Starting phenix.real_space_refine on Sun Jul 5 21:13:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6f_33639/07_2026/7y6f_33639_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6f_33639/07_2026/7y6f_33639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y6f_33639/07_2026/7y6f_33639_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6f_33639/07_2026/7y6f_33639_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y6f_33639/07_2026/7y6f_33639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6f_33639/07_2026/7y6f_33639.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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): 0.02s 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: 6.61, per 1000 atoms: 0.21 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: 2.70 Conformation dependent library (CDL) restraints added in 1.1 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: 0.69 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: 5.72 Time building geometry restraints manager: 3.50 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 25.910 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 712 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 712 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 MET cc_start: 0.5264 (mtm) cc_final: 0.5010 (mtm) REVERT: L 129 HIS cc_start: 0.7173 (m-70) cc_final: 0.6953 (m90) REVERT: S 146 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8137 (mm-30) outliers start: 0 outliers final: 0 residues processed: 712 average time/residue: 0.6208 time to fit residues: 518.9072 Evaluate side-chains 655 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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: 10.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.0170 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 9.9990 overall best weight: 1.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 112 HIS D 156 GLN ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 156 GLN T 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.152234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.146496 restraints weight = 25364.175| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 0.31 r_work: 0.3367 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.499 31999 Z= 0.194 Angle : 0.554 12.530 43354 Z= 0.267 Chirality : 0.033 0.149 4806 Planarity : 0.003 0.088 5596 Dihedral : 6.940 85.834 4204 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.72 % Allowed : 7.24 % Favored : 91.04 % 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: 4.03 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.59 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 45 TYR 0.044 0.001 TYR T 71 PHE 0.039 0.002 PHE F 49 TRP 0.009 0.001 TRP H 37 HIS 0.004 0.001 HIS Q 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.19 (31968) covalent geometry : angle 0.55390 / 0.27 (43354) hydrogen bonds : bond 0.10582 / 7.18 ( 2579) hydrogen bonds : angle 3.64411 / 2.71 ( 7737) Misc. bond : bond 0.15075 / 8.41 ( 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 712 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 655 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 66 ASP cc_start: 0.7936 (t70) cc_final: 0.7592 (t0) REVERT: L 129 HIS cc_start: 0.7619 (m-70) cc_final: 0.7412 (m90) REVERT: L 155 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7686 (mt-10) REVERT: Q 66 ASP cc_start: 0.8203 (t0) cc_final: 0.7959 (t0) REVERT: S 66 ASP cc_start: 0.8198 (t0) cc_final: 0.7944 (t0) REVERT: S 146 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8434 (mm-30) REVERT: W 66 ASP cc_start: 0.8270 (t0) cc_final: 0.8005 (t0) outliers start: 57 outliers final: 3 residues processed: 662 average time/residue: 0.6503 time to fit residues: 502.0491 Evaluate side-chains 646 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 643 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain W residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 278 optimal weight: 7.9990 chunk 242 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 156 GLN H 54 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.135511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.127952 restraints weight = 23212.115| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 0.39 r_work: 0.3164 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.473 31999 Z= 0.252 Angle : 0.645 24.118 43354 Z= 0.314 Chirality : 0.036 0.206 4806 Planarity : 0.004 0.072 5596 Dihedral : 7.192 84.822 4204 