Starting phenix.real_space_refine on Fri Jul 3 21:21:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oo0_13003/07_2026/7oo0_13003.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oo0_13003/07_2026/7oo0_13003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oo0_13003/07_2026/7oo0_13003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oo0_13003/07_2026/7oo0_13003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oo0_13003/07_2026/7oo0_13003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oo0_13003/07_2026/7oo0_13003.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7oo0_13003/07_2026/7oo0_13003.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oo0_13003/07_2026/7oo0_13003.cif" } resolution = 3.1 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= 0.013 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 P 7 5.49 5 S 42 5.16 5 C 10402 2.51 5 N 2450 2.21 5 O 3115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 16016 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "B" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "C" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "D" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "E" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "F" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "G" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1996 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain: "A" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 292 Unusual residues: {'LMT': 7, 'PEE': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 257 Unusual residues: {'LMT': 6, 'PEE': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 327 Unusual residues: {'LMT': 8, 'PEE': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 3.73, per 1000 atoms: 0.23 Number of scatterers: 16016 At special positions: 0 Unit cell: (97.842, 98.9055, 137.192, 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) S 42 16.00 P 7 15.00 O 3115 8.00 N 2450 7.00 C 10402 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=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 580.7 milliseconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 15 sheets defined 56.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 20 through 59 removed outlier: 4.406A pdb=" N LEU A 24 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 89 Processing helix chain 'A' and resid 92 through 128 removed outlier: 5.421A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.539A pdb=" N GLY A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'B' and resid 20 through 59 removed outlier: 4.405A pdb=" N LEU B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 89 Processing helix chain 'B' and resid 92 through 128 removed outlier: 5.421A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 removed outlier: 3.540A pdb=" N GLY B 173 " --> pdb=" O LYS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'C' and resid 20 through 59 removed outlier: 4.405A pdb=" N LEU C 24 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 89 Processing helix chain 'C' and resid 92 through 128 removed outlier: 5.420A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 removed outlier: 3.540A pdb=" N GLY C 173 " --> pdb=" O LYS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'D' and resid 20 through 59 removed outlier: 4.405A pdb=" N LEU D 24 " --> pdb=" O ASN D 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 89 Processing helix chain 'D' and resid 92 through 128 removed outlier: 5.421A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 removed outlier: 3.540A pdb=" N GLY D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 245 through 265 Processing helix chain 'E' and resid 20 through 59 removed outlier: 4.406A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 89 Processing helix chain 'E' and resid 92 through 128 removed outlier: 5.421A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 removed outlier: 3.540A pdb=" N GLY E 173 " --> pdb=" O LYS E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 245 through 265 Processing helix chain 'F' and resid 20 through 59 removed outlier: 4.406A pdb=" N LEU F 24 " --> pdb=" O ASN F 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 89 Processing helix chain 'F' and resid 92 through 128 removed outlier: 5.421A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 removed outlier: 3.539A pdb=" N GLY F 173 " --> pdb=" O LYS F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 245 through 265 Processing helix chain 'G' and resid 20 through 59 removed outlier: 4.406A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 