Starting phenix.real_space_refine on Sat Aug 23 13:58:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twv_41672/08_2025/8twv_41672.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twv_41672/08_2025/8twv_41672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8twv_41672/08_2025/8twv_41672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twv_41672/08_2025/8twv_41672.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8twv_41672/08_2025/8twv_41672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twv_41672/08_2025/8twv_41672.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.220 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 8305 2.51 5 N 2115 2.21 5 O 2275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12720 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2540 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: E, B, D, C Time building chain proxies: 1.80, per 1000 atoms: 0.14 Number of scatterers: 12720 At special positions: 0 Unit cell: (92.352, 91.168, 124.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 2275 8.00 N 2115 7.00 C 8305 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: 0.78 Conformation dependent library (CDL) restraints added in 482.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2930 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 34.2% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.678A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.961A pdb=" N THR A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.718A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 287 Processing helix chain 'A' and resid 299 through 320 removed outlier: 3.618A pdb=" N ALA A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Proline residue: A 305 - end of helix removed outlier: 3.505A pdb=" N GLY A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 removed outlier: 3.678A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 221 Processing helix chain 'E' and resid 227 through 245 removed outlier: 3.961A pdb=" N THR E 234 " --> pdb=" O GLU E 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.718A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 287 Processing helix chain 'E' and resid 299 through 320 removed outlier: 3.617A pdb=" N ALA E 303 " --> pdb=" O ARG E 299 " (cutoff:3.500A) Proline residue: E 305 - end of helix removed outlier: 3.506A pdb=" N GLY E 312 " --> pdb=" O PHE E 308 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E 315 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.678A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 227 through 245 removed outlier: 3.961A pdb=" N THR B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.718A pdb=" N ILE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 287 Processing helix chain 'B' and resid 299 through 320 removed outlier: 3.618A pdb=" N ALA B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Proline residue: B 305 - end of helix removed outlier: 3.505A pdb=" N GLY B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 315 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 70 removed outlier: 3.679A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.960A pdb=" N THR D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.717A pdb=" N ILE D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 287 Processing helix chain 'D' and resid 299 through 320 removed outlier: 3.618A pdb=" N ALA D 303 " --> pdb=" O ARG D 299 " (cutoff:3.500A) Proline residue: D 305 - end of helix removed outlier: 3.505A pdb=" N GLY D 312 " --> pdb=" O PHE D 308 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 315 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.679A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 227 through 245 removed outlier: 3.961A pdb=" N THR C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.717A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 287 Processing helix chain 'C' and resid 299 through 320 removed outlier: 3.618A pdb=" N ALA C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) Proline residue: C 305 - end of helix removed outlier: 3.505A pdb=" N GLY C 312 " --> pdb=" O PHE C 308 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 315 " --> pdb=" O ILE C 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.475A pdb=" N SER A 109 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.056A pdb=" N LYS A 34 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLY A 25 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP A 36 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE A 23 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR A 38 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN A 21 " --> pdb=" O TYR A 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL A 40 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE A 19 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLN A 42 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N SER A 17 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N THR A 44 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N SER A 15 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL A 16 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A 145 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE A 18 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL A 147 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE A 20 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.511A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE A 188 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER A 171 