIS P 130 HIS R 130 HIS X 130 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.032881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.026435 restraints weight = 221802.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.027474 restraints weight = 139589.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.028230 restraints weight = 98527.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.028847 restraints weight = 75014.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.029318 restraints weight = 59381.666| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.741 31999 Z= 0.187 Angle : 0.640 16.617 43354 Z= 0.298 Chirality : 0.033 0.141 4806 Planarity : 0.002 0.031 5596 Dihedral : 6.929 87.054 4204 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.33 % Allowed : 10.83 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.37 (0.13), residues: 3724 helix: 3.75 (0.08), residues: 3067 sheet: None (None), residues: 0 loop : -1.86 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 45 TYR 0.029 0.001 TYR T 71 PHE 0.020 0.001 PHE S 26 TRP 0.004 0.001 TRP R 37 HIS 0.003 0.001 HIS N 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (31968) covalent geometry : angle 0.63969 / 0.30 (43354) hydrogen bonds : bond 0.06703 / 4.54 ( 2579) hydrogen bonds : angle 3.85497 / 2.86 ( 7737) Misc. bond : bond 0.16455 / 8.10 ( 31) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 1.294 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: A 86 MET cc_start: 0.9239 (mtm) cc_final: 0.8809 (mpp) REVERT: A 108 MET cc_start: 0.8710 (ptm) cc_final: 0.8462 (ppp) REVERT: C 108 MET cc_start: 0.8846 (ptm) cc_final: 0.8412 (ppp) REVERT: D 86 MET cc_start: 0.9416 (mtt) cc_final: 0.9203 (mtt) REVERT: D 108 MET cc_start: 0.8711 (ptm) cc_final: 0.8374 (ppp) REVERT: E 53 ARG cc_start: 0.8926 (mtt90) cc_final: 0.8546 (mtm-85) REVERT: E 108 MET cc_start: 0.8803 (ptm) cc_final: 0.8532 (ppp) REVERT: F 59 THR cc_start: 0.9431 (m) cc_final: 0.9151 (p) REVERT: F 86 MET cc_start: 0.9249 (mtm) cc_final: 0.8812 (mpp) REVERT: F 108 MET cc_start: 0.8858 (ptm) cc_final: 0.8419 (ppp) REVERT: G 108 MET cc_start: 0.8630 (ptm) cc_final: 0.8379 (ppp) REVERT: H 52 MET cc_start: 0.7805 (mtm) cc_final: 0.7378 (mtm) REVERT: I 59 THR cc_start: 0.9411 (m) cc_final: 0.9126 (p) REVERT: I 108 MET cc_start: 0.8828 (ptm) cc_final: 0.8345 (ppp) REVERT: J 53 ARG cc_start: 0.8886 (mtt90) cc_final: 0.8571 (mtm-85) REVERT: J 86 MET cc_start: 0.9419 (mtt) cc_final: 0.9212 (mtt) REVERT: J 108 MET cc_start: 0.8840 (ptm) cc_final: 0.8340 (ppp) REVERT: K 52 MET cc_start: 0.8041 (mtm) cc_final: 0.7693 (mtp) REVERT: K 59 THR cc_start: 0.9424 (m) cc_final: 0.9153 (p) REVERT: K 108 MET cc_start: 0.8678 (ptm) cc_final: 0.8455 (ppp) REVERT: L 108 MET cc_start: 0.8992 (ptm) cc_final: 0.8392 (ppp) REVERT: M 53 ARG cc_start: 0.8877 (mtt90) cc_final: 0.8535 (mtm-85) REVERT: M 108 MET cc_start: 0.8997 (ptm) cc_final: 0.8526 (ppp) REVERT: N 86 MET cc_start: 0.9420 (mtt) cc_final: 0.9214 (mtt) REVERT: N 108 MET cc_start: 0.8864 (ptm) cc_final: 0.8583 (ppp) REVERT: O 59 THR cc_start: 0.9392 (m) cc_final: 0.9118 (p) REVERT: O 108 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.9109 (ptm) REVERT: P 108 MET cc_start: 0.8674 (ptm) cc_final: 0.8416 (ppp) REVERT: Q 108 MET cc_start: 0.8743 (ptm) cc_final: 0.8405 (ppp) REVERT: R 86 MET cc_start: 0.9223 (mtm) cc_final: 0.8764 (mpp) REVERT: R 108 MET cc_start: 0.8784 (ptm) cc_final: 0.8347 (ppp) REVERT: S 59 THR cc_start: 0.9446 (m) cc_final: 0.9189 (p) REVERT: S 86 MET cc_start: 0.9223 (mtm) cc_final: 0.8804 (mpp) REVERT: T 86 MET cc_start: 0.9234 (mtm) cc_final: 0.8791 (mpp) REVERT: T 108 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8984 (ptm) REVERT: U 108 MET cc_start: 0.8792 (ptm) cc_final: 0.8445 (ppp) REVERT: V 108 