89 Processing helix chain 'G' and resid 92 through 128 removed outlier: 5.421A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 173 removed outlier: 3.539A pdb=" N GLY G 173 " --> pdb=" O LYS G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 211 Processing helix chain 'G' and resid 245 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 166 removed outlier: 7.074A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 176 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.054A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TRP A 240 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET A 221 " --> pdb=" O TRP A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 279 removed outlier: 7.289A pdb=" N VAL B 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE B 277 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS A 278 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ARG B 279 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C 275 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASN B 276 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE C 277 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS B 278 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ARG C 279 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL D 275 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASN C 276 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE D 277 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS C 278 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ARG D 279 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL E 275 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN D 276 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE E 277 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS D 278 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ARG E 279 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL F 275 " --> pdb=" O ASP E 274 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASN E 276 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE F 277 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS E 278 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ARG F 279 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL G 275 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN F 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE G 277 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS F 278 " --> pdb=" O PHE G 277 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ARG G 279 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 275 " --> pdb=" O LYS G 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 162 through 166 removed outlier: 7.074A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 176 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.054A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TRP B 240 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET B 221 " --> pdb=" O TRP B 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 162 through 166 removed outlier: 7.074A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 176 " --> pdb=" O ASP C 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.053A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N TRP C 240 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N MET C 221 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 162 through 166 removed outlier: 7.074A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 176 " --> pdb=" O ASP D 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.053A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TRP D 240 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET D 221 " --> pdb=" O TRP D 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 162 through 166 removed outlier: 7.075A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 176 " --> pdb=" O ASP E 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.053A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N TRP E 240 " --> pdb=" O MET E 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET E 221 " --> pdb=" O TRP E 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 162 through 166 removed outlier: 7.075A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE F 176 " --> pdb=" O ASP F 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.053A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TRP F 240 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET F 221 " --> pdb=" O TRP F 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 162 through 166 removed outlier: 7.075A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE G 176 " --> pdb=" O ASP G 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.053A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N TRP G 240 " --> pdb=" O MET G 221 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET G 221 " --> pdb=" O TRP G 240 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2961 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: 2.24 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2312 1.32 - 1.44: 4180 1.44 - 1.56: 9643 1.56 - 1.68: 14 1.68 - 1.80: 84 Bond restraints: 16233 Sorted by residual: bond pdb=" C4 PEE D 302 " pdb=" O4P PEE D 302 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.15e+00 bond pdb=" C4 PEE E 302 " pdb=" O4P PEE E 302 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C4 PEE F 302 " pdb=" O4P PEE F 302 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C4 PEE B 302 " pdb=" O4P PEE B 302 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 3.98e+00 bond pdb=" C4 PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 3.94e+00 ... (remaining 16228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 21120 2.27 - 4.54: 692 4.54 - 6.82: 28 6.82 - 9.09: 0 9.09 - 11.36: 7 Bond angle restraints: 21847 Sorted by residual: angle pdb=" O3P PEE E 302 " pdb=" P PEE E 302 " pdb=" O4P PEE E 302 " ideal model delta sigma weight residual 92.91 104.27 -11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3P PEE D 302 " pdb=" P PEE D 302 " pdb=" O4P PEE D 302 " ideal model delta sigma weight residual 92.91 104.26 -11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3P PEE A 301 " pdb=" P PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 92.91 104.25 -11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3P PEE F 302 " pdb=" P PEE F 302 " pdb=" O4P PEE F 302 " ideal model delta sigma weight residual 92.91 104.24 -11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3P PEE C 302 " pdb=" P PEE C 302 " pdb=" O4P PEE C 302 " ideal model delta sigma weight residual 92.91 104.24 -11.33 3.00e+00 1.11e-01 1.43e+01 ... (remaining 21842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.91: 9037 27.91 - 55.81: 217 55.81 - 83.72: 7 83.72 - 111.62: 7 111.62 - 139.53: 7 Dihedral angle restraints: 9275 sinusoidal: 4018 harmonic: 5257 Sorted by residual: dihedral pdb=" C23 PEE B 302 " pdb=" C24 PEE B 302 " pdb=" C25 PEE B 302 " pdb=" C26 PEE B 302 " ideal model delta sinusoidal sigma weight residual -179.89 -40.36 -139.53 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" C23 PEE D 302 " pdb=" C24 PEE D 302 " pdb=" C25 PEE D 302 " pdb=" C26 PEE D 302 " ideal model delta sinusoidal sigma weight residual -179.89 -40.42 -139.47 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" C23 PEE C 302 " pdb=" C24 PEE C 302 " pdb=" C25 PEE C 302 " pdb=" C26 PEE C 302 " ideal model delta sinusoidal sigma weight residual -179.89 -40.42 -139.47 1 3.00e+01 1.11e-03 1.88e+01 ... (remaining 9272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1715 0.038 - 0.075: 813 0.075 - 0.113: 254 0.113 - 0.151: 53 0.151 - 0.188: 21 Chirality restraints: 2856 Sorted by residual: chirality pdb=" C2 PEE G 404 " pdb=" C1 PEE G 404 " pdb=" C3 PEE G 404 " pdb=" O2 PEE G 404 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" C2 PEE D 302 " pdb=" C1 PEE D 302 " pdb=" C3 PEE D 302 " pdb=" O2 PEE D 302 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" C2 PEE F 302 " pdb=" C1 PEE F 302 " pdb=" C3 PEE F 302 " pdb=" O2 PEE F 302 " both_signs ideal model delta sigma weight residual False -2.33 -2.51 0.19 2.00e-01 2.50e+01 8.73e-01 ... (remaining 2853 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 83 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C ILE F 83 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE F 83 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA F 84 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 83 " 0.009 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C ILE C 83 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE C 83 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA C 84 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 83 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C ILE A 83 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 83 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA A 84 " -0.010 2.00e-02 2.50e+03 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 311 2.68 - 3.24: 15368 3.24 - 3.79: 24084 3.79 - 4.35: 32887 4.35 - 4.90: 56743 Nonbonded interactions: 129393 Sorted by model distance: nonbonded pdb=" O3' LMT B 308 " pdb=" O2B LMT C 308 