Starting phenix.real_space_refine on Thu Jul 2 23:03:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u5m_26355/07_2026/7u5m_26355.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u5m_26355/07_2026/7u5m_26355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u5m_26355/07_2026/7u5m_26355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u5m_26355/07_2026/7u5m_26355.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7u5m_26355/07_2026/7u5m_26355.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u5m_26355/07_2026/7u5m_26355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u5m_26355/07_2026/7u5m_26355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u5m_26355/07_2026/7u5m_26355.map" } resolution = 2.28 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= 0.108 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 8 5.49 5 S 52 5.16 5 C 6448 2.51 5 N 1772 2.21 5 O 2347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 10627 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2513 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 319} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "C" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "D" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Restraints were copied for chains: B, C, D Time building chain proxies: 2.49, per 1000 atoms: 0.23 Number of scatterers: 10627 At special positions: 0 Unit cell: (99.51, 93.09, 82.39, 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 52 16.00 P 8 15.00 O 2347 8.00 N 1772 7.00 C 6448 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: 0.89 Conformation dependent library (CDL) restraints added in 384.2 milliseconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 39.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 10 through 24 Processing helix chain 'A' and resid 37 through 47 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 102 through 112 removed outlier: 3.817A pdb=" N ALA A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N HIS A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 149 through 166 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.923A pdb=" N GLY A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 223 Processing helix chain 'A' and resid 252 through 266 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 315 through 332 Processing helix chain 'B' and resid 10 through 24 Processing helix chain 'B' and resid 37 through 47 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.816A pdb=" N ALA B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N HIS B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 149 through 166 Proline residue: B 157 - end of helix Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.923A pdb=" N GLY B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 223 Processing helix chain 'B' and resid 252 through 266 Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 315 through 332 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 37 through 47 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 84 through 89 Processing helix chain 'C' and resid 102 through 112 removed outlier: 3.817A pdb=" N ALA C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N HIS C 109 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 149 through 166 Proline residue: C 157 - end of helix Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.923A pdb=" N GLY C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 223 Processing helix chain 'C' and resid 252 through 266 Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'D' and resid 10 through 24 Processing helix chain 'D' and resid 37 through 47 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 102 through 112 removed outlier: 3.817A pdb=" N ALA D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N HIS D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 138 Processing helix chain 'D' and resid 149 through 166 Proline residue: D 157 - end of helix Processing helix chain 'D' and resid 193 through 198 Processing helix chain 'D' and resid 210 through 219 removed outlier: 3.923A pdb=" N GLY D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 223 Processing helix chain 'D' and resid 252 through 266 Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 315 through 332 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 61 removed outlier: 10.194A pdb=" N ASP A 27 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N THR A 73 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 29 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE A 75 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 31 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL A 6 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE A 31 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL A 93 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 208 removed outlier: 9.303A pdb=" N THR A 227 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY A 171 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N MET A 229 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET A 173 " --> pdb=" O MET A 229 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE A 231 " --> pdb=" O MET A 173 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR A 175 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 170 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A 309 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 297 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N TRP A 311 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N ALA A 295 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 11.812A pdb=" N ASP A 313 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 12.302A pdb=" N PHE A 293 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61 removed outlier: 10.194A pdb=" N ASP B 27 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N THR B 73 " --> pdb=" O ASP B 27 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 29 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE B 75 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 31 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL B 6 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE B 31 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL B 93 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 205 through 208 removed outlier: 9.303A pdb=" N THR B 227 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY B 171 " --> pdb=" O THR B 227 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N MET B 229 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET B 173 " --> pdb=" O MET B 229 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE B 231 " --> pdb=" O MET B 173 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR B 175 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU B 170 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE B 309 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA B 297 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 10.840A pdb=" N TRP B 311 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N ALA B 295 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 11.812A pdb=" N ASP B 313 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 12.302A pdb=" N PHE B 293 " --> pdb=" O ASP B 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 61 removed outlier: 10.195A pdb=" N ASP C 27 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 9.589A pdb=" N THR C 73 " --> pdb=" O ASP C 27 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 29 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE C 75 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 31 " --> pdb=" O PHE C 75 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL C 6 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE C 31 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL C 93 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 205 through 208 removed outlier: 9.303A pdb=" N THR C 227 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY C 171 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N MET C 229 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET C 173 " --> pdb=" O MET C 229 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE C 231 " --> pdb=" O MET C 173 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR C 175 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 170 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE C 309 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA C 297 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N TRP C 311 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N ALA C 295 " --> pdb=" O TRP C 311 " (cutoff:3.500A) removed outlier: 11.812A pdb=" N ASP C 313 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 12.302A pdb=" N PHE C 293 " --> pdb=" O ASP C 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 61 removed outlier: 10.194A pdb=" N ASP D 27 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N THR D 73 " --> pdb=" O ASP D 27 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL D 29 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE D 75 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE D 31 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL D 6 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE D 31 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL D 93 " --> pdb=" O ILE D 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 205 through 208 removed outlier: 9.303A pdb=" N THR D 227 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY D 171 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N MET D 229 " --> pdb=" O GLY D 171 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N MET D 173 " --> pdb=" O MET D 229 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE D 231 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR D 175 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU D 170 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE D 309 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA D 297 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N TRP D 311 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N ALA D 295 " --> pdb=" O TRP D 311 " (cutoff:3.500A) removed outlier: 11.812A pdb=" N ASP D 313 " --> pdb=" O PHE D 293 " (cutoff:3.500A) removed outlier: 12.302A pdb=" N PHE D 293 " --> pdb=" O ASP D 313 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1212 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: 1.85 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1708 1.30 - 1.43: 2633 1.43 - 1.56: 5971 1.56 - 1.69: 36 1.69 - 1.82: 96 Bond restraints: 10444 Sorted by residual: bond pdb=" O5D NAD B 401 " pdb=" PN NAD B 401 " ideal model delta sigma weight residual 1.637 1.773 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" O5D NAD A 401 " pdb=" PN NAD A 401 " ideal model delta sigma weight residual 1.637 1.773 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" O5D NAD C 401 " pdb=" PN NAD C 401 " ideal model delta sigma weight residual 1.637 1.773 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" O5D NAD D 401 " pdb=" PN NAD D 401 " ideal model delta sigma weight residual 1.637 1.773 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" O5B NAD C 401 " pdb=" PA NAD C 401 " ideal model delta sigma weight residual 1.638 1.766 -0.128 2.00e-02 2.50e+03 4.08e+01 ... (remaining 10439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 14004 3.56 - 7.12: 128 7.12 - 10.68: 28 10.68 - 14.24: 8 14.24 - 17.80: 8 Bond angle restraints: 14176 Sorted by residual: angle pdb=" N ASN A 203 " pdb=" CA ASN A 203 " pdb=" C ASN A 203 " ideal model delta sigma weight residual 109.50 127.30 -17.80 1.58e+00 4.01e-01 1.27e+02 angle pdb=" N ASN C 203 " pdb=" CA ASN C 203 " pdb=" C ASN C 203 " ideal model delta sigma weight residual 109.50 127.30 -17.80 1.58e+00 4.01e-01 1.27e+02 angle pdb=" N ASN D 203 " pdb=" CA ASN D 203 " pdb=" C ASN D 203 " ideal model delta sigma weight residual 109.50 127.30 -17.80 1.58e+00 4.01e-01 1.27e+02 angle pdb=" N ASN B 203 " pdb=" CA ASN B 203 " pdb=" C ASN B 203 " ideal model delta sigma weight residual 109.50 127.28 -17.78 1.58e+00 4.01e-01 1.27e+02 angle pdb=" N GLN B 202 " pdb=" CA GLN B 202 " pdb=" C GLN B 202 " ideal model delta sigma weight residual 111.82 119.98 -8.16 1.16e+00 7.43e-01 4.94e+01 ... (remaining 14171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 5772 17.44 - 34.89: 244 34.89 - 52.33: 64 52.33 - 69.77: 16 69.77 - 87.21: 12 Dihedral angle restraints: 6108 sinusoidal: 2348 harmonic: 3760 Sorted by residual: dihedral pdb=" CA ASN A 237 " pdb=" C ASN A 237 " pdb=" N VAL A 238 " pdb=" CA VAL A 238 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASN D 237 " pdb=" C ASN D 237 " pdb=" N VAL D 238 " pdb=" CA VAL D 238 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASN C 237 " pdb=" C ASN C 237 " pdb=" N VAL C 238 " pdb=" CA VAL C 238 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 6105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1392 0.082 - 0.164: 176 0.164 - 0.246: 16 0.246 - 0.328: 20 0.328 - 0.410: 8 Chirality restraints: 1612 Sorted by residual: chirality pdb=" C2D NAD B 401 " pdb=" C1D NAD B 401 " pdb=" C3D NAD B 401 " pdb=" O2D NAD B 401 " both_signs ideal model delta sigma weight residual False -2.56 -2.97 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C2D NAD D 401 " pdb=" C1D NAD D 401 " pdb=" C3D NAD D 401 " pdb=" O2D NAD D 401 " both_signs ideal model delta sigma weight residual False -2.56 -2.97 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C2D NAD C 401 " pdb=" C1D NAD C 401 " pdb=" C3D NAD C 401 " pdb=" O2D NAD C 401 " both_signs ideal model delta sigma weight residual False -2.56 -2.97 0.41 2.00e-01 2.50e+01 4.21e+00 ... (remaining 1609 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 196 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C ASP C 196 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP C 196 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY C 197 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 196 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C ASP B 196 " 0.049 2.00e-02 2.50e+03 pdb=" O ASP B 196 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 197 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 196 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C ASP D 196 " 0.049 2.00e-02 2.50e+03 pdb=" O ASP D 196 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY D 197 " -0.017 2.00e-02 2.50e+03 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3183 2.82 - 3.34: 10416 3.34 - 3.86: 21685 3.86 - 4.38: 24737 4.38 - 4.90: 39436 Nonbonded interactions: 99457 Sorted by model distance: nonbonded pdb=" O TRP D 194 " pdb=" O HOH D 501 " model vdw 2.296 3.040 nonbonded pdb=" O1N NAD D 401 " pdb=" O HOH D 502 " model vdw 2.297 3.040 nonbonded