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG A 190 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N HIS A 169 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR A 192 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER A 167 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ARG A 194 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS A 165 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP A 196 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 56 through 58 removed outlier: 4.475A pdb=" N SER E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 58 removed outlier: 4.056A pdb=" N LYS E 34 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLY E 25 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP E 36 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE E 23 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR E 38 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN E 21 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL E 40 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N PHE E 19 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLN E 42 " --> pdb=" O SER E 17 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N SER E 17 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N THR E 44 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N SER E 15 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL E 16 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE E 145 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE E 18 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL E 147 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE E 20 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.512A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE E 188 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER E 171 " --> pdb=" O PHE E 188 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG E 190 " --> pdb=" O HIS E 169 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N HIS E 169 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR E 192 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER E 167 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG E 194 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS E 165 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP E 196 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 58 removed outlier: 4.475A pdb=" N SER B 109 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 56 through 58 removed outlier: 4.055A pdb=" N LYS B 34 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLY B 25 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP B 36 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE B 23 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR B 38 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN B 21 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL B 40 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N PHE B 19 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLN B 42 " --> pdb=" O SER B 17 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N SER B 17 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N THR B 44 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N SER B 15 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL B 16 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE B 145 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE B 18 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 147 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE B 20 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.511A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE B 188 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER B 171 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG B 190 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HIS B 169 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR B 192 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER B 167 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG B 194 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS B 165 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP B 196 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.475A pdb=" N SER D 109 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.056A pdb=" N LYS D 34 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLY D 25 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP D 36 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE D 23 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N TYR D 38 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN D 21 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL D 40 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE D 19 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLN D 42 " --> pdb=" O SER D 17 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N SER D 17 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N THR D 44 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N SER D 15 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL D 16 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE D 145 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE D 18 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL D 147 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE D 20 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.512A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE D 188 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER D 171 " --> pdb=" O PHE D 188 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG D 190 " --> pdb=" O HIS D 169 