Starting phenix.real_space_refine on Wed Jul 30 15:39:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twv_41672/07_2025/8twv_41672.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twv_41672/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8twv_41672/07_2025/8twv_41672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twv_41672/07_2025/8twv_41672.map" model { file = "/net/cci-nas-00/data/ceres_data/8twv_41672/07_2025/8twv_41672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twv_41672/07_2025/8twv_41672.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, E, D Time building chain proxies: 5.48, per 1000 atoms: 0.43 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: 2.97 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.67 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: 3.88 Time building geometry restraints manager: 3.35 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 27.750 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- 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 : 11.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.001 TRP A 206 HIS 0.006 0.001 HIS A 285 PHE 0.040 0.002 PHE B 208 TYR 0.009 0.001 TYR B 38 ARG 0.010 0.001 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.12954 ( 535) hydrogen bonds : angle 6.72788 ( 1680) covalent geometry : bond 0.00409 (13065) covalent geometry : angle 0.72721 (17780) *********************** 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 : 1.443 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: 0.2517 time to fit residues: 53.0576 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 : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 0.0270 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.7642 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.153938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116755 restraints weight = 15397.572| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.95 r_work: 0.2842 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13065 Z= 0.178 Angle : 0.549 7.273 17780 Z= 0.280 Chirality : 0.046 0.133 1955 Planarity : 0.003 0.022 2265 Dihedral : 4.293 14.832 1715 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.45 % Allowed : 18.84 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1540 helix: 0.54 (0.24), residues: 505 sheet: 1.06 (0.25), residues: 480 loop : -1.92 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 206 HIS 0.004 0.001 HIS A 285 PHE 0.011 0.001 PHE A 208 TYR 0.011 0.001 TYR D 33 ARG 0.003 0.000 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 535) hydrogen bonds : angle 5.05561 ( 1680) covalent geometry : bond 0.00405 (13065) covalent geometry : angle 0.54948 (17780) *********************** 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 158 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: E 34 LYS cc_start: 0.8920 (mttp) cc_final: 0.8704 (mttm) REVERT: E 185 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8514 (pt0) REVERT: E 231 ARG cc_start: 0.7136 (mtm180) cc_final: 0.6891 (mtt-85) REVERT: B 86 ASP cc_start: 0.8848 (t70) cc_final: 0.8353 (t70) REVERT: B 151 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.7895 (m110) REVERT: B 225 LEU cc_start: 0.8805 (mp) cc_final: 0.8520 (mp) REVERT: B 231 ARG cc_start: 0.7041 (mtm180) cc_final: 0.6202 (mpt-90) REVERT: D 30 GLU cc_start: 0.8925 (pm20) cc_final: 0.8263 (pm20) REVERT: D 151 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.7574 (t0) REVERT: D 231 ARG cc_start: 0.7152 (mtm180) cc_final: 0.6829 (mtt-85) REVERT: D 264 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8251 (mt0) REVERT: C 151 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8234 (t0) REVERT: C 185 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8581 (pt0) outliers start: 34 outliers final: 16 residues processed: 158 average time/residue: 0.2396 time to fit residues: 55.9348 Evaluate side-chains 138 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 E residue 29 LEU 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 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 9 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.158007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.120052 restraints weight = 15465.338| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.03 r_work: 0.2885 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13065 Z= 0.109 Angle : 0.472 6.345 17780 Z= 0.240 Chirality : 0.044 0.128 1955 Planarity : 0.003 0.021 2265 Dihedral : 4.047 16.885 1715 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.37 % Allowed : 20.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1540 helix: 1.06 (0.24), residues: 505 sheet: 1.04 (0.25), residues: 475 loop : -1.84 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.004 0.001 HIS A 285 PHE 0.008 0.001 PHE A 208 TYR 0.010 0.001 TYR D 38 ARG 0.003 0.000 ARG D 231 Details of bonding type rmsd hydrogen bonds : bond 0.02872 ( 535) hydrogen bonds : angle 4.66324 ( 1680) covalent geometry : bond 0.00238 (13065) covalent geometry : angle 0.47229 (17780) *********************** 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 142 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ASP cc_start: 0.8895 (t70) cc_final: 0.8660 (t70) REVERT: A 264 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8144 (mt0) REVERT: E 129 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: E 264 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: B 86 ASP cc_start: 0.8944 (t70) cc_final: 0.8574 (t70) REVERT: D 231 ARG cc_start: 0.7214 (mtm180) cc_final: 0.6573 (mtt180) outliers start: 19 outliers final: 12 residues processed: 140 average