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR F 27 " pdb=" O2B LMT F 305 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR C 27 " pdb=" O2B LMT C 305 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR D 27 " pdb=" O2B LMT D 305 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR E 27 " pdb=" O2B LMT E 305 " model vdw 2.241 3.040 ... (remaining 129388 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 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'B' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'C' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'D' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'E' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'F' and (resid 19 through 280 or resid 303 or resid 305 through 307)) selection = (chain 'G' and (resid 19 through 280 or resid 403 or resid 405 through 407)) } 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.150 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 0.041 16233 Z= 0.384 Angle : 0.864 11.360 21847 Z= 0.397 Chirality : 0.049 0.188 2856 Planarity : 0.005 0.030 2450 Dihedral : 12.748 139.528 5887 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.16), residues: 1820 helix: -1.29 (0.10), residues: 1036 sheet: -1.80 (0.25), residues: 273 loop : 0.04 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 219 TYR 0.010 0.002 TYR E 75 PHE 0.012 0.002 PHE B 277 TRP 0.004 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00879 / 0.38 (16233) covalent geometry : angle 0.86427 / 0.40 (21847) hydrogen bonds : bond 0.12342 / 8.22 ( 994) hydrogen bonds : angle 5.85397 / 4.22 ( 2961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.324 Fit side-chains REVERT: A 128 ARG cc_start: 0.7767 (mmt180) cc_final: 0.7423 (mmt180) REVERT: A 227 GLU cc_start: 0.8357 (tt0) cc_final: 0.7968 (tt0) REVERT: B 128 ARG cc_start: 0.7636 (mmt180) cc_final: 0.7155 (mmt180) REVERT: C 128 ARG cc_start: 0.7845 (mmt180) cc_final: 0.7520 (mmt180) REVERT: C 255 GLU cc_start: 0.7821 (tt0) cc_final: 0.7561 (tt0) REVERT: D 128 ARG cc_start: 0.7634 (mmt180) cc_final: 0.7315 (mmt180) REVERT: D 202 LYS cc_start: 0.7942 (mtpt) cc_final: 0.7667 (mtpt) REVERT: D 227 GLU cc_start: 0.8124 (tt0) cc_final: 0.7904 (tt0) REVERT: E 126 MET cc_start: 0.8160 (mtp) cc_final: 0.7933 (ttm) REVERT: E 128 ARG cc_start: 0.7848 (mmt180) cc_final: 0.7513 (mmt180) REVERT: E 187 GLU cc_start: 0.7938 (tt0) cc_final: 0.7664 (tt0) REVERT: E 221 MET cc_start: 0.8755 (mtm) cc_final: 0.8313 (mtm) REVERT: F 128 ARG cc_start: 0.7686 (mmt180) cc_final: 0.7263 (mmt180) REVERT: G 128 ARG cc_start: 0.7786 (mmt180) cc_final: 0.7420 (mmt180) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1498 time to fit residues: 29.1034 Evaluate side-chains 125 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.140024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.113053 restraints weight = 17011.960| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.68 r_work: 0.3022 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 16233 Z= 0.112 Angle : 0.502 4.622 21847 Z= 0.244 Chirality : 0.040 0.123 2856 Planarity : 0.003 0.022 2450 Dihedral : 12.619 130.831 2758 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.54 % Allowed : 5.05 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.18), residues: 1820 helix: 1.86 (0.14), residues: 1036 sheet: -1.24 (0.26), residues: 308 loop : -0.22 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 219 TYR 0.008 0.001 TYR C 27 PHE 0.008 0.001 PHE D 235 TRP 0.002 0.001 TRP A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (16233) covalent geometry : angle 0.50208 / 0.24 (21847) hydrogen bonds : bond 0.03980 / 2.76 ( 994) hydrogen bonds : angle 4.00385 / 2.89 ( 2961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.536 Fit side-chains REVERT: A 128 ARG cc_start: 0.7882 (mmt180) cc_final: 0.7451 (mmt180) REVERT: B 128 ARG cc_start: 0.7778 (mmt180) cc_final: 0.7278 (mmt180) REVERT: C 128 ARG cc_start: 0.7985 (mmt180) cc_final: 0.7673 (mmt180) REVERT: C 255 GLU cc_start: 0.8067 (tt0) cc_final: 0.7838 (tt0) REVERT: D 128 ARG cc_start: 0.7858 (mmt180) cc_final: 0.7490 (mmt180) REVERT: E 221 MET cc_start: 0.8787 (mtm) cc_final: 0.8431 (mtm) REVERT: F 128 ARG cc_start: 0.7589 (mmt180) cc_final: 0.7116 (mmt180) REVERT: F 137 ASP cc_start: 0.8281 (t0) cc_final: 0.8057 (t0) REVERT: G 128 ARG cc_start: 0.7921 (mmt180) cc_final: 0.7717 (mmt180) REVERT: G 187 GLU cc_start: 0.8613 (tt0) cc_final: 0.8394 (tt0) outliers start: 8 outliers final: 5 residues processed: 147 average time/residue: 0.1365 time to fit residues: 29.7289 Evaluate