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N HIS D 169 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR D 192 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER D 167 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG D 194 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS D 165 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP D 196 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 56 through 58 removed outlier: 4.476A pdb=" N SER C 109 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 56 through 58 removed outlier: 4.056A pdb=" N LYS C 34 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLY C 25 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP C 36 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE C 23 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR C 38 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN C 21 " --> pdb=" O TYR C 38 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL C 40 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N PHE C 19 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLN C 42 " --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N SER C 17 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N THR C 44 " --> pdb=" O SER C 15 " (cutoff:3.500A) removed outlier: 9.610A pdb=" N SER C 15 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL C 16 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE C 145 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE C 18 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL C 147 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE C 20 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.512A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE C 188 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER C 171 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG C 190 " --> pdb=" O HIS C 169 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N HIS C 169 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR C 192 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER C 167 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG C 194 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LYS C 165 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP C 196 " --> pdb=" O ARG C 163 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1680 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: 1.43 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4020 1.34 - 1.46: 2849 1.46 - 1.57: 6146 1.57 - 1.69: 5 1.69 - 1.81: 45 Bond restraints: 13065 Sorted by residual: bond pdb=" CA PHE B 208 " pdb=" CB PHE B 208 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.69e-02 3.50e+03 3.10e+00 bond pdb=" CA PHE A 208 " pdb=" CB PHE A 208 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.69e-02 3.50e+03 3.07e+00 bond pdb=" CA PHE E 208 " pdb=" CB PHE E 208 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.69e-02 3.50e+03 3.06e+00 bond pdb=" CA PHE C 208 " pdb=" CB PHE C 208 " ideal model delta sigma weight residual 1.530 1.560 -0.029 1.69e-02 3.50e+03 3.02e+00 bond pdb=" CA PHE D 208 " pdb=" CB PHE D 208 " ideal model delta sigma weight residual 1.530 1.560 -0.029 1.69e-02 3.50e+03 3.01e+00 ... (remaining 13060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 17116 1.61 - 3.22: 494 3.22 - 4.83: 115 4.83 - 6.44: 40 6.44 - 8.05: 15 Bond angle restraints: 17780 Sorted by residual: angle pdb=" N ARG D 299 " pdb=" CA ARG D 299 " pdb=" C ARG D 299 " ideal model delta sigma weight residual 113.20 107.78 5.42 1.21e+00 6.83e-01 2.01e+01 angle pdb=" N ARG B 299 " pdb=" CA ARG B 299 " pdb=" C ARG B 299 " ideal model delta sigma weight residual 113.20 107.81 5.39 1.21e+00 6.83e-01 1.99e+01 angle pdb=" N ARG A 299 " pdb=" CA ARG A 299 " pdb=" C ARG A 299 " ideal model delta sigma weight residual 113.20 107.82 5.38 1.21e+00 6.83e-01 1.98e+01 angle pdb=" N ARG C 299 " pdb=" CA ARG C 299 " pdb=" C ARG C 299 " ideal model delta sigma weight residual 113.20 107.83 5.37 1.21e+00 6.83e-01 1.97e+01 angle pdb=" N ARG E 299 " pdb=" CA ARG E 299 " pdb=" C ARG E 299 " ideal model delta sigma weight residual 113.20 107.86 5.34 1.21e+00 6.83e-01 1.95e+01 ... (remaining 17775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 6675 17.64 - 35.27: 696 35.27 - 52.91: 179 52.91 - 70.55: 45 70.55 - 88.19: 10 Dihedral angle restraints: 7605 sinusoidal: 3060 harmonic: 4545 Sorted by residual: dihedral pdb=" CA ASP D 115 " pdb=" CB ASP D 115 " pdb=" CG ASP D 115 " pdb=" OD1 ASP D 115 " ideal model delta sinusoidal sigma weight residual -30.00 -88.59 58.59 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP B 115 " pdb=" CB ASP B 115 " pdb=" CG ASP B 115 " pdb=" OD1 ASP B 115 " ideal model delta sinusoidal sigma weight residual -30.00 -88.58 58.58 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP E 115 " pdb=" CB ASP E 115 " pdb=" CG ASP E 115 " pdb=" OD1 ASP E 115 " ideal model delta sinusoidal sigma weight residual -30.00 -88.56 58.56 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 7602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1255 0.042 - 0.083: 446 0.083 - 0.125: 201 0.125 - 0.166: 38 0.166 - 0.208: 15 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CA THR A 61 " pdb=" N THR A 61 " pdb=" C THR A 61 " pdb=" CB THR A 61 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA THR C 61 " pdb=" N THR C 61 " pdb=" C THR C 61 " pdb=" CB THR C 61 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA THR D 61 " pdb=" N THR D 61 " pdb=" C THR D 61 " pdb=" CB THR D 61 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1952 