time/residue: 0.2560 time to fit residues: 52.8927 Evaluate side-chains 126 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 81 VAL Chi-restraints excluded: chain A residue 191 ILE 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 129 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D 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 5 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 110 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.132466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.099068 restraints weight = 15821.058| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.68 r_work: 0.2888 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13065 Z= 0.116 Angle : 0.467 7.040 17780 Z= 0.237 Chirality : 0.044 0.126 1955 Planarity : 0.002 0.020 2265 Dihedral : 3.995 17.187 1715 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.60 % Allowed : 19.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1540 helix: 1.34 (0.24), residues: 505 sheet: 1.08 (0.25), residues: 475 loop : -1.72 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.004 0.001 HIS A 285 PHE 0.006 0.001 PHE C 228 TYR 0.010 0.001 TYR D 38 ARG 0.002 0.000 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.02809 ( 535) hydrogen bonds : angle 4.53087 ( 1680) covalent geometry : bond 0.00257 (13065) covalent geometry : angle 0.46683 (17780) *********************** 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 164 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8451 (pt0) REVERT: A 264 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8260 (mt0) REVERT: E 129 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: E 185 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8433 (pt0) REVERT: E 231 ARG cc_start: 0.7622 (mtt180) cc_final: 0.7213 (mtt-85) REVERT: E 264 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7784 (mt0) REVERT: B 36 ASP cc_start: 0.8788 (t70) cc_final: 0.8548 (t0) REVERT: B 86 ASP cc_start: 0.8862 (t70) cc_final: 0.8537 (t70) REVERT: B 129 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8027 (mt-10) REVERT: D 230 GLU cc_start: 0.7158 (mp0) cc_final: 0.6643 (pm20) REVERT: D 231 ARG cc_start: 0.7280 (mtm180) cc_final: 0.7043 (mtm180) REVERT: C 129 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8128 (mt-10) REVERT: C 239 MET cc_start: 0.8522 (ttt) cc_final: 0.8310 (ttt) outliers start: 36 outliers final: 21 residues processed: 163 average time/residue: 0.2466 time to fit residues: 59.2318 Evaluate side-chains 148 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 185 GLN 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 129 GLU Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 264 GLN 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 39 ILE Chi-restraints excluded: chain D residue 60 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 C residue 60 ASN Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 138 optimal weight: 0.4980 chunk 146 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 124 optimal weight: 0.0060 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 298 GLN E 298 GLN B 298 GLN C 251 ASN C 298 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.132244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.098234 restraints weight = 15920.699| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.77 r_work: 0.3167 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13065 Z= 0.120 Angle : 0.468 6.865 17780 Z= 0.237 Chirality : 0.044 0.127 1955 Planarity : 0.002 0.021 2265 Dihedral : 3.971 16.578 1715 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.10 % Allowed : 18.70 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1540 helix: 1.46 (0.24), residues: 505 sheet: 1.12 (0.25), residues: 475 loop : -1.68 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.004 0.001 HIS D 285 PHE 0.006 0.001 PHE C 228 TYR 0.010 0.001 TYR D 38 ARG 0.002 0.000 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.02787 ( 535) hydrogen bonds : angle 4.47957 ( 1680) covalent geometry : bond 0.00272 (13065) covalent geometry : angle 0.46791 (17780) *********************** 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 167 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: A 151 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7914 (m110) REVERT: A 264 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8441 (mt0) REVERT: E 129 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: E 185 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8408 (pt0) REVERT: E 231 ARG cc_start: 0.7546 (mtt180) cc_final: 0.6954 (mtt-85) REVERT: E 264 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7886 (mt0) REVERT: B 86 ASP cc_start: 0.8749 (t70) cc_final: 0.8451 (t70) REVERT: B 129 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: D 248 TYR cc_start: 0.8875 (t80) cc_final: 0.8665 (t80) REVERT: C 129 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: C 239 MET cc_start: 0.8589 (ttt) cc_final: 0.8355 (ttt) outliers start: 43 outliers final: 25 residues processed: 161 average time/residue: 0.2950 time to fit residues: 70.2136 Evaluate side-chains 152 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 151 ASN 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 129 GLU 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 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 185 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 60 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 C residue 60 ASN Chi-restraints excluded: chain C residue 129 GLU 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 61 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 0.0570 chunk 51 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 298 GLN C 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.161432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.125093 restraints weight = 15725.619| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.08 r_work: 0.3140 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13065 Z= 0.121 Angle : 0.476 6.943 17780 Z= 0.241 Chirality : 0.044 0.143 1955 Planarity : 0.002 0.021 2265 Dihedral : 3.962 19.217 1715 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.39 % Allowed : 18.