MET cc_start: 0.9264 (ptp) cc_final: 0.9027 (ptm) REVERT: W 59 THR cc_start: 0.9491 (m) cc_final: 0.9242 (p) REVERT: W 86 MET cc_start: 0.9261 (mtm) cc_final: 0.8789 (mpp) REVERT: W 108 MET cc_start: 0.8779 (ptm) cc_final: 0.8469 (ppp) REVERT: X 86 MET cc_start: 0.9282 (mtm) cc_final: 0.8901 (mpp) REVERT: X 108 MET cc_start: 0.8817 (ptm) cc_final: 0.8596 (ppp) outliers start: 44 outliers final: 26 residues processed: 194 average time/residue: 0.1967 time to fit residues: 63.4605 Evaluate side-chains 197 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain T residue 108 MET Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain X residue 98 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 155 optimal weight: 5.9990 chunk 60 optimal weight: 30.0000 chunk 323 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 202 optimal weight: 30.0000 chunk 38 optimal weight: 0.0970 chunk 132 optimal weight: 6.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 HIS B 130 HIS C 130 HIS N 130 HIS O 130 HIS P 130 HIS R 130 HIS X 130 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.034100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.027619 restraints weight = 223188.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.028684 restraints weight = 139779.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.029471 restraints weight = 98227.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.030097 restraints weight = 74089.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.030562 restraints weight = 58549.183| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.814 31999 Z= 0.138 Angle : 0.581 14.707 43354 Z= 0.266 Chirality : 0.032 0.118 4806 Planarity : 0.002 0.026 5596 Dihedral : 6.893 88.660 4204 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.48 % Allowed : 11.10 % Favored : 88.41 % 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 are not related in a simple way. whole: 4.63 (0.13), residues: 3724 helix: 3.91 (0.08), residues: 3067 sheet: None (None), residues: 0 loop : -1.69 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 73 TYR 0.026 0.001 TYR T 71 PHE 0.017 0.001 PHE S 26 TRP 0.007 0.001 TRP O 37 HIS 0.002 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (31968) covalent geometry : angle 0.58106 / 0.27 (43354) hydrogen bonds : bond 0.05777 / 3.91 ( 2579) hydrogen bonds : angle 3.56439 / 2.64 ( 7737) Misc. bond : bond 0.17291 / 8.17 ( 31) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 1.330 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 86 MET cc_start: 0.9163 (mtm) cc_final: 0.8764 (mpp) REVERT: C 108 MET cc_start: 0.8741 (ptm) cc_final: 0.8372 (ppp) REVERT: D 108 MET cc_start: 0.8606 (ptm) cc_final: 0.8393 (ppp) REVERT: E 53 ARG cc_start: 0.8961 (mtt90) cc_final: 0.8572 (mtm-85) REVERT: F 59 THR cc_start: 0.9363 (m) cc_final: 0.9066 (p) REVERT: F 86 MET cc_start: 0.9163 (mtm) cc_final: 0.8761 (mpp) REVERT: F 108 MET cc_start: 0.8727 (ptm) cc_final: 0.8523 (ppp) REVERT: H 52 MET cc_start: 0.7869 (mtm) cc_final: 0.7490 (mtm) REVERT: I 108 MET cc_start: 0.8710 (ptm) cc_final: 0.8254 (ppp) REVERT: J 53 ARG cc_start: 0.8906 (mtt90) cc_final: 0.8582 (mtm-85) REVERT: J 108 MET cc_start: 0.8765 (ptm) cc_final: 0.8313 (ppp) REVERT: K 52 MET cc_start: 0.8188 (mtm) cc_final: 0.7844 (mtp) REVERT: L 108 MET cc_start: 0.8934 (ptm) cc_final: 0.8381 (ppp) REVERT: M 53 ARG cc_start: 0.8905 (mtt90) cc_final: 0.8548 (mtm-85) REVERT: M 108 MET cc_start: 0.8928 (ptm) cc_final: 0.8496 (ppp) REVERT: N 108 MET cc_start: 0.8750 (ptm) cc_final: 0.8534 (ppp) REVERT: O 59 THR cc_start: 0.9316 (m) cc_final: 0.9028 (p) REVERT: O 108 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.8959 (tmm) REVERT: Q 108 MET cc_start: 0.8640 (ptm) cc_final: 0.8412 (ppp) REVERT: R 86 MET cc_start: 0.9153 (mtm) cc_final: 0.8747 (mpp) REVERT: R 108 MET cc_start: 0.8695 (ptm) cc_final: 0.8293 (ppp) REVERT: S 59 THR cc_start: 0.9404 (m) cc_final: 0.9119 (p) REVERT: S 86 MET cc_start: 0.9152 (mtm) cc_final: 0.8762 (mpp) REVERT: T 86 MET cc_start: 0.9155 (mtm) cc_final: 0.8745 (mpp) REVERT: T 108 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8945 (ptm) REVERT: U 108 MET cc_start: 0.8669 (ptm) cc_final: 0.8414 (ppp) REVERT: V 108 MET cc_start: 0.9230 (ptp) cc_final: 0.9012 (ptm) REVERT: W 59 THR cc_start: 0.9430 (m) cc_final: 0.9172 (p) REVERT: W 86 MET cc_start: 0.9190 (mtm) cc_final: 0.8763 (mpp) REVERT: W 108 MET cc_start: 0.8642 (ptm) cc_final: 0.8436 (ppp) outliers start: 16 outliers final: 8 residues processed: 189 average time/residue: 0.1819 time to fit residues: 58.9720 Evaluate side-chains 177 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain T residue 108 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 307 optimal weight: 30.0000 chunk 214 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 245 optimal weight: 9.9990 chunk 330 optimal weight: 30.0000 chunk 94 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 302 optimal weight: 5.9990 chunk 318 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 HIS B 130 HIS C 130 HIS N 130 HIS O 130 HIS R 130 HIS V 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.033140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.026744 restraints weight = 221991.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.027788 restraints weight = 139704.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.028559 restraints weight = 98425.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.029176 restraints weight = 74356.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.029641 restraints weight = 58752.506| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.860 31999 Z= 0.173 Angle : 0.614 14.400 43354 Z= 0.285 Chirality : 0.033 0.124 4806 Planarity : 0.002 0.030 5596 Dihedral : 6.895 89.740 4204 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.84 % Allowed : 11.32 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.47 (0.13), residues: 3724 helix: 3.79 (0.08), residues: 3067 sheet: None (None), residues: 0 loop : -1.65 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 73 TYR 0.028 0.001 TYR T 71 PHE 0.019 0.001 PHE S 26 TRP 0.004 0.001 TRP K 37 HIS 0.003 0.001 HIS L 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (31968) covalent geometry : angle 0.61410 / 0.29 (43354) hydrogen bonds : bond 0.06274 / 4.25 ( 2579) hydrogen bonds : angle 3.73047 / 2.76 ( 7737) Misc. bond : bond 0.18222 / 8.65 ( 31) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 1.343 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: A 86 MET cc_start: 0.9234 (mtm) cc_final: 0.8858 (mpp) REVERT: C 108 MET cc_start: 0.8801 (ptm) cc_final: 0.8393 (ppp) REVERT: D 86 MET cc_start: 0.9412 (mtt) cc_final: 0.8798 (mpp) REVERT: D 108 MET cc_start: 0.8664 (ptm) cc_final: 0.8415 (ppp) REVERT: E 53 ARG cc_start: 0.8933 (mtt90) cc_final: 0.8532 (mtm-85) REVERT: F 86 MET cc_start: 0.9249 (mtm) cc_final: 0.8830 (mpp) REVERT: F 108 MET cc_start: 0.8776 (ptm) cc_final: 0.8388 (ppp) REVERT: H 52 MET cc_start: 0.7895 (mtm) cc_final: 0.7522 (mtm) REVERT: I 108 MET cc_start: 0.8785 (ptm) cc_final: 0.8339 (ppp) REVERT: J 53 ARG cc_start: 0.8905 (mtt90) cc_final: 0.8576 (mtm-85) REVERT: J 86 MET cc_start: 0.9419 (mtt) cc_final: 0.8811 (mpp) REVERT: J 108 MET cc_start: 0.8817 (ptm) cc_final: 0.8360 (ppp) REVERT: K 52 MET cc_start: 0.8112 (mtm) cc_final: 0.7805 (mtp) REVERT: L 108 MET cc_start: 0.8974 (ptm) cc_final: 0.8403 (ppp) REVERT: M 53 ARG cc_start: 0.8890 (mtt90) cc_final: 0.8540 (mtm-85) REVERT: M 108 MET cc_start: 0.8951 (ptm) cc_final: 0.8530 (ppp) REVERT: N 86 MET