not shown) Planarity restraints: 2265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 208 " 0.011 2.00e-02 2.50e+03 1.79e-02 5.63e+00 pdb=" CG PHE C 208 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 208 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE C 208 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE C 208 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 208 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 208 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 208 " 0.011 2.00e-02 2.50e+03 1.79e-02 5.62e+00 pdb=" CG PHE B 208 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 208 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 208 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE B 208 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 208 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 208 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 208 " 0.011 2.00e-02 2.50e+03 1.79e-02 5.59e+00 pdb=" CG PHE E 208 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE E 208 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE E 208 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE E 208 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 208 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE E 208 " -0.000 2.00e-02 2.50e+03 ... (remaining 2262 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2493 2.78 - 3.31: 11409 3.31 - 3.84: 21313 3.84 - 4.37: 25170 4.37 - 4.90: 43579 Nonbonded interactions: 103964 Sorted by model distance: nonbonded pdb=" OE2 GLU D 59 " pdb=" OG SER C 134 " model vdw 2.244 3.040 nonbonded pdb=" OE2 GLU E 59 " pdb=" OG SER D 134 " model vdw 2.256 3.040 nonbonded pdb=" O THR E 61 " pdb=" OG1 THR E 61 " model vdw 2.303 3.040 nonbonded pdb=" O THR A 61 " pdb=" OG1 THR A 61 " model vdw 2.304 3.040 nonbonded pdb=" O THR B 61 " pdb=" OG1 THR B 61 " model vdw 2.304 3.040 ... (remaining 103959 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'B' selection = chain 'D' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.000 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.004 0.054 13065 Z= 0.216 Angle : 0.727 8.046 17780 Z= 0.437 Chirality : 0.053 0.208 1955 Planarity : 0.005 0.062 2265 Dihedral : 15.797 88.185 4675 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.07 % Allowed : 19.13 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.21), residues: 1540 helix: -1.61 (0.19), residues: 525 sheet: 1.36 (0.27), residues: 430 loop : -2.25 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 231 TYR 0.009 0.001 TYR B 38 PHE 0.040 0.002 PHE B 208 TRP 0.016 0.001 TRP A 206 HIS 0.006 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00409 (13065) covalent geometry : angle 0.72721 (17780) hydrogen bonds : bond 0.12954 ( 535) hydrogen bonds : angle 6.72788 ( 1680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ARG cc_start: 0.6869 (mtm180) cc_final: 0.6411 (mpt-90) REVERT: E 34 LYS cc_start: 0.8971 (mttp) cc_final: 0.8762 (mttm) REVERT: E 208 PHE cc_start: 0.8704 (t80) cc_final: 0.8396 (t80) REVERT: E 230 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6983 (mp0) REVERT: E 231 ARG cc_start: 0.6850 (mtm180) cc_final: 0.6450 (mpt-90) REVERT: B 225 LEU cc_start: 0.8615 (mp) cc_final: 0.8385 (mp) REVERT: B 231 ARG cc_start: 0.6871 (mtm180) cc_final: 0.6335 (mpt-90) REVERT: D 86 ASP cc_start: 0.8750 (t70) cc_final: 0.8482 (t70) REVERT: D 230 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7121 (mp0) REVERT: D 231 ARG cc_start: 0.6980 (mtm180) cc_final: 0.6661 (mpt-90) REVERT: C 113 ASP cc_start: 0.8233 (m-30) cc_final: 0.7625 (p0) REVERT: C 208 PHE cc_start: 0.8676 (t80) cc_final: 0.8473 (t80) REVERT: C 231 ARG cc_start: 0.6807 (mtm180) cc_final: 0.6369 (mpt-90) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.1039 time to fit residues: 22.1362 Evaluate side-chains 116 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.155396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.117257 restraints weight = 15503.192| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.01 r_work: 0.2821 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 13065 Z= 0.199 Angle : 0.565 7.010 17780 Z= 0.289 Chirality : 0.046 0.136 1955 Planarity : 0.003 0.022 2265 Dihedral : 4.377 14.775 1715 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.74 % Allowed : 18.84 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.22), residues: 1540 helix: 0.55 (0.24), residues: 505 sheet: 1.02 (0.25), residues: 480 loop : -1.91 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 231 TYR 0.012 0.002 TYR D 33 PHE 0.011 0.001 PHE A 208 TRP 0.013 0.001 TRP D 206 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00460 (13065) covalent geometry : angle 0.56522 (17780) hydrogen bonds : bond 0.03502 ( 535) hydrogen bonds : angle 5.10475 ( 1680) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8562 (pt0) REVERT: A 264 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8292 (mt0) REVERT: E 185 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8523 (pt0) REVERT: E 231 ARG cc_start: 0.7195 (mtm180) cc_final: 0.6749 (mtt180) REVERT: E 264 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: B 86 ASP cc_start: 0.8853 (t70) cc_final: 0.8386 (t70) REVERT: B 151 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.7938 (m110) REVERT: B 225 LEU cc_start: 0.8812 (mp) cc_final: 0.8529 (mp) REVERT: B 231 ARG cc_start: 0.7046 (mtm180) cc_final: 0.6213 (mpt-90) REVERT: D 151 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8038 (m-40) REVERT: D 231 ARG cc_start: 0.7197 (mtm180) cc_final: 0.6834 (mtt-85) REVERT: D 264 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8215 (mt0) REVERT: C 151 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8326 (t0) REVERT: C 185 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8557 (pt0) outliers start: 38 outliers final: 15 residues processed: 163 average time/residue: 0.0846 time to fit residues: 20.6803 Evaluate side-chains 140 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 214 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 110 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 298 GLN E 125 GLN E 298 GLN B 298 GLN D 125 GLN D 298 GLN C 251 ASN C 298 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.153528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.116603 restraints weight = 15910.294| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.92 r_work: 0.2751 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 13065 Z= 0.308 Angle : 0.622 7.932 17780 Z= 0.321 Chirality : 0.049 0.138 1955 Planarity : 0.003 0.023 2265 Dihedral : 4.734 23.549 1715 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.48 % Allowed : 17.62 % Favored : 77.91 % 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 aren not related in a simple way. whole: -0.11 (0.22), residues: 1540 helix: 0.87 (0.23), residues: 500 sheet: 0.93 (0.25), residues: 470 loop : -1.84 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 105 TYR 0.015 0.002 TYR E 204 PHE 0.012 0.001 PHE C 133 TRP 0.011 0.001 TRP A 206 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00731 (13065) covalent geometry : angle 0.62157 (17780) hydrogen bonds : bond 0.03900 ( 535) hydrogen bonds : angle 5.15889 ( 1680) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 124 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7933 (tpp80) REVERT: A 129 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: A 185 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8576 (pt0) REVERT: A 264 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8507 (mt0) REVERT: E 86 ASP cc_start: 0.8895 (t70) cc_final: 0.8448 (t70) REVERT: E 185 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8502 (pt0) REVERT: E 264 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8492 (mt0) REVERT: B 86 ASP cc_start: 0.8883 (t70) cc_final: 0.8654 (t70) REVERT: B 129 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8448 (mt-10) REVERT: B 151 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8195 (m110) REVERT: B 225 LEU cc_start: 0.8724 (mp) cc_final: 0.8472 (mp) REVERT: B 231 ARG cc_start: 0.7263 (mtm180) cc_final: 0.7003 (mtt180) REVERT: D 30 GLU cc_start: 0.9114 (pm20) cc_final: 0.8783 (pm20) REVERT: D 151 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8122 (m-40) REVERT: D 245 TYR cc_start: 0.7981 (m-10) cc_final: 0.7770 (m-80) REVERT: D 264 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8349 (mt0) REVERT: C 151 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8347 (t0) REVERT: C 161 TRP cc_start: 0.8462 (m-10) cc_final: 0.8213 (m-90) REVERT: C 184 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8322 (m-40) REVERT: C 185 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8589 (pt0) outliers start: 62 outliers final: 33 residues processed: 184 average time/residue: 0.0906 time to fit residues: 24.8247 Evaluate side-chains 166 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 103 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.130288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.096610 restraints weight = 16124.039| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.74 r_work: 0.2842 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 13065 Z= 0.113 Angle : 0.487 6.222 17780 Z= 0.248 Chirality : 0.045 0.128 1955 Planarity : 0.003 0.022 2265 Dihedral : 4.276 19.309 1715 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.52 % Allowed : 20.22 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.22), residues: 1540 helix: 1.23 (0.24), residues: 505 sheet: 0.98 (0.25), residues: 465 loop : -1.74 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.010 0.001 TYR D 38 PHE 0.006 0.001 PHE A 116 TRP 0.015 0.001 TRP A 206 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00249 (13065) covalent geometry : angle 0.48693 (17780) hydrogen bonds : bond 0.02934 ( 535) hydrogen bonds : angle 4.76433 ( 1680) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7873 (tpp80) REVERT: E 231 ARG cc_start: 0.7398 (mtt180) cc_final: 0.6968 (mtt180) REVERT: B 30 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8531 (pm20) REVERT: B 36 ASP cc_start: 0.8855 (t70) cc_final: 0.8581 (t0) REVERT: B 151 ASN cc_start: 0.8355 (m-40) cc_final: 0.7978 (m110) REVERT: B 161 TRP cc_start: 0.8479 (m-10) cc_final: 0.7990 (m-90) REVERT: B 225 LEU cc_start: 0.8737 (mp) cc_final: 0.8416 (mp) REVERT: D 125 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8498 (pt0) REVERT: D 230 GLU cc_start: 0.7126 (mp0) cc_final: 0.6747 (pm20) REVERT: D 231 ARG cc_start: 0.7484 (mtm180) cc_final: 0.6888 (mtm-85) REVERT: D 245 TYR cc_start: 0.7784 (m-10) cc_final: 0.7569 (m-80) REVERT: D 248 TYR cc_start: 0.8974 (t80) cc_final: 0.8735 (t80) REVERT: C 30 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8555 (pm20) REVERT: C 161 TRP cc_start: 0.8402 (m-10) cc_final: 0.8190 (m-90) REVERT: C 187 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7777 (mt-10) outliers start: 21 outliers final: 11 residues processed: 157 average time/residue: 0.0864 time to fit residues: 19.8004 Evaluate side-chains 142 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 