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1540 helix: 1.52 (0.24), residues: 505 sheet: 1.11 (0.25), residues: 475 loop : -1.72 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 206 HIS 0.004 0.001 HIS A 285 PHE 0.010 0.001 PHE A 142 TYR 0.010 0.001 TYR D 38 ARG 0.002 0.000 ARG D 231 Details of bonding type rmsd hydrogen bonds : bond 0.02783 ( 535) hydrogen bonds : angle 4.45864 ( 1680) covalent geometry : bond 0.00275 (13065) covalent geometry : angle 0.47585 (17780) *********************** 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 171 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: A 151 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7876 (m110) REVERT: A 264 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8403 (mt0) REVERT: E 86 ASP cc_start: 0.8616 (t70) cc_final: 0.8362 (t70) REVERT: E 129 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: E 185 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8378 (pt0) REVERT: E 264 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7824 (mt0) REVERT: B 82 VAL cc_start: 0.9209 (t) cc_final: 0.8976 (t) REVERT: B 129 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: D 65 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7397 (ttm-80) REVERT: D 231 ARG cc_start: 0.7385 (mtm180) cc_final: 0.7129 (mtm-85) REVERT: D 248 TYR cc_start: 0.8840 (t80) cc_final: 0.8636 (t80) REVERT: C 129 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7931 (mt-10) REVERT: C 239 MET cc_start: 0.8512 (ttt) cc_final: 0.8245 (ttt) outliers start: 47 outliers final: 28 residues processed: 163 average time/residue: 0.3214 time to fit residues: 83.0531 Evaluate side-chains 156 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 2.181 ------------------------------------------------------------------------------- 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 151 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 29 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 129 GLU 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 B residue 29 LEU 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 39 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 145 ILE 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 C residue 60 ASN Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 145 ILE 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 84 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 61 optimal weight: 0.0670 chunk 121 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.1520 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.131595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.098076 restraints weight = 15960.693| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.69 r_work: 0.2872 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13065 Z= 0.127 Angle : 0.477 7.319 17780 Z= 0.242 Chirality : 0.044 0.126 1955 Planarity : 0.002 0.021 2265 Dihedral : 3.936 19.554 1715 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.96 % Allowed : 19.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1540 helix: 1.54 (0.24), residues: 505 sheet: 1.09 (0.25), residues: 475 loop : -1.76 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 161 HIS 0.004 0.001 HIS A 285 PHE 0.009 0.001 PHE B 142 TYR 0.009 0.001 TYR D 38 ARG 0.002 0.000 ARG D 231 Details of bonding type rmsd hydrogen bonds : bond 0.02797 ( 535) hydrogen bonds : angle 4.45931 ( 1680) covalent geometry : bond 0.00289 (13065) covalent geometry : angle 0.47665 (17780) *********************** 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 165 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8036 (mmm-85) cc_final: 0.7824 (tpp80) REVERT: A 113 ASP cc_start: 0.8232 (m-30) cc_final: 0.7723 (p0) REVERT: A 129 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: A 151 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.8003 (m110) REVERT: A 264 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8482 (mt0) REVERT: E 86 ASP cc_start: 0.8758 (t70) cc_final: 0.8443 (t70) REVERT: E 185 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8478 (pt0) REVERT: E 264 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7829 (mt0) REVERT: B 82 VAL cc_start: 0.9173 (t) cc_final: 0.8942 (t) REVERT: B 129 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: B 184 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7773 (m-40) REVERT: D 30 GLU cc_start: 0.8860 (pm20) cc_final: 0.8598 (pm20) REVERT: D 65 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7451 (ttm-80) REVERT: D 231 ARG cc_start: 0.7342 (mtm180) cc_final: 0.7078 (mtm-85) REVERT: D 248 TYR cc_start: 0.8936 (t80) cc_final: 0.8721 (t80) REVERT: C 129 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: C 151 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8113 (m110) REVERT: C 239 MET cc_start: 0.8544 (ttt) cc_final: 0.8327 (ttt) outliers start: 41 outliers final: 28 residues processed: 160 average time/residue: 0.2692 time to fit residues: 63.2606 Evaluate side-chains 157 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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 