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.11 % Allowed : 8.21 % Favored : 89.68 % 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: 4.33 (0.13), residues: 3724 helix: 3.82 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.02 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 45 TYR 0.043 0.002 TYR T 71 PHE 0.036 0.003 PHE O 120 TRP 0.005 0.002 TRP C 37 HIS 0.005 0.001 HIS Q 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.25 (31968) covalent geometry : angle 0.64537 / 0.31 (43354) hydrogen bonds : bond 0.13960 / 9.47 ( 2579) hydrogen bonds : angle 3.89954 / 2.88 ( 7737) Misc. bond : bond 0.16995 / 9.53 ( 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 832 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 762 time to evaluate : 1.041 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: A 68 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8493 (mt) REVERT: C 4 ASP cc_start: 0.7640 (m-30) cc_final: 0.7384 (t70) REVERT: C 68 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8448 (mt) REVERT: D 4 ASP cc_start: 0.7640 (m-30) cc_final: 0.7391 (t70) REVERT: E 68 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8477 (mt) REVERT: E 81 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: F 4 ASP cc_start: 0.7591 (m-30) cc_final: 0.7329 (t70) REVERT: G 81 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7823 (mt0) REVERT: H 68 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8476 (mt) REVERT: I 81 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7829 (mt0) REVERT: J 68 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8450 (mt) REVERT: L 66 ASP cc_start: 0.8272 (t70) cc_final: 0.7788 (t0) REVERT: M 66 ASP cc_start: 0.8445 (t70) cc_final: 0.8010 (t0) REVERT: N 4 ASP cc_start: 0.7597 (m-30) cc_final: 0.7377 (t70) REVERT: N 66 ASP cc_start: 0.8477 (t0) cc_final: 0.8145 (t0) REVERT: N 68 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8463 (mt) REVERT: O 66 ASP cc_start: 0.8076 (t70) cc_final: 0.7654 (t0) REVERT: O 68 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8523 (mt) REVERT: P 68 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8480 (mt) REVERT: Q 66 ASP cc_start: 0.8517 (t0) cc_final: 0.8138 (t0) REVERT: Q 68 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8462 (mt) REVERT: Q 81 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7898 (mt0) REVERT: R 81 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7555 (mt0) REVERT: S 4 ASP cc_start: 0.7626 (m-30) cc_final: 0.7397 (t70) REVERT: S 66 ASP cc_start: 0.8498 (t0) cc_final: 0.8133 (t0) REVERT: S 68 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8501 (mt) REVERT: S 81 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7675 (mt0) REVERT: U 81 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: V 66 ASP cc_start: 0.8069 (t0) cc_final: 0.7736 (t0) REVERT: W 4 ASP cc_start: 0.7604 (m-30) cc_final: 0.7359 (t70) REVERT: W 66 ASP cc_start: 0.8570 (t0) cc_final: 0.8190 (t0) REVERT: X 4 ASP cc_start: 0.7633 (m-30) cc_final: 0.7397 (t70) REVERT: X 66 ASP cc_start: 0.8493 (t0) cc_final: 0.8057 (t0) outliers start: 70 outliers final: 5 residues processed: 770 average time/residue: 0.6719 time to fit residues: 597.7799 Evaluate side-chains 773 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 751 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 81 GLN Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain W residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 272 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 264 optimal weight: 0.8980 chunk 278 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 336 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.140859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.133444 restraints weight = 23478.691| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 0.39 r_work: 0.3242 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.410 31999 Z= 0.217 Angle : 0.601 24.028 43354 Z= 0.286 Chirality : 0.034 0.197 4806 Planarity : 0.003 0.055 5596 Dihedral : 7.321 86.324 4204 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.08 % Allowed : 10.92 % Favored : 86.99 % 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: 4.50 (0.13), residues: 3724 helix: 3.95 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.03 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 45 TYR 0.031 0.002 TYR T 71 PHE 0.017 0.002 PHE K 120 TRP 0.003 0.001 TRP P 37 HIS 0.004 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.22 (31968) covalent geometry : angle 