236 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain C residue 30 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 104 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN D 251 ASN C 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.129102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.095754 restraints weight = 16107.777| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.70 r_work: 0.3004 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13065 Z= 0.143 Angle : 0.494 7.484 17780 Z= 0.251 Chirality : 0.045 0.128 1955 Planarity : 0.003 0.021 2265 Dihedral : 4.195 19.001 1715 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.89 % Allowed : 19.13 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.22), residues: 1540 helix: 1.34 (0.24), residues: 505 sheet: 1.01 (0.25), residues: 470 loop : -1.71 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 65 TYR 0.010 0.001 TYR D 38 PHE 0.007 0.001 PHE C 121 TRP 0.014 0.001 TRP A 206 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00328 (13065) covalent geometry : angle 0.49381 (17780) hydrogen bonds : bond 0.03021 ( 535) hydrogen bonds : angle 4.68280 ( 1680) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7908 (tpp80) REVERT: A 129 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: A 264 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8565 (mt0) REVERT: E 185 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8470 (pt0) REVERT: E 231 ARG cc_start: 0.7508 (mtt180) cc_final: 0.6937 (mtt180) REVERT: B 30 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: B 129 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: B 231 ARG cc_start: 0.7514 (mtm180) cc_final: 0.6896 (mtt-85) REVERT: D 30 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8668 (pm20) REVERT: D 125 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8538 (pt0) REVERT: D 129 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: D 231 ARG cc_start: 0.7499 (mtm180) cc_final: 0.7273 (mtm180) REVERT: D 245 TYR cc_start: 0.7879 (m-10) cc_final: 0.7608 (m-80) REVERT: D 248 TYR cc_start: 0.8935 (t80) cc_final: 0.8730 (t80) REVERT: C 30 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8488 (pm20) REVERT: C 187 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7843 (mt-10) outliers start: 40 outliers final: 24 residues processed: 163 average time/residue: 0.0857 time to fit residues: 20.5402 Evaluate side-chains 159 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 236 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 152 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN D 251 ASN C 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.093249 restraints weight = 16313.879| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.68 r_work: 0.2792 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13065 Z= 0.216 Angle : 0.544 6.776 17780 Z= 0.278 Chirality : 0.046 0.130 1955 Planarity : 0.003 0.021 2265 Dihedral : 4.420 20.429 1715 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.61 % Allowed : 18.99 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.22), residues: 1540 helix: 1.31 (0.24), residues: 505 sheet: 1.06 (0.26), residues: 455 loop : -1.81 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 105 TYR 0.012 0.002 TYR C 204 PHE 0.009 0.001 PHE D 133 TRP 0.017 0.001 TRP C 161 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00510 (13065) covalent geometry : angle 0.54414 (17780) hydrogen bonds : bond 0.03315 ( 535) hydrogen bonds : angle 4.81041 ( 1680) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8118 (mmm-85) cc_final: 0.7878 (tpp80) REVERT: A 129 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8283 (mt-10) REVERT: A 264 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8535 (mt0) REVERT: A 304 PHE cc_start: 0.5011 (OUTLIER) cc_final: 0.4215 (t80) REVERT: E 30 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8613 (pm20) REVERT: E 185 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8535 (pt0) REVERT: E 231 ARG cc_start: 0.7475 (mtt180) cc_final: 0.6907 (mtt180) REVERT: B 30 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8556 (pm20) REVERT: B 129 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8356 (mt-10) REVERT: B 231 ARG cc_start: 0.7443 (mtm180) cc_final: 0.7060 (mtt180) REVERT: D 30 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8738 (pm20) REVERT: D 129 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8337 (mt-10) REVERT: D 230 GLU cc_start: 0.7154 (mp0) cc_final: 0.6375 (pm20) REVERT: D 231 ARG cc_start: 0.7449 (mtm180) cc_final: 0.6899 (mtm-85) REVERT: D 245 TYR cc_start: 0.7940 (m-10) cc_final: 0.7693 (m-80) REVERT: D 264 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8470 (mt0) REVERT: C 30 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8551 (pm20) outliers start: 50 outliers final: 29 residues processed: 168 average time/residue: 0.0906 time to fit residues: 22.4807 Evaluate side-chains 163 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 25 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN D 251 ASN C 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097399 restraints weight = 16036.143| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.71 r_work: 0.2850 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13065 Z= 0.110 Angle : 0.480 7.363 17780 Z= 0.242 Chirality : 0.044 0.126 1955 Planarity : 0.002 0.024 2265 Dihedral : 4.084 16.631 1715 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.10 % Allowed : 19.71 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.22), residues: 