side-chains 133 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN F 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.138897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.111501 restraints weight = 17369.143| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.71 r_work: 0.3003 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16233 Z= 0.133 Angle : 0.477 4.850 21847 Z= 0.234 Chirality : 0.039 0.133 2856 Planarity : 0.002 0.036 2450 Dihedral : 12.238 121.987 2758 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.74 % Allowed : 6.60 % Favored : 92.65 % 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: 1.71 (0.18), residues: 1820 helix: 2.55 (0.14), residues: 1036 sheet: -0.90 (0.27), residues: 308 loop : -0.63 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 59 TYR 0.005 0.001 TYR F 75 PHE 0.008 0.001 PHE G 277 TRP 0.002 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (16233) covalent geometry : angle 0.47658 / 0.23 (21847) hydrogen bonds : bond 0.03948 / 2.74 ( 994) hydrogen bonds : angle 3.86262 / 2.79 ( 2961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.548 Fit side-chains REVERT: A 128 ARG cc_start: 0.7852 (mmt180) cc_final: 0.7398 (mmt180) REVERT: A 227 GLU cc_start: 0.8632 (tt0) cc_final: 0.8355 (tt0) REVERT: B 128 ARG cc_start: 0.7772 (mmt180) cc_final: 0.7245 (mmt180) REVERT: C 128 ARG cc_start: 0.7967 (mmt180) cc_final: 0.7649 (mmt180) REVERT: C 255 GLU cc_start: 0.8103 (tt0) cc_final: 0.7895 (tt0) REVERT: D 128 ARG cc_start: 0.7792 (mmt180) cc_final: 0.7455 (mmt180) REVERT: E 128 ARG cc_start: 0.8000 (mmt180) cc_final: 0.7497 (mmt180) REVERT: E 221 MET cc_start: 0.8828 (mtm) cc_final: 0.8467 (mtm) REVERT: F 128 ARG cc_start: 0.7629 (mmt180) cc_final: 0.7174 (mmt180) REVERT: F 137 ASP cc_start: 0.8308 (t0) cc_final: 0.8093 (t0) REVERT: G 128 ARG cc_start: 0.7864 (mmt180) cc_final: 0.7651 (mmt180) REVERT: G 187 GLU cc_start: 0.8625 (tt0) cc_final: 0.8410 (tt0) outliers start: 11 outliers final: 8 residues processed: 152 average time/residue: 0.1440 time to fit residues: 32.1663 Evaluate side-chains 146 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.138271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.111027 restraints weight = 17182.342| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.67 r_work: 0.2995 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 16233 Z= 0.153 Angle : 0.499 4.782 21847 Z= 0.242 Chirality : 0.040 0.129 2856 Planarity : 0.003 0.046 2450 Dihedral : 12.205 115.398 2758 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.15 % Allowed : 7.35 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.19), residues: 1820 helix: 2.74 (0.15), residues: 1036 sheet: -0.67 (0.27), residues: 308 loop : -0.93 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 59 TYR 0.006 0.001 TYR F 75 PHE 0.009 0.001 PHE G 277 TRP 0.003 0.001 TRP A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (16233) covalent geometry : angle 0.49860 / 0.24 (21847) hydrogen bonds : bond 0.03937 / 2.73 ( 994) hydrogen bonds : angle 3.82245 / 2.77 ( 2961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.541 Fit side-chains REVERT: A 128 ARG cc_start: 0.7902 (mmt180) cc_final: 0.7470 (mmt180) REVERT: A 227 GLU cc_start: 0.8579 (tt0) cc_final: 0.8292 (tt0) REVERT: B 128 ARG cc_start: 0.7814 (mmt180) cc_final: 0.7318 (mmt180) REVERT: C 128 ARG cc_start: 0.8006 (mmt180) cc_final: 0.7710 (mmt180) REVERT: D 128 ARG cc_start: 0.7761 (mmt180) cc_final: 0.7450 (mmt180) REVERT: E 128 ARG cc_start: 0.7983 (mmt180) cc_final: 0.7462 (mmt180) REVERT: E 221 MET cc_start: 0.8847 (mtm) cc_final: 0.8517 (mtm) REVERT: F 128 ARG cc_start: 0.7654 (mmt180) cc_final: 0.7199 (mmt180) REVERT: G 128 ARG cc_start: 0.7888 (mmt180) cc_final: 0.7678 (mmt180) REVERT: G 187 GLU cc_start: 0.8650 (tt0) cc_final: 0.8444 (tt0) outliers start: 17 outliers final: 10 residues processed: 156 average time/residue: 0.1414 time to fit residues: 32.4950 Evaluate side-chains 151 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 8 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.139747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.112669 restraints weight = 17058.835| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.67 r_work: 0.3017 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 16233 Z= 0.111 Angle : 0.461 4.648 21847 Z= 0.224 Chirality : 0.039 0.127 2856 Planarity : 0.003 0.051 2450 Dihedral : 11.876 104.940 2758 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.67 % Allowed : 8.29 % 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: 2.13 (0.19), residues: 