pdb=" O TRP C 194 " pdb=" O HOH C 501 " model vdw 2.301 3.040 nonbonded pdb=" O TRP A 194 " pdb=" O HOH A 501 " model vdw 2.301 3.040 nonbonded pdb=" O ASP B 294 " pdb=" O HOH B 501 " model vdw 2.310 3.040 ... (remaining 99452 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.130 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.260 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.136 10444 Z= 0.457 Angle : 0.961 17.802 14176 Z= 0.511 Chirality : 0.068 0.410 1612 Planarity : 0.005 0.039 1804 Dihedral : 12.190 87.213 3708 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.87 % Allowed : 5.60 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.23), residues: 1320 helix: 0.98 (0.26), residues: 392 sheet: -0.92 (0.31), residues: 264 loop : -0.27 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 232 TYR 0.014 0.002 TYR C 318 PHE 0.020 0.002 PHE D 231 TRP 0.004 0.001 TRP D 194 HIS 0.004 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00802 / 0.46 (10444) covalent geometry : angle 0.96135 / 0.51 (14176) hydrogen bonds : bond 0.16727 / 11.18 ( 464) hydrogen bonds : angle 7.18341 / 5.23 ( 1212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.407 Fit side-chains REVERT: A 41 MET cc_start: 0.8276 (mtp) cc_final: 0.7962 (mtp) REVERT: A 103 MET cc_start: 0.7867 (mmm) cc_final: 0.7537 (mmm) REVERT: A 131 MET cc_start: 0.8693 (mmm) cc_final: 0.8409 (mmm) REVERT: A 170 GLU cc_start: 0.8668 (pt0) cc_final: 0.8182 (pt0) REVERT: B 41 MET cc_start: 0.8277 (mtp) cc_final: 0.7964 (mtp) REVERT: B 103 MET cc_start: 0.7877 (mmm) cc_final: 0.7559 (mmm) REVERT: B 131 MET cc_start: 0.8687 (mmm) cc_final: 0.8400 (mmm) REVERT: B 170 GLU cc_start: 0.8656 (pt0) cc_final: 0.8166 (pt0) REVERT: C 41 MET cc_start: 0.8267 (mtp) cc_final: 0.7953 (mtp) REVERT: C 103 MET cc_start: 0.7858 (mmm) cc_final: 0.7522 (mmm) REVERT: C 131 MET cc_start: 0.8691 (mmm) cc_final: 0.8402 (mmm) REVERT: C 170 GLU cc_start: 0.8656 (pt0) cc_final: 0.8176 (pt0) REVERT: D 41 MET cc_start: 0.8275 (mtp) cc_final: 0.7961 (mtp) REVERT: D 103 MET cc_start: 0.7872 (mmm) cc_final: 0.7528 (mmm) REVERT: D 131 MET cc_start: 0.8693 (mmm) cc_final: 0.8410 (mmm) REVERT: D 170 GLU cc_start: 0.8654 (pt0) cc_final: 0.8180 (pt0) outliers start: 20 outliers final: 12 residues processed: 224 average time/residue: 0.6820 time to fit residues: 163.0010 Evaluate side-chains 204 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 55 ASN A 68 ASN A 237 ASN A 289 HIS A 328 HIS B 22 ASN B 55 ASN B 68 ASN B 237 ASN B 289 HIS B 328 HIS C 22 ASN C 55 ASN C 68 ASN C 237 ASN C 289 HIS C 328 HIS D 22 ASN D 55 ASN D 68 ASN D 237 ASN D 289 HIS D 328 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.173719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.155752 restraints weight = 8859.083| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 0.75 r_work: 0.3583 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 10444 Z= 0.228 Angle : 0.637 5.229 14176 Z= 0.355 Chirality : 0.052 0.182 1612 Planarity : 0.005 0.035 1804 Dihedral : 8.812 81.220 1440 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.15 % Allowed : 10.82 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.49 (0.23), residues: 1320 helix: 0.68 (0.24), residues: 408 sheet: -1.28 (0.31), residues: 264 loop : -0.43 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 232 TYR 0.022 0.003 TYR D 318 PHE 0.013 0.002 PHE B 284 TRP 0.004 0.002 TRP B 194 HIS 0.005 0.002 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 (10444) covalent geometry : angle 0.63733 / 0.35 (14176) hydrogen bonds : bond 0.05260 / 3.53 ( 464) hydrogen bonds : angle 6.09537 / 4.39 ( 1212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.429 Fit side-chains REVERT: A 37 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6729 (p0) REVERT: A 41 MET cc_start: 0.8638 (mtp) cc_final: 0.8310 (mtp) REVERT: A 75 PHE cc_start: 0.8464 (m-80) cc_final: 0.8078 (m-80) REVERT: A 131 MET cc_start: 0.8804 (mmm) cc_final: 0.8540 (mmm) REVERT: A 170 GLU cc_start: 0.8896 (pt0) cc_final: 0.8568 (pt0) REVERT: A 316 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8246 (t80) REVERT: B 37 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6711 (p0) REVERT: B 41 MET cc_start: 0.8643 (mtp) cc_final: 0.8320 (mtp) REVERT: B 75 PHE cc_start: 0.8494 (m-80) cc_final: 0.8157 (m-80) REVERT: B 131 MET cc_start: 0.8779 (mmm) cc_final: 0.8516 (mmm) REVERT: B 170 GLU cc_start: 0.8877 (pt0) cc_final: 0.8551 (pt0) REVERT: B 316 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8257 (t80) REVERT: C 37 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6716 (p0) REVERT: C 41 MET cc_start: 0.8638 (mtp) cc_final: 0.8311 (mtp) REVERT: C 75 PHE cc_start: 0.8467 (m-80) cc_final: 0.8142 (m-80) REVERT: C 103 MET cc_start: 0.8006 (mmm) cc_final: 0.7569 (mmm) REVERT: C 131 MET cc_start: 0.8784 (mmm) cc_final: 0.8518 (mmm) REVERT: C 170 GLU cc_start: 0.8883 (pt0) cc_final: 0.8557 (pt0) REVERT: C 316 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8261 (t80) REVERT: D 37 ASP cc_start: 0.7128 (OUTLIER) cc_final: 0.6734 (p0) REVERT: D 41 MET cc_start: 0.8637 (mtp) cc_final: 0.8311 (mtp) REVERT: D 75 PHE cc_start: 0.8465 (m-80) cc_final: 0.8075 (m-80) REVERT: D 103 MET cc_start: 0.8013 (mmm) cc_final: 0.7565 (mmm) REVERT: D 131 MET cc_start: 0.8796 (mmm) cc_final: 0.8531 (mmm) REVERT: D 170 GLU cc_start: 0.8876 (pt0) cc_final: 0.8555 (pt0) REVERT: D 316 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8248 (t80) outliers start: 23 outliers final: 10 residues processed: 196 average time/residue: 0.6760 time to fit residues: 141.5617 Evaluate side-chains 204 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 0.3980 chunk 95 optimal weight: 0.7980 chunk 109 optimal weight: 0.3980 chunk 66 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.178447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.161315 restraints weight = 8766.718| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 0.73 r_work: 0.3473 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10444 Z= 0.118 Angle : 0.503 4.895 14176 Z= 0.277 Chirality : 0.047 0.164 1612 Planarity : 0.004 0.032 1804 Dihedral : 8.313 78.924 1436 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.33 % Allowed : 11.75 % Favored : 85.91 % 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: -0.40 (0.23), residues: 1320 helix: 0.83 (0.25), residues: 416 sheet: -1.39 (0.31), residues: 272 loop : -0.35 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.015 0.002 TYR B 318 PHE 0.010 0.001 PHE C 284 TRP 0.005 0.001 TRP D 85 HIS 0.003 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (10444) covalent geometry : angle 0.50338 / 0.28 (14176) hydrogen bonds : bond 0.03842 / 2.59 ( 464) hydrogen bonds : angle 5.74418 / 4.12 ( 1212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.8597 (mtp) cc_final: 0.8274 (mtp) REVERT: A 75 PHE cc_start: 0.8460 (m-80) cc_final: 0.8035 (m-80) REVERT: A 103 MET cc_start: 0.7761 (mmm) cc_final: 0.7306 (mmm) REVERT: A 131 MET cc_start: 0.8857 (mmm) cc_final: 0.8616 (mmm) REVERT: A 170 GLU cc_start: 0.8879 (pt0) cc_final: 0.8479 (pt0) REVERT: A 316 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8197 (t80) REVERT: B 37 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6821 (p0) REVERT: B 41 MET cc_start: 0.8595 (mtp) cc_final: 0.8307 (mtp) REVERT: B 75 PHE cc_start: 0.8465 (m-80) cc_final: 0.8038 (m-80) REVERT: B 131 MET cc_start: 0.8829 (mmm) cc_final: 0.8588 (mmm) REVERT: B 170 GLU cc_start: 0.8875 (pt0) cc_final: 0.8469 (pt0) REVERT: B 316 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8160 (t80) REVERT: C 37 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6838 (p0) REVERT: C 41 MET cc_start: 0.8605 (mtp) cc_final: 0.8292 (mtp) REVERT: C 75 PHE cc_start: 0.8465 (m-80) cc_final: 0.8039 (m-80) REVERT: C 103 MET cc_start: 0.7757 (mmm) cc_final: 0.7411 (mmm) REVERT: C 131 MET cc_start: 0.8843 (mmm) cc_final: 0.8604 (mmm) REVERT: C 170 GLU cc_start: 0.8862 (pt0) cc_final: 0.8455 (pt0) REVERT: C 316 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8160 (t80) REVERT: D 41 MET cc_start: 0.8601 (mtp) cc_final: 0.8275 (mtp) REVERT: D 75 PHE cc_start: 0.8457 (m-80) cc_final: 0.8034 (m-80) REVERT: D 103 MET cc_start: 0.7736 (mmm) cc_final: 0.7386 (mmm) REVERT: D 131 MET cc_start: 0.8838 (mmm) cc_final: 0.8599 (mmm) REVERT: D 170 GLU cc_start: 0.8869 (pt0) cc_final: 0.8475 (pt0) REVERT: D 316 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.8170 (t80) outliers start: 25 outliers final: 7 residues processed: 203 average time/residue: 0.6453 time to fit residues: 140.4238 Evaluate side-chains 201 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN A 278 GLN B 68 ASN B 278 GLN C 68 ASN C 278 GLN D 68 ASN D 278 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.172730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.154694 restraints weight = 8894.875| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 0.75 r_work: 0.3569 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 10444 Z= 0.267 Angle : 0.680 5.889 14176 Z= 0.376 Chirality : 0.054 0.214 1612 Planarity : 0.005 0.034 1804 Dihedral : 8.831 79.349 1436 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.43 % Allowed : 12.31 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.68 (0.23), residues: 1320 helix: 0.60 (0.25), residues: 408 sheet: -1.49 (0.31), residues: 264 loop : -0.56 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 18 TYR 0.025 0.004 TYR A 318 PHE 0.013 0.003 PHE A 284 TRP 0.007 0.002 TRP D 311 HIS 0.006 0.002 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.27 (10444) covalent geometry : angle 0.68010 / 0.38 (14176) hydrogen bonds : bond 0.05324 / 3.57 ( 464) hydrogen bonds : angle 6.07868 / 4.37 ( 1212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.428 Fit side-chains REVERT: A 131 MET cc_start: 0.8797 (mmm) cc_final: 0.8561 (mmm) REVERT: A 316 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8282 (t80) REVERT: B 37 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6736 (p0) REVERT: B 131 MET cc_start: 0.8769 (mmm) cc_final: 0.8537 (mmm) REVERT: B 316 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8289 (t80) REVERT: C 37 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6745 (p0) REVERT: C 103 MET cc_start: 0.7963 (mmm) cc_final: 0.7464 (mmm) REVERT: C 131 MET cc_start: 0.8780 (mmm) cc_final: 0.8539 (mmm) REVERT: C 316 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8293 (t80) REVERT: D 37 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6754 (p0) REVERT: D 59 LYS cc_start: 0.8330 (pttm) cc_final: 0.7955 (pttm) REVERT: D 75 PHE cc_start: 0.8568 (m-80) cc_final: 0.8142 (m-80) REVERT: D 103 MET cc_start: 0.7954 (mmm) cc_final: 0.7435 (mmm) REVERT: D 110 LEU cc_start: 0.7895 (mt) cc_final: 0.7691 (mt) REVERT: D 111 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6932 (mtpt) REVERT: D 131 MET cc_start: 0.8809 (mmm) cc_final: 0.8567 (mmm) REVERT: D 316 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8276 (t80) outliers start: 26 outliers final: 11 residues processed: 192 average time/residue: 0.6976 time to fit residues: 142.8762 Evaluate side-chains 193 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.177352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.160129 restraints weight = 8816.091| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 0.73 r_work: 0.3651 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10444 Z= 0.128 Angle : 0.526 5.097 14176 Z= 0.289 Chirality : 0.047 0.163 1612 Planarity : 0.004 0.031 1804 Dihedral : 8.384 77.710 1436 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.68 % Allowed : 13.62 % Favored : 84.70 % 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: -0.54 (0.23), residues: 1320 helix: 0.79 (0.25), residues: 416 sheet: -1.52 (0.31), residues: 272 loop : -0.47 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 78 TYR 0.015 0.002 TYR D 318 PHE 0.010 0.001 PHE C 231 TRP 0.005 0.001 TRP C 85 HIS 0.004 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (10444) covalent geometry : angle 0.52578 / 0.29 (14176) hydrogen bonds : bond 0.03919 / 2.63 ( 464) hydrogen bonds : angle 5.71922 / 4.11 ( 1212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8376 (m-80) cc_final: 0.8057 (m-80) REVERT: A 316 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.8230 (t80) REVERT: B 75 PHE cc_start: 0.8392 (m-80) cc_final: 0.8070 (m-80) REVERT: B 131 MET cc_start: 0.8824 (mmm) cc_final: 0.8607 (mmm) REVERT: B 316 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8209 (t80) REVERT: C 103 MET cc_start: 0.7811 (mmm) cc_final: 0.7301 (mmm) REVERT: C 131 MET cc_start: 0.8846 (mmm) cc_final: 0.8630 (mmm) REVERT: C 316 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8211 (t80) REVERT: D 75 PHE cc_start: 0.8513 (m-80) cc_final: 0.8071 (m-80) REVERT: D 131 MET cc_start: 0.8846 (mmm) cc_final: 0.8629 (mmm) REVERT: D 316 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.8211 (t80) outliers start: 18 outliers final: 11 residues processed: 201 average time/residue: 0.6618 time to fit residues: 142.4323 Evaluate side-chains 204 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 0.0060 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.179093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.161672 restraints weight = 8896.722| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 0.75 r_work: 0.3655 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10444 Z= 0.128 Angle : 0.528 5.271 14176 Z= 0.289 Chirality : 0.047 0.164 1612 Planarity : 0.004 0.031 1804 Dihedral : 8.332 77.259 1436 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.77 % Allowed : 12.87 % Favored : 85.35 % 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: -0.53 (0.23), residues: 1320 helix: 0.88 (0.25), residues: 416 sheet: -1.55 (0.31), residues: 272 loop : -0.51 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 78 TYR 0.015 0.002 TYR C 318 PHE 0.010 0.001 PHE A 231 TRP 0.005 0.001 TRP C 85 HIS 0.004 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (10444) covalent geometry : angle 0.52802 / 0.29 (14176) hydrogen bonds : bond 0.03837 / 2.58 ( 464) hydrogen bonds : angle 5.70534 / 4.10 ( 1212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 75 PHE cc_start: 0.8422 (m-80) cc_final: 0.8062 (m-80) REVERT: A 103 MET cc_start: 0.7659 (mmm) cc_final: 0.7450 (mmm) REVERT: A 316 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8231 (t80) REVERT: B 75 PHE cc_start: 0.8423 (m-80) cc_final: 0.8061 (m-80) REVERT: B 131 MET cc_start: 0.8810 (mmm) cc_final: 0.8591 (mmm) REVERT: B 316 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8241 (t80) REVERT: C 103 MET cc_start: 0.7728 (mmm) cc_final: 0.7431 (mmm) REVERT: C 131 MET cc_start: 0.8826 (mmm) cc_final: 0.8600 (mmm) REVERT: C 316 