0.60135 / 0.29 (43354) hydrogen bonds : bond 0.12155 / 8.24 ( 2579) hydrogen bonds : angle 3.72228 / 2.75 ( 7737) Misc. bond : bond 0.15793 / 8.65 ( 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 743 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 674 time to evaluate : 1.239 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: B 4 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7138 (t70) REVERT: B 81 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7761 (mt0) REVERT: D 81 GLN cc_start: 0.8433 (mt0) cc_final: 0.8166 (mt0) REVERT: E 4 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7211 (t70) REVERT: E 81 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: G 81 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: I 4 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7222 (t70) REVERT: I 81 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: J 4 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7132 (t70) REVERT: J 81 GLN cc_start: 0.8435 (mt0) cc_final: 0.8164 (mt0) REVERT: K 81 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7792 (mt0) REVERT: L 66 ASP cc_start: 0.8262 (t70) cc_final: 0.7840 (t0) REVERT: L 68 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8495 (mt) REVERT: M 66 ASP cc_start: 0.8260 (t70) cc_final: 0.7846 (t0) REVERT: N 66 ASP cc_start: 0.8353 (t0) cc_final: 0.8005 (t0) REVERT: N 81 GLN cc_start: 0.8411 (mt0) cc_final: 0.8136 (mt0) REVERT: P 4 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7150 (t70) REVERT: P 81 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7646 (mt0) REVERT: Q 66 ASP cc_start: 0.8392 (t0) cc_final: 0.8037 (t0) REVERT: R 4 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7242 (t70) REVERT: R 68 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8405 (mt) REVERT: R 155 GLU cc_start: 0.7766 (tt0) cc_final: 0.7549 (tt0) REVERT: S 66 ASP cc_start: 0.8389 (t0) cc_final: 0.8033 (t0) REVERT: T 4 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7139 (t70) REVERT: T 68 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8408 (mt) REVERT: U 4 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7061 (t70) REVERT: U 81 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: W 66 ASP cc_start: 0.8436 (t0) cc_final: 0.8043 (t0) outliers start: 69 outliers final: 5 residues processed: 695 average time/residue: 0.6409 time to fit residues: 519.3509 Evaluate side-chains 695 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 672 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain J residue 4 ASP Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain O residue 4 ASP Chi-restraints excluded: chain P residue 4 ASP Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain T residue 4 ASP Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain U residue 4 ASP Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain W residue 44 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 84 optimal weight: 8.9990 chunk 343 optimal weight: 0.9990 chunk 251 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 357 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.132378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.124667 restraints weight = 23149.023| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 0.39 r_work: 0.3125 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.432 31999 Z= 0.266 Angle : 0.672 27.485 43354 Z= 0.323 Chirality : 0.037 0.211 4806 Planarity : 0.004 0.066 5596 Dihedral : 7.470 89.171 4204 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.29 % Allowed : 11.53 % Favored : 86.18 % 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: 4.17 (0.13), residues: 3724 helix: 3.72 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.15 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 45 TYR 0.038 0.002 TYR T 71 PHE 0.016 0.002 PHE L 120 TRP 0.006 0.002 TRP P 37 HIS 0.008 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.26 (31968) covalent geometry : angle 0.67159 / 0.32 (43354) hydrogen bonds : bond 0.14648 / 9.93 ( 2579) hydrogen bonds : angle 3.91433 / 2.89 ( 7737) Misc. bond : bond 0.16694 / 9.13 ( 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 854 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 778 time to evaluate : 1.197 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: B 68 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8469 (mt) REVERT: B 81 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7906 (mt0) REVERT: C 4 ASP cc_start: 0.7648 (m-30) cc_final: 0.7396 (t70) REVERT: C 81 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7932 (mt0) REVERT: D 4 ASP cc_start: 0.7651 (m-30) cc_final: 0.7420 (t70) REVERT: D 68 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8465 (mt) REVERT: D 81 GLN cc_start: 0.8514 (mt0) cc_final: 0.8247 (mt0) REVERT: E 81 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7827 (mt0) REVERT: F 4 ASP cc_start: 0.7599 (m-30) cc_final: 0.7387 (t70) REVERT: G 68 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8486 (mt) REVERT: G 81 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7812 (mt0) REVERT: I 68 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8470 (mt) REVERT: I 81 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7887 (mt0) REVERT: J 81 GLN cc_start: 0.8499 (mt0) cc_final: 0.8213 (mt0) REVERT: K 68 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8473 (mt) REVERT: K 81 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: L 66 ASP cc_start: 0.8397 (t70) cc_final: 0.7887 (t0) REVERT: L 68 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8519 (mt) REVERT: M 1 MET cc_start: 0.6254 (mmp) cc_final: 0.5718 (mmm) REVERT: M 66 ASP cc_start: 0.8490 (t70) cc_final: 0.7995 (t0) REVERT: N 81 GLN cc_start: 0.8510 (mt0) cc_final: 0.8246 (mt0) REVERT: O 66 ASP cc_start: 0.8160 (t70) cc_final: 0.7661 (t0) REVERT: P 81 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: Q 35 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8454 (mtmm) REVERT: Q 81 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: R 81 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7590 (mt0) REVERT: R 155 GLU cc_start: 0.7866 (tt0) cc_final: 0.7642 (tt0) REVERT: S 4 ASP cc_start: 0.7614 (m-30) cc_final: 0.7395 (t70) REVERT: S 66 ASP cc_start: 0.8510 (t0) cc_final: 0.8065 (t0) REVERT: T 68 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8452 (mt) REVERT: U 81 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: V 66 ASP cc_start: 0.8176 (t0) cc_final: 0.7783 (t0) REVERT: V 68 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8513 (mt) REVERT: W 4 ASP cc_start: 0.7625 (m-30) cc_final: 0.7409 (t70) REVERT: W 66 ASP cc_start: 0.8553 (t0) cc_final: 0.8123 (t0) REVERT: X 4 ASP cc_start: 0.7645 (m-30) cc_final: 0.7428 (t70) outliers start: 76 outliers final: 13 residues processed: 789 average time/residue: 0.6799 time to fit residues: 621.4119 Evaluate side-chains 791 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 759 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 13 GLU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 4 ASP Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain Q residue 35 LYS Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain W residue 44 THR 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: 0.7980 chunk 126 optimal weight: 9.9990 chunk 290 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 142 optimal weight: 0.5980 chunk 308 optimal weight: 5.9990 chunk 344 optimal weight: 4.9990 chunk 317 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 238 optimal weight: 0.8980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.142185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.134640 restraints weight = 23470.269| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 0.39 r_work: 0.3260 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.551 31999 Z= 0.209 Angle : 0.596 30.589 43354 Z= 0.281 Chirality : 0.034 0.167 4806 Planarity : 0.003 0.049 5596 Dihedral : 7.493 88.197 4204 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.38 % Allowed : 13.10 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.54 (0.13), residues: 3724 helix: 3.99 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.06 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 100 TYR 0.022 0.001 TYR T 71 PHE 0.014 0.001 PHE N 26 TRP 0.003 0.001 TRP P 37 HIS 0.004 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.21 (31968) covalent geometry : angle 0.59631 / 0.28 (43354) hydrogen bonds : bond 0.11669 / 7.91 ( 2579) hydrogen bonds : angle 3.66992 / 2.71 ( 7737) Misc. bond : bond 0.16903 / 8.80 ( 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 742 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 663 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7138 (t70) REVERT: B 68 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8430 (mt) REVERT: B 81 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7786 (mt0) REVERT: D 81 GLN cc_start: 0.8416 (mt0) cc_final: 0.8135 (mt0) REVERT: E 68 