1820 helix: 3.02 (0.15), residues: 1036 sheet: -0.47 (0.27), residues: 308 loop : -1.00 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 59 TYR 0.004 0.001 TYR F 75 PHE 0.008 0.001 PHE G 277 TRP 0.002 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (16233) covalent geometry : angle 0.46074 / 0.22 (21847) hydrogen bonds : bond 0.03610 / 2.51 ( 994) hydrogen bonds : angle 3.68074 / 2.66 ( 2961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.538 Fit side-chains REVERT: A 128 ARG cc_start: 0.7853 (mmt180) cc_final: 0.7456 (mmt180) REVERT: A 227 GLU cc_start: 0.8536 (tt0) cc_final: 0.8250 (tt0) REVERT: B 128 ARG cc_start: 0.7822 (mmt180) cc_final: 0.7319 (mmt180) REVERT: C 128 ARG cc_start: 0.8005 (mmt180) cc_final: 0.7700 (mmt180) REVERT: D 128 ARG cc_start: 0.7764 (mmt180) cc_final: 0.7428 (mmt180) REVERT: E 128 ARG cc_start: 0.8000 (mmt180) cc_final: 0.7498 (mmt180) REVERT: E 221 MET cc_start: 0.8787 (mtm) cc_final: 0.8448 (mtm) REVERT: F 128 ARG cc_start: 0.7676 (mmt180) cc_final: 0.7235 (mmt180) REVERT: G 128 ARG cc_start: 0.7890 (mmt180) cc_final: 0.7682 (mmt180) REVERT: G 187 GLU cc_start: 0.8665 (tt0) cc_final: 0.8456 (tt0) outliers start: 10 outliers final: 7 residues processed: 155 average time/residue: 0.1322 time to fit residues: 30.4772 Evaluate side-chains 152 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 149 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 146 optimal weight: 0.0470 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.138935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.111843 restraints weight = 17149.550| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.67 r_work: 0.3005 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16233 Z= 0.131 Angle : 0.476 4.684 21847 Z= 0.231 Chirality : 0.039 0.129 2856 Planarity : 0.003 0.055 2450 Dihedral : 11.669 95.471 2758 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.62 % Allowed : 7.82 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.19), residues: 1820 helix: 3.02 (0.15), residues: 1036 sheet: -0.39 (0.26), residues: 308 loop : -1.08 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 59 TYR 0.005 0.001 TYR C 75 PHE 0.009 0.001 PHE D 188 TRP 0.003 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (16233) covalent geometry : angle 0.47567 / 0.23 (21847) hydrogen bonds : bond 0.03696 / 2.57 ( 994) hydrogen bonds : angle 3.70699 / 2.68 ( 2961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.557 Fit side-chains REVERT: A 24 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6888 (mp) REVERT: A 128 ARG cc_start: 0.7813 (mmt180) cc_final: 0.7416 (mmt180) REVERT: A 137 ASP cc_start: 0.8313 (t70) cc_final: 0.8033 (t0) REVERT: A 227 GLU cc_start: 0.8523 (tt0) cc_final: 0.8235 (tt0) REVERT: B 128 ARG cc_start: 0.7798 (mmt180) cc_final: 0.7304 (mmt180) REVERT: C 24 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.7017 (mp) REVERT: C 128 ARG cc_start: 0.7900 (mmt180) cc_final: 0.7579 (mmt180) REVERT: D 24 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6734 (mp) REVERT: D 128 ARG cc_start: 0.7651 (mmt180) cc_final: 0.7313 (mmt180) REVERT: E 128 ARG cc_start: 0.7903 (mmt180) cc_final: 0.7389 (mmt180) REVERT: E 221 MET cc_start: 0.8823 (mtm) cc_final: 0.8506 (mtm) REVERT: F 128 ARG cc_start: 0.7658 (mmt180) cc_final: 0.7217 (mmt180) REVERT: G 187 GLU cc_start: 0.8710 (tt0) cc_final: 0.8488 (tt0) outliers start: 24 outliers final: 11 residues processed: 174 average time/residue: 0.1263 time to fit residues: 32.6738 Evaluate side-chains 161 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 106 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.139769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.112647 restraints weight = 17030.224| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.68 r_work: 0.3016 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 16233 Z= 0.115 Angle : 0.464 4.681 21847 Z= 0.225 Chirality : 0.039 0.129 2856 Planarity : 0.003 0.051 2450 Dihedral : 11.292 84.539 2758 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.01 % Allowed : 8.63 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.19), residues: 1820 helix: 3.14 (0.15), residues: 1036 sheet: -0.30 (0.26), residues: 308 loop : -1.08 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 59 TYR 0.004 0.001 TYR C 75 PHE 0.009 0.001 PHE D 188 TRP 0.002 0.001 TRP A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (16233) covalent geometry : angle 0.46402 / 0.22 (21847) hydrogen bonds : bond 0.03554 / 2.47 ( 994) hydrogen bonds : angle 3.64126 / 2.64 ( 