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8242 (t80) REVERT: D 75 PHE cc_start: 0.8546 (m-80) cc_final: 0.8104 (m-80) REVERT: D 103 MET cc_start: 0.7802 (mmm) cc_final: 0.7417 (mmm) REVERT: D 131 MET cc_start: 0.8829 (mmm) cc_final: 0.8604 (mmm) REVERT: D 316 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8227 (t80) outliers start: 19 outliers final: 11 residues processed: 198 average time/residue: 0.6529 time to fit residues: 138.5469 Evaluate side-chains 200 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.172460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.154738 restraints weight = 8829.700| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 0.73 r_work: 0.3576 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 10444 Z= 0.268 Angle : 0.693 5.691 14176 Z= 0.381 Chirality : 0.054 0.213 1612 Planarity : 0.005 0.034 1804 Dihedral : 8.856 80.254 1436 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.96 % Allowed : 12.78 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.69 (0.23), residues: 1320 helix: 0.70 (0.25), residues: 404 sheet: -1.54 (0.31), residues: 264 loop : -0.62 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 18 TYR 0.024 0.004 TYR B 318 PHE 0.012 0.003 PHE B 284 TRP 0.007 0.002 TRP B 311 HIS 0.006 0.002 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.27 (10444) covalent geometry : angle 0.69254 / 0.38 (14176) hydrogen bonds : bond 0.05262 / 3.54 ( 464) hydrogen bonds : angle 6.04059 / 4.35 ( 1212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.399 Fit side-chains REVERT: A 103 MET cc_start: 0.7930 (mmm) cc_final: 0.7498 (mmm) REVERT: A 316 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8282 (t80) REVERT: B 75 PHE cc_start: 0.8510 (m-80) cc_final: 0.8056 (m-80) REVERT: B 131 MET cc_start: 0.8775 (mmm) cc_final: 0.8547 (mmm) REVERT: B 316 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8282 (t80) REVERT: C 131 MET cc_start: 0.8781 (mmm) cc_final: 0.8551 (mmm) REVERT: C 316 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8292 (t80) REVERT: D 75 PHE cc_start: 0.8554 (m-80) cc_final: 0.8114 (m-80) REVERT: D 103 MET cc_start: 0.8042 (mmm) cc_final: 0.7650 (mmm) REVERT: D 131 MET cc_start: 0.8793 (mmm) cc_final: 0.8560 (mmm) REVERT: D 316 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8266 (t80) outliers start: 21 outliers final: 9 residues processed: 188 average time/residue: 0.5742 time to fit residues: 115.6891 Evaluate side-chains 189 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 125 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.177467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.160068 restraints weight = 8774.096| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 0.74 r_work: 0.3625 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10444 Z= 0.158 Angle : 0.571 5.959 14176 Z= 0.313 Chirality : 0.049 0.164 1612 Planarity : 0.004 0.033 1804 Dihedral : 8.589 79.581 1436 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.31 % Allowed : 13.25 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.56 (0.23), residues: 1320 helix: 0.73 (0.25), residues: 416 sheet: -1.45 (0.31), residues: 264 loop : -0.51 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 78 TYR 0.017 0.002 TYR A 318 PHE 0.011 0.002 PHE D 284 TRP 0.005 0.001 TRP C 85 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (10444) covalent geometry : angle 0.57066 / 0.31 (14176) hydrogen bonds : bond 0.04253 / 2.87 ( 464) hydrogen bonds : angle 5.83703 / 4.20 ( 1212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.364 Fit side-chains REVERT: A 103 MET cc_start: 0.7706 (mmm) cc_final: 0.7436 (mmm) REVERT: A 316 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.8263 (t80) REVERT: B 75 PHE cc_start: 0.8481 (m-80) cc_final: 0.8079 (m-80) REVERT: B 131 MET cc_start: 0.8815 (mmm) cc_final: 0.8612 (mmm) REVERT: B 316 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8270 (t80) REVERT: C 103 MET cc_start: 0.7821 (mmm) cc_final: 0.7469 (mmm) REVERT: C 131 MET cc_start: 0.8806 (mmm) cc_final: 0.8601 (mmm) REVERT: C 316 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8266 (t80) REVERT: D 75 PHE cc_start: 0.8557 (m-80) cc_final: 0.8095 (m-80) REVERT: D 103 MET cc_start: 0.7936 (mmm) cc_final: 0.7510 (mmm) REVERT: D 131 MET cc_start: 0.8816 (mmm) cc_final: 0.8606 (mmm) REVERT: D 316 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8257 (t80) outliers start: 14 outliers final: 9 residues processed: 192 average time/residue: 0.6305 time to fit residues: 129.6109 Evaluate side-chains 196 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 81 optimal weight: 0.5980 chunk 83 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 92 optimal weight: 0.0770 chunk 29 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 0.0070 chunk 99 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.179211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.161999 restraints weight = 