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8484 (mt) REVERT: E 81 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: G 4 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7066 (t70) REVERT: G 68 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8458 (mt) REVERT: G 81 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7735 (mt0) REVERT: H 4 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7147 (t70) REVERT: I 68 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8421 (mt) REVERT: J 4 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7080 (t70) REVERT: J 68 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8463 (mt) REVERT: J 81 GLN cc_start: 0.8404 (mt0) cc_final: 0.8119 (mt0) REVERT: K 4 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7114 (t70) REVERT: K 68 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8418 (mt) REVERT: K 81 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: L 66 ASP cc_start: 0.8213 (t70) cc_final: 0.7781 (t0) REVERT: M 1 MET cc_start: 0.6363 (mmp) cc_final: 0.5802 (mmm) REVERT: M 66 ASP cc_start: 0.8219 (t70) cc_final: 0.7817 (t0) REVERT: N 1 MET cc_start: 0.4522 (OUTLIER) cc_final: 0.4061 (mmm) REVERT: N 4 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7170 (t70) REVERT: N 66 ASP cc_start: 0.8300 (t0) cc_final: 0.7952 (t0) REVERT: N 81 GLN cc_start: 0.8404 (mt0) cc_final: 0.8131 (mt0) REVERT: P 81 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7627 (mt0) REVERT: Q 35 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8429 (mtmm) REVERT: Q 66 ASP cc_start: 0.8331 (t0) cc_final: 0.7971 (t0) REVERT: Q 81 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: R 4 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7306 (t0) REVERT: R 81 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7458 (mt0) REVERT: R 155 GLU cc_start: 0.7842 (tt0) cc_final: 0.7602 (tt0) REVERT: S 66 ASP cc_start: 0.8338 (t0) cc_final: 0.7969 (t0) REVERT: T 4 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7119 (t70) REVERT: T 68 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8438 (mt) REVERT: W 66 ASP cc_start: 0.8399 (t0) cc_final: 0.8019 (t0) REVERT: X 1 MET cc_start: 0.4582 (OUTLIER) cc_final: 0.4252 (mmm) REVERT: X 155 GLU cc_start: 0.7936 (tt0) cc_final: 0.7730 (tt0) outliers start: 79 outliers final: 10 residues processed: 688 average time/residue: 0.6809 time to fit residues: 544.9456 Evaluate side-chains 694 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 659 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain G residue 4 ASP Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 4 ASP Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 4 ASP Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 4 ASP Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 4 ASP Chi-restraints excluded: chain O residue 4 ASP Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain Q residue 35 LYS Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain S residue 155 GLU Chi-restraints excluded: chain T residue 4 ASP Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 323 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.132286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.124510 restraints weight = 23223.493| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 0.39 r_work: 0.3121 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.523 31999 Z= 0.266 Angle : 0.672 23.007 43354 Z= 0.325 Chirality : 0.037 0.164 4806 Planarity : 0.004 0.066 5596 Dihedral : 7.567 86.345 4204 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.90 % Allowed : 13.25 % Favored : 83.86 % 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: 4.17 (0.13), residues: 3724 helix: 3.72 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.16 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 73 TYR 0.032 0.002 TYR T 71 PHE 0.013 0.002 PHE S 26 TRP 0.006 0.002 TRP J 37 HIS 0.008 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.26 (31968) covalent geometry : angle 0.67186 / 0.32 (43354) hydrogen bonds : bond 0.14635 / 9.92 ( 2579) hydrogen bonds : angle 3.91170 / 2.89 ( 7737) Misc. bond : bond 0.16932 / 8.95 ( 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 844 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 748 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8531 (t0) cc_final: 0.8304 (t70) REVERT: B 4 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7445 (t0) REVERT: B 81 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7900 (mt0) REVERT: C 4 ASP cc_start: 