2961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.446 Fit side-chains REVERT: A 128 ARG cc_start: 0.7842 (mmt180) cc_final: 0.7427 (mmt180) REVERT: A 137 ASP cc_start: 0.8301 (t70) cc_final: 0.8032 (t0) REVERT: A 227 GLU cc_start: 0.8573 (tt0) cc_final: 0.8298 (tt0) REVERT: B 128 ARG cc_start: 0.7840 (mmt180) cc_final: 0.7350 (mmt180) REVERT: C 24 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.7000 (mp) REVERT: C 128 ARG cc_start: 0.7883 (mmt180) cc_final: 0.7572 (mmt180) REVERT: D 24 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6741 (mp) REVERT: D 128 ARG cc_start: 0.7678 (mmt180) cc_final: 0.7353 (mmt180) REVERT: E 128 ARG cc_start: 0.7934 (mmt180) cc_final: 0.7427 (mmt180) REVERT: E 221 MET cc_start: 0.8768 (mtm) cc_final: 0.8432 (mtm) REVERT: F 128 ARG cc_start: 0.7671 (mmt180) cc_final: 0.7243 (mmt180) REVERT: G 187 GLU cc_start: 0.8759 (tt0) cc_final: 0.8539 (tt0) outliers start: 15 outliers final: 10 residues processed: 166 average time/residue: 0.1310 time to fit residues: 32.0866 Evaluate side-chains 161 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 106 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.136684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.109092 restraints weight = 17396.930| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.71 r_work: 0.2973 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16233 Z= 0.199 Angle : 0.535 4.875 21847 Z= 0.258 Chirality : 0.041 0.134 2856 Planarity : 0.003 0.058 2450 Dihedral : 11.663 82.542 2758 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.48 % Allowed : 8.42 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.19), residues: 1820 helix: 2.83 (0.15), residues: 1036 sheet: -0.21 (0.26), residues: 308 loop : -1.19 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 59 TYR 0.008 0.002 TYR B 250 PHE 0.012 0.002 PHE E 188 TRP 0.005 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.20 (16233) covalent geometry : angle 0.53480 / 0.26 (21847) hydrogen bonds : bond 0.04089 / 2.83 ( 994) hydrogen bonds : angle 3.85805 / 2.79 ( 2961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.534 Fit side-chains REVERT: A 24 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7019 (mp) REVERT: A 128 ARG cc_start: 0.7936 (mmt180) cc_final: 0.7531 (mmt180) REVERT: A 137 ASP cc_start: 0.8240 (t70) cc_final: 0.7981 (t0) REVERT: A 227 GLU cc_start: 0.8568 (tt0) cc_final: 0.8291 (tt0) REVERT: B 128 ARG cc_start: 0.7823 (mmt180) cc_final: 0.7378 (mmt180) REVERT: C 24 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7038 (mp) REVERT: C 128 ARG cc_start: 0.7920 (mmt180) cc_final: 0.7626 (mmt180) REVERT: C 255 GLU cc_start: 0.8220 (tt0) cc_final: 0.7993 (tt0) REVERT: D 24 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6735 (mp) REVERT: D 128 ARG cc_start: 0.7758 (mmt180) cc_final: 0.7472 (mmt180) REVERT: E 128 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7365 (mmt180) REVERT: E 221 MET cc_start: 0.8859 (mtm) cc_final: 0.8533 (mtm) REVERT: F 128 ARG cc_start: 0.7661 (mmt180) cc_final: 0.7282 (mmt180) REVERT: G 187 GLU cc_start: 0.8777 (tt0) cc_final: 0.8569 (tt0) outliers start: 22 outliers final: 15 residues processed: 170 average time/residue: 0.1371 time to fit residues: 34.4835 Evaluate side-chains 166 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 125 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 143 optimal weight: 0.6980 chunk 118 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.140035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.112913 restraints weight = 17080.345| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.68 r_work: 0.3017 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 16233 Z= 0.100 Angle : 0.463 5.153 21847 Z= 0.226 Chirality : 0.039 0.175 2856 Planarity : 0.003 0.052 2450 Dihedral : 11.240 75.933 2758 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.01 % Allowed : 8.96 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.19), residues: 1820 helix: 3.20 (0.15), residues: 1036 sheet: -0.16 (0.26), residues: 308 loop : -1.16 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 59 TYR 0.005 0.001 TYR A 135 PHE 0.009 0.001 PHE F 188 TRP 0.002 0.001 TRP A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (16233) covalent geometry : angle 0.46279 / 0.23 (21847) hydrogen bonds : bond 0.03494 / 2.43 ( 994) hydrogen bonds : angle 3.63042 / 2.63 ( 2961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.558 Fit side-chains REVERT: A 24 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6922 (mp) REVERT: A 128 ARG cc_start: 0.7839 (mmt180) cc_final: 