1540 helix: 1.41 (0.24), residues: 505 sheet: 1.12 (0.26), residues: 450 loop : -1.82 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 105 TYR 0.009 0.001 TYR D 38 PHE 0.007 0.001 PHE C 228 TRP 0.018 0.001 TRP C 161 HIS 0.004 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00246 (13065) covalent geometry : angle 0.47985 (17780) hydrogen bonds : bond 0.02804 ( 535) hydrogen bonds : angle 4.57107 ( 1680) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: E 30 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8612 (pm20) REVERT: E 231 ARG cc_start: 0.7462 (mtt180) cc_final: 0.6967 (mtt180) REVERT: E 304 PHE cc_start: 0.4769 (OUTLIER) cc_final: 0.3400 (t80) REVERT: B 30 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8543 (pm20) REVERT: B 34 LYS cc_start: 0.9032 (mttp) cc_final: 0.8817 (mttm) REVERT: B 129 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: B 304 PHE cc_start: 0.5423 (OUTLIER) cc_final: 0.4320 (t80) REVERT: D 30 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8633 (pm20) REVERT: D 125 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8526 (pt0) REVERT: D 230 GLU cc_start: 0.7214 (mp0) cc_final: 0.6487 (pm20) REVERT: D 231 ARG cc_start: 0.7371 (mtm180) cc_final: 0.6806 (mtm-85) REVERT: D 245 TYR cc_start: 0.7734 (m-10) cc_final: 0.7483 (m-80) REVERT: D 248 TYR cc_start: 0.8979 (t80) cc_final: 0.8689 (t80) REVERT: D 304 PHE cc_start: 0.5027 (OUTLIER) cc_final: 0.3778 (t80) REVERT: C 30 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8513 (pm20) REVERT: C 184 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8169 (m-40) REVERT: C 304 PHE cc_start: 0.5448 (OUTLIER) cc_final: 0.4255 (t80) outliers start: 43 outliers final: 21 residues processed: 168 average time/residue: 0.0861 time to fit residues: 21.3469 Evaluate side-chains 158 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 236 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 304 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 154 ASN E 62 GLN E 154 ASN B 62 GLN D 62 GLN D 154 ASN D 251 ASN C 62 GLN C 154 ASN C 251 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.131405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.097742 restraints weight = 15973.456| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.75 r_work: 0.2858 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13065 Z= 0.110 Angle : 0.479 7.542 17780 Z= 0.241 Chirality : 0.044 0.127 1955 Planarity : 0.003 0.024 2265 Dihedral : 3.983 15.335 1715 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.47 % Allowed : 19.35 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.22), residues: 1540 helix: 1.47 (0.24), residues: 505 sheet: 1.01 (0.26), residues: 460 loop : -1.79 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 65 TYR 0.010 0.001 TYR D 38 PHE 0.007 0.001 PHE C 228 TRP 0.018 0.001 TRP C 161 HIS 0.004 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00248 (13065) covalent geometry : angle 0.47945 (17780) hydrogen bonds : bond 0.02779 ( 535) hydrogen bonds : angle 4.47723 ( 1680) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8447 (pm20) REVERT: A 129 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: A 264 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8229 (mt0) REVERT: A 304 PHE cc_start: 0.5044 (OUTLIER) cc_final: 0.4193 (t80) REVERT: E 30 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8578 (pm20) REVERT: E 231 ARG cc_start: 0.7363 (mtt180) cc_final: 0.6897 (mtt180) REVERT: E 304 PHE cc_start: 0.4891 (OUTLIER) cc_final: 0.3342 (t80) REVERT: B 34 LYS cc_start: 0.8986 (mttp) cc_final: 0.8757 (mttm) REVERT: B 82 VAL cc_start: 0.9181 (t) cc_final: 0.8937 (t) REVERT: B 129 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: B 161 TRP cc_start: 0.8476 (m-90) cc_final: 0.8202 (m-10) REVERT: B 304 PHE cc_start: 0.5309 (OUTLIER) cc_final: 0.4230 (t80) REVERT: D 30 GLU cc_start: 0.8915 (pm20) cc_final: 0.8621 (pm20) REVERT: D 65 ARG cc_start: 0.7849 (mmm-85) cc_final: 0.7486 (ttm-80) REVERT: D 125 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8486 (pt0) REVERT: D 248 TYR cc_start: 0.8978 (t80) cc_final: 0.8685 (t80) REVERT: C 30 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8413 (pm20) REVERT: C 184 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8138 (m-40) REVERT: C 304 PHE cc_start: 0.5394 (OUTLIER) cc_final: 0.4191 (t80) outliers start: 48 outliers final: 23 residues processed: 167 average time/residue: 0.0898 time to fit residues: 21.9629 Evaluate side-chains 158 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 304 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 154 ASN E 62 GLN E 154 ASN B 62 GLN B 154 ASN D 62 GLN D 154 ASN D 251 ASN C 62 GLN C 154 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.098314 restraints weight = 15993.792| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.69 r_work: 0.3146 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13065 Z= 0.114 Angle : 0.483 7.042 17780 Z= 0.245 Chirality : 0.044 0.128 1955 Planarity : 0.002 0.024 2265 Dihedral : 3.966 16.169 1715 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.32 % Allowed : 19.64 % Favored : 77.04 % 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 aren not related in a simple way. whole: 0.26 (0.22), residues: 1540 helix: 1.48 (0.24), residues: 505 sheet: 1.02 (0.26), residues: 460 loop : -1.81 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 231 TYR 0.012 0.001 TYR D 38 PHE 0.007 0.001 PHE E 228 TRP 0.022 0.001 TRP C 161 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00260 (13065) covalent geometry : angle 0.48341 (17780) hydrogen bonds : bond 0.02759 ( 535) hydrogen bonds : angle 4.43932 ( 1680) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: A 129 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: A 304 PHE cc_start: 0.5185 (OUTLIER) cc_final: 0.4246 (t80) REVERT: E 30 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8545 (pm20) REVERT: E 304 PHE cc_start: 0.5038 (OUTLIER) cc_final: 0.3346 (t80) REVERT: B 30 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: B 82 VAL cc_start: 0.9264 (t) cc_final: 0.9011 (t) REVERT: B 129 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: B 161 TRP cc_start: 0.8544 (m-90) cc_final: 0.8269 (m-10) REVERT: B 304 PHE cc_start: 0.5444 (OUTLIER) cc_final: 0.4321 (t80) REVERT: D 30 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8619 (pm20) REVERT: D 65 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7581 (ttm-80) REVERT: D 125 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8390 (pt0) REVERT: D 248 TYR cc_start: 0.8891 (t80) cc_final: 0.8624 (t80) REVERT: D 304 PHE cc_start: 0.5091 (OUTLIER) cc_final: 0.3786 (t80) REVERT: C 30 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8392 (pm20) REVERT: C 184 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.8177 (m-40) REVERT: C 304 PHE cc_start: 0.5451 (OUTLIER) cc_final: 0.4253 (t80) outliers start: 46 outliers final: 25 residues processed: 157 average time/residue: 0.0985 time to fit residues: 22.8535 Evaluate side-chains 161 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 304 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 75 optimal weight: 0.0980 chunk 125 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 113 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 154 ASN E 62 GLN E 154 ASN B 62 GLN B 154 ASN D 62 GLN D 154 ASN D 251 ASN C 154 ASN C 251 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.130129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.096272 restraints weight = 16089.577| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.75 r_work: 0.3015 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13065 Z= 0.141 Angle : 0.504 7.116 17780 Z= 0.256 Chirality : 0.045 0.127 1955 Planarity : 0.003 0.023 2265 Dihedral : 4.092 19.401 1715 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.54 % Allowed : 19.57 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.22), residues: 1540 helix: 1.46 (0.24), residues: 505 sheet: 1.13 (0.25), residues: 455 loop : -1.88 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 231 TYR 0.012 0.001 TYR D 38 PHE 0.011 0.001 PHE E 228 TRP 0.022 0.001 TRP C 161 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00327 (13065) covalent geometry : angle 0.50350 (17780) hydrogen bonds : bond 0.02904 ( 535) hydrogen bonds : angle 4.49251 ( 1680) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: A 129 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8166 (mt-10) REVERT: A 304 PHE cc_start: 0.5176 (OUTLIER) cc_final: 0.4244 (t80) REVERT: E 30 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8552 (pm20) REVERT: E 230 GLU cc_start: 0.7110 (mp0) cc_final: 0.6655 (pm20) REVERT: E 304 PHE cc_start: 0.5057 (OUTLIER) cc_final: 0.3357 (t80) REVERT: B 30 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: B 82 VAL cc_start: 0.9254 (t) cc_final: 0.9006 (t) REVERT: B 129 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: B 161 TRP cc_start: 0.8595 (m-90) cc_final: 0.8323 (m-10) REVERT: B 304 PHE cc_start: 0.5554 (OUTLIER) cc_final: 0.4300 (t80) REVERT: D 30 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8638 (pm20) REVERT: D 65 ARG cc_start: 0.7903 (mmm-85) cc_final: 0.7574 (ttm-80) REVERT: D 125 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8501 (pt0) REVERT: D 129 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: D 248 TYR cc_start: 0.8930 (t80) cc_final: 0.8637 (t80) REVERT: D 304 PHE cc_start: 0.5033 (OUTLIER) cc_final: 0.3749 (t80) REVERT: C 30 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8413 (pm20) REVERT: C 184 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8153 (m-40) REVERT: C 304 PHE cc_start: 0.5464 (OUTLIER) cc_final: 0.4271 (t80) outliers start: 49 outliers final: 30 residues processed: 165 average time/residue: 0.1007 time to fit residues: 24.3105 Evaluate side-chains 171 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 304 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 154 ASN E 62 GLN E 154 ASN B 62 GLN B 154 ASN D 62 GLN D 154 ASN D 251 ASN C 154 ASN C 251 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.094184 restraints weight = 16111.118| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.70 r_work: 0.2804 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13065 Z= 0.198 Angle : 0.540 7.417 17780 Z= 0.276 Chirality : 0.046 0.130 1955 Planarity : 0.003 0.022 2265 Dihedral : 4.283 20.545 1715 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.68 % Allowed : 19.49 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.22), residues: 1540 helix: 1.39 (0.24), residues: 505 sheet: 1.05 (0.26), residues: 455 loop : -1.87 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 105 TYR 0.012 0.002 TYR B 245 PHE 0.012 0.001 PHE B 208 TRP 0.025 0.002 TRP C 161 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00470 (13065) covalent geometry : angle 0.53997 (17780) hydrogen bonds : bond 0.03157 ( 535) hydrogen bonds : angle 4.62488 ( 1680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.86 seconds wall clock time: 38 minutes 34.88 seconds (2314.88 seconds total)