0.7632 (m-30) cc_final: 0.7370 (t70) REVERT: C 35 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8272 (mtmm) REVERT: C 81 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7925 (mt0) REVERT: D 4 ASP cc_start: 0.7627 (m-30) cc_final: 0.7404 (t70) REVERT: D 81 GLN cc_start: 0.8531 (mt0) cc_final: 0.8262 (mt0) REVERT: E 81 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7819 (mt0) REVERT: F 4 ASP cc_start: 0.7616 (m-30) cc_final: 0.7387 (t70) REVERT: G 81 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: I 68 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8493 (mt) REVERT: J 81 GLN cc_start: 0.8470 (mt0) cc_final: 0.8186 (mt0) REVERT: K 81 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7835 (mt0) REVERT: L 66 ASP cc_start: 0.8402 (t70) cc_final: 0.7863 (t0) REVERT: M 1 MET cc_start: 0.6418 (mmp) cc_final: 0.5965 (mmm) REVERT: M 66 ASP cc_start: 0.8500 (t70) cc_final: 0.7999 (t0) REVERT: M 68 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8503 (mt) REVERT: N 1 MET cc_start: 0.4609 (OUTLIER) cc_final: 0.4091 (mmm) REVERT: N 81 GLN cc_start: 0.8527 (mt0) cc_final: 0.8258 (mt0) REVERT: O 35 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8333 (mtmm) REVERT: O 66 ASP cc_start: 0.8309 (t70) cc_final: 0.7817 (t0) REVERT: P 81 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7782 (mt0) REVERT: Q 35 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8447 (mtmm) REVERT: Q 81 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7906 (mt0) REVERT: R 81 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: R 155 GLU cc_start: 0.7894 (tt0) cc_final: 0.7687 (tt0) REVERT: S 4 ASP cc_start: 0.7627 (m-30) cc_final: 0.7395 (t70) REVERT: T 68 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8467 (mt) REVERT: V 66 ASP cc_start: 0.8223 (t70) cc_final: 0.7808 (t0) REVERT: W 4 ASP cc_start: 0.7671 (m-30) cc_final: 0.7424 (t70) REVERT: W 66 ASP cc_start: 0.8543 (t0) cc_final: 0.8111 (t0) REVERT: X 4 ASP cc_start: 0.7693 (m-30) cc_final: 0.7435 (t70) REVERT: X 35 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8547 (mtmm) REVERT: X 155 GLU cc_start: 0.7918 (tt0) cc_final: 0.7716 (tt0) outliers start: 96 outliers final: 19 residues processed: 779 average time/residue: 0.7025 time to fit residues: 634.9185 Evaluate side-chains 773 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 737 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 13 GLU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 4 ASP Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain P residue 13 GLU Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain Q residue 13 GLU Chi-restraints excluded: chain Q residue 35 LYS Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 35 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 307 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 173 optimal weight: 6.9990 chunk 149 optimal weight: 0.2980 chunk 245 optimal weight: 2.9990 chunk 330 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 302 optimal weight: 5.9990 chunk 318 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.142670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.135168 restraints weight = 23690.460| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 0.39 r_work: 0.3260 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.512 31999 Z= 0.209 Angle : 0.643 31.532 43354 Z= 0.291 Chirality : 0.034 0.208 4806 Planarity : 0.003 0.042 5596 Dihedral : 7.574 89.265 4204 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.14 % Allowed : 14.21 % Favored : 83.65 % 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: 4.52 (0.13), residues: 3724 helix: 3.97 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.06 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 73 TYR 0.020 0.001 TYR T 71 PHE 0.027 0.001 PHE F 49 TRP 0.003 0.001 TRP P 37 HIS 0.004 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.21 (31968) covalent geometry : angle 0.64267 / 0.29 (43354) hydrogen bonds : bond 0.11572 / 7.85 ( 2579) hydrogen bonds : angle 3.68467 / 2.72 ( 7737) Misc. bond : bond 0.16273 / 8.58 ( 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 731 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 660 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7279 (t0) REVERT: C 35 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8202 (mtmm) REVERT: D 81 GLN cc_start: 0.8414 (mt0) cc_final: 0.8150 (mt0) REVERT: E 4 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7324 (t0) REVERT: E 81 