cc_start: 0.9427 (mtt) cc_final: 0.8827 (mpp) REVERT: N 108 MET cc_start: 0.8805 (ptm) cc_final: 0.8385 (ppp) REVERT: O 59 THR cc_start: 0.9357 (m) cc_final: 0.9074 (p) REVERT: O 108 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.9089 (ptm) REVERT: Q 108 MET cc_start: 0.8689 (ptm) cc_final: 0.8435 (ppp) REVERT: R 86 MET cc_start: 0.9227 (mtm) cc_final: 0.8815 (mpp) REVERT: R 108 MET cc_start: 0.8751 (ptm) cc_final: 0.8330 (ppp) REVERT: S 59 THR cc_start: 0.9443 (m) cc_final: 0.9163 (p) REVERT: S 86 MET cc_start: 0.9230 (mtm) cc_final: 0.8867 (mpp) REVERT: T 86 MET cc_start: 0.9224 (mtm) cc_final: 0.8839 (mpp) REVERT: T 108 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8971 (ptm) REVERT: U 108 MET cc_start: 0.8717 (ptm) cc_final: 0.8283 (ppp) REVERT: V 108 MET cc_start: 0.9257 (ptp) cc_final: 0.9044 (ptm) REVERT: W 59 THR cc_start: 0.9460 (m) cc_final: 0.9211 (p) REVERT: W 86 MET cc_start: 0.9253 (mtm) cc_final: 0.8795 (mpp) REVERT: W 108 MET cc_start: 0.8705 (ptm) cc_final: 0.8316 (ppp) REVERT: X 86 MET cc_start: 0.9197 (mtm) cc_final: 0.8809 (mpp) outliers start: 28 outliers final: 24 residues processed: 174 average time/residue: 0.1780 time to fit residues: 53.2491 Evaluate side-chains 192 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain T residue 108 MET Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain X residue 98 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 41 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 346 optimal weight: 9.9990 chunk 232 optimal weight: 8.9990 chunk 172 optimal weight: 30.0000 chunk 354 optimal weight: 8.9990 chunk 120 optimal weight: 30.0000 chunk 334 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 130 HIS F 130 HIS P 130 HIS U 130 HIS X 130 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.032432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.025967 restraints weight = 215817.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.026979 restraints weight = 136611.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.027715 restraints weight = 96741.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.028331 restraints weight = 73750.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.028805 restraints weight = 58399.660| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.888 31999 Z= 0.190 Angle : 0.631 15.028 43354 Z= 0.296 Chirality : 0.033 0.131 4806 Planarity : 0.002 0.030 5596 Dihedral : 6.916 88.557 4204 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.84 % Allowed : 11.41 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.38 (0.13), residues: 3724 helix: 3.73 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -1.74 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 73 TYR 0.028 0.001 TYR T 71 PHE 0.020 0.001 PHE S 26 TRP 0.004 0.001 TRP K 37 HIS 0.003 0.001 HIS P 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (31968) covalent geometry : angle 0.63132 / 0.30 (43354) hydrogen bonds : bond 0.06709 / 4.55 ( 2579) hydrogen bonds : angle 3.82530 / 2.83 ( 7737) Misc. bond : bond 0.18693 / 8.72 ( 31) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 1.450 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: A 86 MET cc_start: 0.9278 (mtm) cc_final: 0.8895 (mpp) REVERT: C 108 MET cc_start: 0.8822 (ptm) cc_final: 0.8393 (ppp) REVERT: D 86 MET cc_start: 0.9423 (mtt) cc_final: 0.8806 (mpp) REVERT: D 108 MET cc_start: 0.8703 (ptm) cc_final: 0.8276 (ppp) REVERT: E 53 ARG cc_start: 0.8936 (mtt90) cc_final: 0.8537 (mtm-85) REVERT: F 86 MET cc_start: 0.9292 (mtm) cc_final: 0.8892 (mpp) REVERT: F 108 MET cc_start: 0.8810 (ptm) cc_final: 0.8424 (ppp) REVERT: H 52 MET cc_start: 0.7850 (mtm) cc_final: 0.7421 (mtm) REVERT: I 108 MET cc_start: 0.8810 (ptm) cc_final: 0.8380 (ppp) REVERT: J 53 ARG cc_start: 0.8895 (mtt90) cc_final: 0.8568 (mtm-85) REVERT: J 86 MET cc_start: 0.9425 (mtt) cc_final: 0.8805 (mpp) REVERT: J 108 MET cc_start: 0.8842 (ptm) cc_final: 0.8403 (ppp) REVERT: K 52 MET cc_start: 0.8083 (mtm) cc_final: 0.7781 (mtp) REVERT: L 108 MET cc_start: 0.8995 (ptm) cc_final: 0.8443 (ppp) REVERT: M 53 ARG cc_start: 0.8879 (mtt90) cc_final: 0.8527 (mtm-85) REVERT: M 108 MET cc_start: 0.8961 (ptm) cc_final: 0.8563 (ppp) REVERT: N 86 MET cc_start: 0.9442 (mtt) cc_final: 0.8825 (mpp) REVERT: N 108 MET cc_start: 0.8843 (ptm) cc_final: 0.8426 (ppp) REVERT: O 59 THR cc_start: 0.9384 (m) cc_final: 0.9109 (p) REVERT: O 108 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.8967 (tmm) REVERT: Q 108 MET cc_start: 0.8723 (ptm) cc_final: 0.8305 (ppp) REVERT: R 86 MET cc_start: 0.9262 (mtm) cc_final: 0.8870 (mpp) REVERT: R 108 MET cc_start: 0.8754 (ptm) cc_final: 0.8344 (ppp) REVERT: S 59 THR cc_start: 0.9452 (m) cc_final: 0.9184 (p) REVERT: S 86 MET cc_start: 0.9271 (mtm) cc_final: 0.8896 (mpp) REVERT: T 86 MET cc_start: 0.9271 (mtm) cc_final: 0.8880 (mpp) REVERT: T 108 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8982 (ptm) REVERT: U 108 MET cc_start: 0.8757 (ptm) cc_final: 0.8304 (ppp) REVERT: V 108 MET cc_start: 0.9258 (ptp) cc_final: 0.9055 (ptm) REVERT: W 59 THR cc_start: 0.9470 (m) cc_final: 0.9224 (p) REVERT: W 86 MET cc_start: 0.9299 (mtm) cc_final: 0.8894 (mpp) REVERT: W 108 MET cc_start: 0.8727 (ptm) cc_final: 0.8327 (ppp) REVERT: X 86 MET cc_start: 0.9242 (mtm) cc_final: 0.8772 (mpp) outliers start: 28 outliers final: 25 residues processed: 174 average time/residue: 0.1711 time to fit residues: 52.0775 Evaluate side-chains 190 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain T residue 108 MET Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain X residue 98 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 56 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 326 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 236 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 45 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 HIS C 130 HIS D 130 HIS F 130 HIS U 130 HIS X 130 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.033213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.026838 restraints weight = 221698.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.027883 restraints weight = 139591.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.028650 restraints weight = 98275.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.029269 restraints weight = 74280.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.029738 restraints weight = 58722.190| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.876 31999 Z= 0.162 Angle : 0.618 14.638 43354 Z= 0.286 Chirality : 0.033 0.132 4806 Planarity : 0.002 0.028 5596 Dihedral : 6.909 88.134 4204 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.75 % Allowed : 11.68 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.46 (0.13), residues: 3724 helix: 3.78 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -1.74 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 73 TYR 0.026 0.001 TYR T 71 PHE 0.018 0.001 PHE S 26 TRP 0.005 0.001 TRP K 37 HIS 0.002 0.001 HIS P 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (31968) covalent geometry : angle 0.61787 / 0.29 (43354) hydrogen bonds : bond 0.06237 / 4.23 ( 2579) hydrogen bonds : angle 3.69429 / 2.73 ( 7737) Misc. bond : bond 0.18643 / 8.76 ( 31) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 1.353 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 86 MET cc_start: 0.9246 (mtm) cc_final: 0.8874 (mpp) REVERT: C 108 MET cc_start: 0.8772 (ptm) cc_final: 0.8364 (ppp) REVERT: D 86 MET cc_start: 0.9414 (mtt) cc_final: 0.8796 (mpp) REVERT: D 108 MET cc_start: 0.8641 (ptm) cc_final: 0.8411 (ppp) REVERT: E 53 ARG cc_start: 0.8938 (mtt90) cc_final: 0.8532 (mtm-85) REVERT: F 86 MET cc_start: 0.9262 (mtm) cc_final: 0.8858 (mpp) REVERT: F 108 MET cc_start: 0.8759 (ptm) cc_final: 0.8411 (ppp) REVERT: H 52 MET cc_start: 0.7927 (mtm) cc_final: 0.7503 (mtm) REVERT: I 108 MET cc_start: 0.8771 (ptm) cc_final: 0.8349 (ppp) REVERT: J 53 ARG cc_start: 0.8920 (mtt90) cc_final: 0.8591 (mtm-85) REVERT: J 86 MET cc_start: 0.9414 (mtt) cc_final: 0.8790 (mpp) REVERT: J 108 MET cc_start: 0.8791 (ptm) cc_final: 0.8360 (ppp) REVERT: K 52 MET cc_start: 0.8085 (mtm) cc_final: 0.7787 (mtp) REVERT: L 108 MET cc_start: 0.8960 (ptm) cc_final: 0.8414 (ppp) REVERT: M 53 ARG cc_start: 0.8894 (mtt90) cc_final: 0.8547 (mtm-85) REVERT: M 108 MET cc_start: 0.8922 (ptm) cc_final: 0.8532 (ppp) REVERT: N 86 MET cc_start: 0.9419 (mtt) cc_final: 0.8800 (mpp) REVERT: N 108 MET cc_start: 0.8786 (ptm) cc_final: 0.8392 (ppp) REVERT: O 59 THR cc_start: 0.9349 (m) cc_final: 0.9067 (p) REVERT: O 108 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8961 (ppp) REVERT: Q 108 MET cc_start: 0.8663 (ptm) cc_final: 0.8424 (ppp) REVERT: R 86 MET cc_start: 0.9237 (mtm) cc_final: 0.8849 (mpp) REVERT: R 108 MET cc_start: 0.8729 (ptm) cc_final: 0.8331 (ppp) REVERT: S 59 THR cc_start: 0.9440 (m) cc_final: 0.9157 (p) REVERT: S 86 MET cc_start: 0.9237 (mtm) cc_final: 0.8863 (mpp) REVERT: T 86 MET cc_start: 0.9242 (mtm) cc_final: 0.8856 (mpp) REVERT: T 108 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8874 (ppp) REVERT: U 108 MET cc_start: 0.8698 (ptm) cc_final: 0.8293 (ppp) REVERT: W 59 THR cc_start: 0.9443 (m) cc_final: 0.9189 (p) REVERT: W 86 MET cc_start: 0.9264 (mtm) cc_final: 0.8869 (mpp) REVERT: W 108 MET cc_start: 0.8674 (ptm) cc_final: 0.8306 (ppp) REVERT: X 86 MET cc_start: 0.9193 (mtm) cc_final: 0.8758 (mpp) outliers start: 25 outliers final: 21 residues processed: 174 average time/residue: 0.1789 time to fit residues: 54.1167 Evaluate side-chains 184 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain T residue 108 MET Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 247 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 193 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 338 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 225 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 HIS C 130 HIS X 130 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.033064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.026698 restraints weight = 222425.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.027733 restraints weight = 139714.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.028503 restraints weight = 98453.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.029122 restraints weight = 74238.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.029590 restraints weight = 58708.998| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.897 31999 Z= 0.170 Angle : 0.634 14.807 43354 Z= 0.291 Chirality : 0.033 0.342 4806 Planarity : 0.002 0.025 5596 Dihedral : 6.867 87.403 4204 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.88 % Allowed : 11.59 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.40 (0.13), residues: 3724 helix: 3.75 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -1.77 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 73 TYR 0.026 0.001 TYR T 71 PHE 0.019 0.001 PHE S 26 TRP 0.005 0.001 TRP K 37 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (31968) covalent geometry : angle 0.63427 / 0.29 (43354) hydrogen bonds : bond 0.06297 / 4.27 ( 2579) hydrogen bonds : angle 3.72971 / 2.76 ( 7737) Misc. bond : bond 0.18901 / 8.79 ( 31) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3527.48 seconds wall clock time: 62 minutes 51.82 seconds (3771.82 seconds total)