0.7446 (mmt180) REVERT: A 137 ASP cc_start: 0.8300 (t70) cc_final: 0.8023 (t0) REVERT: A 227 GLU cc_start: 0.8555 (tt0) cc_final: 0.8281 (tt0) REVERT: B 128 ARG cc_start: 0.7830 (mmt180) cc_final: 0.7348 (mmt180) REVERT: C 24 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6917 (mp) REVERT: C 128 ARG cc_start: 0.7883 (mmt180) cc_final: 0.7586 (mmt180) REVERT: D 128 ARG cc_start: 0.7648 (mmt180) cc_final: 0.7329 (mmt180) REVERT: E 128 ARG cc_start: 0.7875 (mmt180) cc_final: 0.7360 (mmt180) REVERT: E 221 MET cc_start: 0.8751 (mtm) cc_final: 0.8501 (mtm) REVERT: F 128 ARG cc_start: 0.7605 (mmt180) cc_final: 0.7195 (mmt180) REVERT: F 149 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7784 (mt0) REVERT: G 187 GLU cc_start: 0.8762 (tt0) cc_final: 0.8551 (tt0) outliers start: 15 outliers final: 9 residues processed: 164 average time/residue: 0.1412 time to fit residues: 34.0619 Evaluate side-chains 159 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 70 optimal weight: 0.8980 chunk 155 optimal weight: 0.0470 chunk 77 optimal weight: 0.0970 chunk 89 optimal weight: 0.0370 chunk 56 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 112 GLN D 112 GLN E 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.143205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.116216 restraints weight = 16845.707| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.67 r_work: 0.3064 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16233 Z= 0.084 Angle : 0.432 4.507 21847 Z= 0.211 Chirality : 0.038 0.124 2856 Planarity : 0.003 0.051 2450 Dihedral : 10.373 59.327 2758 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.61 % Allowed : 9.16 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.19), residues: 1820 helix: 3.52 (0.14), residues: 1036 sheet: -0.05 (0.26), residues: 308 loop : -1.13 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 59 TYR 0.003 0.001 TYR A 135 PHE 0.007 0.001 PHE F 188 TRP 0.002 0.000 TRP A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00170 / 0.08 (16233) covalent geometry : angle 0.43158 / 0.21 (21847) hydrogen bonds : bond 0.03143 / 2.20 ( 994) hydrogen bonds : angle 3.43926 / 2.49 ( 2961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.560 Fit side-chains REVERT: A 128 ARG cc_start: 0.7929 (mmt180) cc_final: 0.7512 (mmt180) REVERT: A 137 ASP cc_start: 0.8294 (t70) cc_final: 0.8030 (t0) REVERT: A 227 GLU cc_start: 0.8536 (tt0) cc_final: 0.8266 (tt0) REVERT: B 128 ARG cc_start: 0.7786 (mmt180) cc_final: 0.7316 (mmt180) REVERT: C 128 ARG cc_start: 0.7856 (mmt180) cc_final: 0.7544 (mmt180) REVERT: D 24 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6703 (mp) REVERT: D 128 ARG cc_start: 0.7717 (mmt180) cc_final: 0.7379 (mmt180) REVERT: E 128 ARG cc_start: 0.7805 (mmt180) cc_final: 0.7283 (mmt180) REVERT: E 221 MET cc_start: 0.8706 (mtm) cc_final: 0.8455 (mtm) REVERT: F 128 ARG cc_start: 0.7647 (mmt180) cc_final: 0.7231 (mmt180) REVERT: F 149 GLN cc_start: 0.8536 (mt0) cc_final: 0.7986 (mm-40) REVERT: G 187 GLU cc_start: 0.8747 (tt0) cc_final: 0.8534 (tt0) outliers start: 9 outliers final: 6 residues processed: 168 average time/residue: 0.1412 time to fit residues: 35.1175 Evaluate side-chains 160 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 171 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 125 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 169 optimal weight: 0.0770 chunk 49 optimal weight: 0.7980 chunk 123 optimal weight: 0.0770 chunk 90 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.142795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.115830 restraints weight = 16856.921| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.67 r_work: 0.3063 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16233 Z= 0.088 Angle : 0.433 4.527 21847 Z= 0.212 Chirality : 0.038 0.126 2856 Planarity : 0.003 0.050 2450 Dihedral : 10.195 59.602 2758 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.61 % Allowed : 9.64 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.19), residues: 1820 helix: 3.54 (0.14), residues: 1036 sheet: -0.01 (0.27), residues: 308 loop : -1.10 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 59 TYR 0.004 0.001 TYR A 27 PHE 0.008 0.001 PHE F 188 TRP 0.002 0.000 TRP A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (16233) covalent geometry : angle 0.43286 / 0.21 (21847) hydrogen bonds : bond 0.03164 / 2.21 ( 994) hydrogen bonds : angle 3.43460 / 2.49 ( 2961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3561.00 seconds wall clock time: 62 minutes 10.75 seconds (3730.75 seconds total)