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: H 4 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7307 (t0) REVERT: I 4 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7241 (t0) REVERT: I 68 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8422 (mt) REVERT: J 4 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7084 (t70) REVERT: J 81 GLN cc_start: 0.8423 (mt0) cc_final: 0.8155 (mt0) REVERT: K 81 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: L 66 ASP cc_start: 0.8159 (t70) cc_final: 0.7756 (t0) REVERT: M 1 MET cc_start: 0.6456 (mmp) cc_final: 0.6080 (mmm) REVERT: N 1 MET cc_start: 0.4509 (OUTLIER) cc_final: 0.4063 (mmm) REVERT: N 4 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7162 (t70) REVERT: N 66 ASP cc_start: 0.8250 (t0) cc_final: 0.7897 (t0) REVERT: N 81 GLN cc_start: 0.8404 (mt0) cc_final: 0.8121 (mt0) REVERT: O 35 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8193 (mtmm) REVERT: P 81 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: Q 35 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8333 (mtmm) REVERT: Q 66 ASP cc_start: 0.8293 (t0) cc_final: 0.7929 (t0) REVERT: Q 81 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: R 81 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7396 (mt0) REVERT: R 155 GLU cc_start: 0.7869 (tt0) cc_final: 0.7641 (tt0) REVERT: S 66 ASP cc_start: 0.8280 (t0) cc_final: 0.7901 (t0) REVERT: T 4 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7076 (t70) REVERT: T 68 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8453 (mt) REVERT: W 66 ASP cc_start: 0.8351 (t0) cc_final: 0.7982 (t0) REVERT: X 1 MET cc_start: 0.4518 (OUTLIER) cc_final: 0.4010 (mmm) REVERT: X 155 GLU cc_start: 0.7888 (tt0) cc_final: 0.7687 (tt0) outliers start: 71 outliers final: 9 residues processed: 691 average time/residue: 0.7119 time to fit residues: 573.5227 Evaluate side-chains 685 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 657 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain H residue 4 ASP Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 4 ASP Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 4 ASP Chi-restraints excluded: chain O residue 4 ASP Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain Q residue 35 LYS Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 81 GLN Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain T residue 4 ASP Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 41 optimal weight: 7.9990 chunk 96 optimal weight: 0.0050 chunk 210 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 346 optimal weight: 5.9990 chunk 232 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 354 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 334 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.150032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.142720 restraints weight = 24078.553| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 0.39 r_work: 0.3452 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.609 31999 Z= 0.182 Angle : 0.607 28.053 43354 Z= 0.268 Chirality : 0.032 0.177 4806 Planarity : 0.003 0.041 5596 Dihedral : 7.406 89.569 4204 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 0.83 % Favored : 99.14 % Rotamer: Outliers : 1.12 % Allowed : 16.29 % Favored : 82.59 % 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: 4.77 (0.13), residues: 3724 helix: 4.17 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.12 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 73 TYR 0.015 0.001 TYR T 71 PHE 0.047 0.001 PHE F 49 TRP 0.005 0.001 TRP M 37 HIS 0.003 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.18 (31968) covalent geometry : angle 0.60736 / 0.27 (43354) hydrogen bonds : bond 0.09822 / 6.66 ( 2579) hydrogen bonds : angle 3.52779 / 2.61 ( 7737) Misc. bond : bond 0.16773 / 8.69 ( 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 699 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 662 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8225 (mtmm) REVERT: D 81 GLN cc_start: 0.8272 (mt0) cc_final: 0.8016 (mt0) REVERT: J 81 GLN cc_start: 0.8261 (mt0) cc_final: 0.7987 (mt0) REVERT: K 4 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7136 (t0) REVERT: K 81 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: M 1 MET cc_start: 0.6398 (mmp) cc_final: 0.6015 (mmm) REVERT: N 81 GLN cc_start: 0.8238 (mt0) cc_final: 0.8009 (mt0) REVERT: O 35 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8065 (mtmm) REVERT: P 81 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7467 (mt0) REVERT: T 4 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.7065 (t0) REVERT: T 66 ASP cc_start: 0.8207 (t0) cc_final: 0.7878 (t0) REVERT: W 66 ASP cc_start: 0.7956 (t0) cc_final: 0.7664 (t0) REVERT: X 1 MET cc_start: 0.4325 (OUTLIER) cc_final: 0.3963 (mmm) outliers start: 37 outliers final: 1 residues processed: 687 average time/residue: 0.7426 time to fit residues: 591.9843 Evaluate side-chains 649 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 641 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain K residue 4 ASP Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain T residue 4 ASP Chi-restraints excluded: chain X residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 56 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 326 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 202 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.141819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.134357 restraints weight = 23651.669| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 0.39 r_work: 0.3261 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.511 31999 Z= 0.214 Angle : 0.673 35.035 43354 Z= 0.298 Chirality : 0.034 0.186 4806 Planarity : 0.003 0.048 5596 Dihedral : 7.305 87.317 4204 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.60 % Allowed : 16.66 % Favored : 82.74 % 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: 4.58 (0.13), residues: 3724 helix: 4.02 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.06 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 73 TYR 0.020 0.001 TYR T 71 PHE 0.033 0.001 PHE F 49 TRP 0.003 0.001 TRP P 37 HIS 0.004 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.21 (31968) covalent geometry : angle 0.67340 / 0.30 (43354) hydrogen bonds : bond 0.11739 / 7.96 ( 2579) hydrogen bonds : angle 3.69426 / 2.73 ( 7737) Misc. bond : bond 0.16964 / 9.89 ( 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 688 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 668 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8232 (mtmm) REVERT: D 81 GLN cc_start: 0.8388 (mt0) cc_final: 0.8117 (mt0) REVERT: E 73 ARG cc_start: 0.8855 (mtm180) cc_final: 0.8651 (ttp-170) REVERT: F 52 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7009 (mpt) REVERT: J 81 GLN cc_start: 0.8350 (mt0) cc_final: 0.8051 (mt0) REVERT: K 81 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: L 1 MET cc_start: 0.6443 (mmm) cc_final: 0.5920 (mmp) REVERT: L 66 ASP cc_start: 0.8235 (t70) cc_final: 0.7874 (t0) REVERT: M 1 MET cc_start: 0.6291 (mmp) cc_final: 0.5930 (mmm) REVERT: N 81 GLN cc_start: 0.8369 (mt0) cc_final: 0.8107 (mt0) REVERT: O 35 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8198 (mtmm) REVERT: P 81 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7660 (mt0) REVERT: T 66 ASP cc_start: 0.8457 (t0) cc_final: 0.8079 (t0) REVERT: X 1 MET cc_start: 0.4531 (OUTLIER) cc_final: 0.3979 (mmm) outliers start: 20 outliers final: 3 residues processed: 674 average time/residue: 0.7299 time to fit residues: 571.5937 Evaluate side-chains 674 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 665 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain X residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 247 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 338 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.133905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.126199 restraints weight = 23406.705| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 0.39 r_work: 0.3136 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.543 31999 Z= 0.260 Angle : 0.800 41.370 43354 Z= 0.348 Chirality : 0.038 0.345 4806 Planarity : 0.004 0.064 5596 Dihedral : 7.502 85.037 4204 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.72 % Allowed : 16.51 % Favored : 82.77 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.24 (0.13), residues: 3724 helix: 3.77 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.15 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG T 73 TYR 0.028 0.002 TYR T 71 PHE 0.032 0.002 PHE F 49 TRP 0.006 0.002 TRP P 37 HIS 0.008 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.26 (31968) covalent geometry : angle 0.80042 / 0.35 (43354) hydrogen bonds : bond 0.14145 / 9.59 ( 2579) hydrogen bonds : angle 3.88409 / 2.87 ( 7737) Misc. bond : bond 0.17573 / 10.27 ( 31) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11320.52 seconds wall clock time: 192 minutes 52.59 seconds (11572.59 seconds total)