151 ASN 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 E residue 29 LEU Chi-restraints excluded: chain E residue 39 ILE 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 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 184 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 39 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 157 ILE 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 C residue 60 ASN Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.128221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.094684 restraints weight = 16319.901| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.69 r_work: 0.2815 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13065 Z= 0.199 Angle : 0.531 7.317 17780 Z= 0.271 Chirality : 0.046 0.131 1955 Planarity : 0.003 0.019 2265 Dihedral : 4.210 19.145 1715 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.54 % Allowed : 18.84 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.22), residues: 1540 helix: 1.49 (0.24), residues: 505 sheet: 1.16 (0.25), residues: 470 loop : -1.80 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 161 HIS 0.003 0.001 HIS A 285 PHE 0.028 0.001 PHE D 228 TYR 0.011 0.002 TYR E 204 ARG 0.001 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 535) hydrogen bonds : angle 4.66049 ( 1680) covalent geometry : bond 0.00471 (13065) covalent geometry : angle 0.53099 (17780) *********************** 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 179 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 130 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8212 (mmm-85) cc_final: 0.8000 (tpp80) REVERT: A 129 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8260 (mt-10) REVERT: A 151 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.8002 (m110) REVERT: A 264 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8575 (mt0) REVERT: A 304 PHE cc_start: 0.5114 (OUTLIER) cc_final: 0.4287 (t80) REVERT: E 86 ASP cc_start: 0.8788 (t70) cc_final: 0.8462 (t70) REVERT: E 185 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8506 (pt0) REVERT: E 264 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8541 (mt0) REVERT: E 304 PHE cc_start: 0.5309 (OUTLIER) cc_final: 0.3700 (t80) REVERT: B 129 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8238 (mt-10) REVERT: B 184 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.8025 (m-40) REVERT: B 304 PHE cc_start: 0.5535 (OUTLIER) cc_final: 0.4327 (t80) REVERT: D 30 GLU cc_start: 0.8954 (pm20) cc_final: 0.8709 (pm20) REVERT: D 65 ARG cc_start: 0.7988 (mmm-85) cc_final: 0.7608 (ttm-80) REVERT: D 231 ARG cc_start: 0.7605 (mtm180) cc_final: 0.7320 (mtm-85) REVERT: D 304 PHE cc_start: 0.4987 (OUTLIER) cc_final: 0.3696 (t80) REVERT: C 30 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: C 151 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8241 (m-40) REVERT: C 304 PHE cc_start: 0.5371 (OUTLIER) cc_final: 0.4214 (t80) outliers start: 49 outliers final: 31 residues processed: 172 average time/residue: 0.2442 time to fit residues: 61.3654 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 : 1.456 ------------------------------------------------------------------------------- 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 151 ASN 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 253 LEU 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 39 ILE 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 304 PHE 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 184 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 B residue 304 PHE 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 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 39 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 151 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 124 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 99 optimal weight: 0.0010 chunk 128 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 154 ASN B 154 ASN D 154 ASN C 154 ASN C 251 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.132243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.098561 restraints weight = 15984.448| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.72 r_work: 0.3173 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13065 Z= 0.106 Angle : 0.474 7.153 17780 Z= 0.240 Chirality : 0.044 0.128 1955 Planarity : 0.002 0.021 2265 Dihedral : 3.910 18.671 1715 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.10 % Allowed : 19.64 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1540 helix: 1.53 (0.24), residues: 505 sheet: 1.31 (0.26), residues: 445 loop : -1.89 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 161 HIS 0.004 0.001 HIS A 285 PHE 0.030 0.001 PHE D 228 TYR 0.010 0.001 TYR C 38 ARG 0.002 0.000 ARG D 231 Details of bonding type rmsd hydrogen bonds : bond 0.02726 ( 535) hydrogen bonds : angle 4.44880 ( 1680) covalent geometry : bond 0.00238 (13065) covalent geometry : angle 0.47398 (17780) *********************** 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 175 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7906 (tpp80) REVERT: A 113 ASP cc_start: 0.8203 (m-30) cc_final: 0.7828 (p0) REVERT: A 129 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: A 151 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.7982 (m110) REVERT: A 264 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8430 (mt0) REVERT: A 304 PHE cc_start: 0.5097 (OUTLIER) cc_final: 0.4201 (t80) REVERT: E 86 ASP cc_start: 0.8711 (t70) cc_final: 0.8458 (t70) REVERT: E 185 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8422 (pt0) REVERT: B 30 