8848.185| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 0.74 r_work: 0.3667 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10444 Z= 0.113 Angle : 0.530 6.169 14176 Z= 0.286 Chirality : 0.047 0.160 1612 Planarity : 0.004 0.030 1804 Dihedral : 8.258 78.141 1436 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.31 % Allowed : 14.27 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.24), residues: 1320 helix: 0.94 (0.26), residues: 416 sheet: -1.54 (0.31), residues: 272 loop : -0.51 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 78 TYR 0.014 0.002 TYR B 318 PHE 0.012 0.001 PHE A 231 TRP 0.005 0.001 TRP A 85 HIS 0.003 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (10444) covalent geometry : angle 0.52998 / 0.29 (14176) hydrogen bonds : bond 0.03596 / 2.43 ( 464) hydrogen bonds : angle 5.60807 / 4.03 ( 1212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.430 Fit side-chains REVERT: A 103 MET cc_start: 0.7820 (mmm) cc_final: 0.7520 (mmm) REVERT: A 316 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.8178 (t80) REVERT: B 75 PHE cc_start: 0.8448 (m-80) cc_final: 0.8032 (m-80) REVERT: B 316 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8186 (t80) REVERT: C 103 MET cc_start: 0.7820 (mmm) cc_final: 0.7617 (mmm) REVERT: C 316 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.8178 (t80) REVERT: D 75 PHE cc_start: 0.8513 (m-80) cc_final: 0.8065 (m-80) REVERT: D 103 MET cc_start: 0.7954 (mmm) cc_final: 0.7534 (mmm) REVERT: D 316 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8171 (t80) outliers start: 14 outliers final: 4 residues processed: 191 average time/residue: 0.5691 time to fit residues: 116.5089 Evaluate side-chains 188 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.1980 chunk 42 optimal weight: 0.0170 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.177942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.160817 restraints weight = 8711.571| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 0.72 r_work: 0.3634 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 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 : 0.004 0.049 10444 Z= 0.162 Angle : 0.597 6.939 14176 Z= 0.323 Chirality : 0.049 0.166 1612 Planarity : 0.004 0.032 1804 Dihedral : 8.423 78.195 1433 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.84 % Allowed : 14.46 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.55 (0.23), residues: 1320 helix: 1.07 (0.26), residues: 396 sheet: -1.62 (0.31), residues: 272 loop : -0.61 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 78 TYR 0.017 0.002 TYR C 318 PHE 0.011 0.002 PHE A 231 TRP 0.006 0.001 TRP C 85 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (10444) covalent geometry : angle 0.59740 / 0.32 (14176) hydrogen bonds : bond 0.04290 / 2.89 ( 464) hydrogen bonds : angle 5.77713 / 4.15 ( 1212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.326 Fit side-chains REVERT: A 103 MET cc_start: 0.7937 (mmm) cc_final: 0.7450 (mmm) REVERT: A 316 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8261 (t80) REVERT: B 75 PHE cc_start: 0.8499 (m-80) cc_final: 0.8057 (m-80) REVERT: B 316 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8284 (t80) REVERT: C 103 MET cc_start: 0.7923 (mmm) cc_final: 0.7559 (mmm) REVERT: C 316 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8282 (t80) REVERT: D 75 PHE cc_start: 0.8561 (m-80) cc_final: 0.8114 (m-80) REVERT: D 103 MET cc_start: 0.7984 (mmm) cc_final: 0.7364 (mmm) REVERT: D 316 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8265 (t80) outliers start: 9 outliers final: 4 residues processed: 181 average time/residue: 0.6324 time to fit residues: 122.2530 Evaluate side-chains 185 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 316 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN B 68 ASN C 68 ASN D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.179009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.161968 restraints weight = 8820.730| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 0.73 r_work: 0.3576 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10444 Z= 0.140 Angle : 0.567 6.633 14176 Z= 0.307 Chirality : 0.048 0.162 1612 Planarity : 0.004 0.031 1804 Dihedral : 8.342 77.253 1433 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.75 % Allowed : 14.93 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.57 (0.23), residues: 1320 helix: 0.92 (0.25), residues: 412 sheet: -1.63 (0.30), residues: 272 loop : -0.56 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 78 TYR 0.016 0.002 TYR A 318 PHE 0.012 0.002 PHE B 231 TRP 0.005 0.001 TRP C 85 HIS 0.004 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (10444) covalent geometry : angle 0.56670 / 0.31 (14176) hydrogen bonds : bond 0.04003 / 2.70 ( 464) hydrogen bonds : angle 5.72956 / 4.12 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4204.98 seconds wall clock time: 72 minutes 44.04 seconds (4364.04 seconds total)