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8395 (mp0) REVERT: B 82 VAL cc_start: 0.9235 (t) cc_final: 0.9015 (t) REVERT: B 129 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: B 184 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7928 (m-40) REVERT: D 65 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7649 (ttm-80) REVERT: D 231 ARG cc_start: 0.7587 (mtm180) cc_final: 0.7275 (mtm-85) REVERT: C 30 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8467 (pm20) REVERT: C 151 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8091 (m110) REVERT: C 187 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7787 (mt-10) outliers start: 43 outliers final: 28 residues processed: 164 average time/residue: 0.2573 time to fit residues: 62.1696 Evaluate side-chains 165 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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 151 ASN 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 253 LEU 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 39 ILE 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 B residue 29 LEU Chi-restraints excluded: chain B residue 30 GLU 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 184 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 157 ILE 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 C residue 30 GLU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 69 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN E 154 ASN B 62 GLN B 154 ASN C 154 ASN C 251 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.131206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.097710 restraints weight = 16013.150| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.70 r_work: 0.3027 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13065 Z= 0.128 Angle : 0.487 7.309 17780 Z= 0.247 Chirality : 0.044 0.126 1955 Planarity : 0.002 0.021 2265 Dihedral : 3.945 17.952 1715 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1540 helix: 1.53 (0.24), residues: 505 sheet: 1.30 (0.26), residues: 450 loop : -1.90 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 161 HIS 0.003 0.001 HIS A 285 PHE 0.030 0.001 PHE D 228 TYR 0.011 0.001 TYR D 38 ARG 0.001 0.000 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.02827 ( 535) hydrogen bonds : angle 4.45270 ( 1680) covalent geometry : bond 0.00296 (13065) covalent geometry : angle 0.48688 (17780) ********************** 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: 46 poor density : 130 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7970 (tpp80) REVERT: A 113 ASP cc_start: 0.8217 (m-30) cc_final: 0.7830 (p0) REVERT: A 129 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: A 151 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7969 (m110) REVERT: A 264 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8412 (mt0) REVERT: A 304 PHE cc_start: 0.5149 (OUTLIER) cc_final: 0.4219 (t80) REVERT: E 86 ASP cc_start: 0.8721 (t70) cc_final: 0.8469 (t70) REVERT: E 185 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8437 (pt0) REVERT: E 304 PHE cc_start: 0.4982 (OUTLIER) cc_final: 0.3375 (t80) REVERT: B 30 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8340 (mp0) REVERT: B 82 VAL cc_start: 0.9194 (t) cc_final: 0.8973 (t) REVERT: B 129 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: B 184 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7912 (m-40) REVERT: D 65 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.7616 (ttt180) REVERT: D 231 ARG cc_start: 0.7612 (mtm180) cc_final: 0.7315 (mtm-85) REVERT: D 304 PHE cc_start: 0.4953 (OUTLIER) cc_final: 0.3647 (t80) REVERT: C 30 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8440 (pm20) REVERT: C 151 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8114 (m110) REVERT: C 187 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7767 (mt-10) outliers start: 46 outliers final: 31 residues processed: 164 average time/residue: 0.2897 time to fit residues: 71.3972 Evaluate side-chains 170 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 151 ASN 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 253 LEU 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 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 154 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 304 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 30 GLU 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 184 ASN Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 157 ILE 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 151 ASN Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN E 154 ASN B 62 GLN B 154 ASN D 154 ASN C 154 ASN C 251 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.094439 restraints weight = 16060.698| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.69 r_work: 0.2814 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13065 Z= 0.202 Angle : 0.536 7.426 17780 Z= 0.275 Chirality : 0.046 0.129 1955 Planarity : 0.003 0.018 2265 Dihedral : 4.181 19.298 1715 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.61 % Allowed : 19.71 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1540 helix: 1.47 (0.24), residues: 505 sheet: 1.23 (0.26), residues: 450 loop : -1.87 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 161 HIS 0.003 0.001 HIS A 285 PHE 0.031 0.001 PHE D 228 TYR 0.012 0.002 TYR C 204 ARG 0.001 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 535) hydrogen bonds : angle 4.63663 ( 1680) covalent geometry : bond 0.00478 (13065) covalent geometry : angle 0.53605 (17780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6316.52 seconds wall clock time: 115 minutes 14.08 seconds (6914.08 seconds total)