Starting phenix.real_space_refine on Fri Jun 5 03:05:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30gd_57742/06_2026/30gd_57742.cif Found real_map, /net/cci-nas-00/data/ceres_data/30gd_57742/06_2026/30gd_57742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/30gd_57742/06_2026/30gd_57742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30gd_57742/06_2026/30gd_57742.map" model { file = "/net/cci-nas-00/data/ceres_data/30gd_57742/06_2026/30gd_57742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30gd_57742/06_2026/30gd_57742.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 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 66 5.16 5 C 10690 2.51 5 N 2985 2.21 5 O 3183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16924 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 310} Chain: "F" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 310} Chain: "B" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2929 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 360} Chain breaks: 1 Chain: "A" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2921 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 1 Chain: "C" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2921 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 1 Chain: "D" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2921 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 359} Chain breaks: 1 Time building chain proxies: 4.13, per 1000 atoms: 0.24 Number of scatterers: 16924 At special positions: 0 Unit cell: (82.88, 100.64, 199.8, 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 66 16.00 O 3183 8.00 N 2985 7.00 C 10690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 762.0 milliseconds 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3982 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 27 sheets defined 40.5% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'E' and resid 38 through 50 removed outlier: 3.607A pdb=" N ALA E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 86 removed outlier: 3.530A pdb=" N ILE E 82 " --> pdb=" O VAL E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 103 Processing helix chain 'E' and resid 105 through 128 removed outlier: 3.746A pdb=" N ASP E 115 " --> pdb=" O GLN E 111 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 157 through 174 Processing helix chain 'E' and resid 191 through 195 removed outlier: 3.579A pdb=" N SER E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 206 Processing helix chain 'E' and resid 224 through 239 Processing helix chain 'E' and resid 257 through 269 Processing helix chain 'E' and resid 272 through 274 No H-bonds generated for 'chain 'E' and resid 272 through 274' Processing helix chain 'E' and resid 297 through 303 Processing helix chain 'E' and resid 310 through 320 removed outlier: 3.592A pdb=" N TRP E 320 " --> pdb=" O LYS E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 98 through 103 Processing helix chain 'F' and resid 105 through 114 Processing helix chain 'F' and resid 114 through 128 Processing helix chain 'F' and resid 138 through 140 No H-bonds generated for 'chain 'F' and resid 138 through 140' Processing helix chain 'F' and resid 157 through 174 Processing helix chain 'F' and resid 191 through 195 removed outlier: 3.756A pdb=" N SER F 195 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 206 Processing helix chain 'F' and resid 224 through 241 Processing helix chain 'F' and resid 257 through 269 Processing helix chain 'F' and resid 297 through 303 Processing helix chain 'F' and resid 310 through 320 removed outlier: 4.110A pdb=" N LYS F 316 " --> pdb=" O ARG F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'B' and resid 29 through 49 removed outlier: 3.826A pdb=" N GLN B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 151 through 170 Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.524A pdb=" N LYS B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 289 through 308 removed outlier: 4.240A pdb=" N ALA B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 353 Processing helix chain 'B' and resid 356 through 365 Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.581A pdb=" N ALA B 375 " --> pdb=" O GLN B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'A' and resid 29 through 49 removed outlier: 3.617A pdb=" N CYS A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 95 through 98 Processing helix chain 'A' and resid 151 through 170 removed outlier: 3.514A pdb=" N ASN A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.564A pdb=" N LYS A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.649A pdb=" N GLN A 256 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 289 through 308 removed outlier: 4.050A pdb=" N ALA A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 353 removed outlier: 3.855A pdb=" N GLU A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 365 removed outlier: 3.576A pdb=" N VAL A 361 " --> pdb=" O PRO A 357 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 4.120A pdb=" N ALA A 376 " --> pdb=" O ARG A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'C' and resid 29 through 49 removed outlier: 4.099A pdb=" N GLN C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 95 through 98 Processing helix chain 'C' and resid 151 through 170 Processing helix chain 'C' and resid 214 through 226 removed outlier: 3.513A pdb=" N LYS C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 253 through 257 Processing helix chain 'C' and resid 265 through 270 Processing helix chain 'C' and resid 289 through 308 removed outlier: 3.764A pdb=" N ALA C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 353 Processing helix chain 'C' and resid 356 through 365 Processing helix chain 'C' and resid 371 through 376 removed outlier: 4.133A pdb=" N ALA C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.726A pdb=" N VAL C 389 " --> pdb=" O PRO C 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 49 removed outlier: 3.895A pdb=" N GLN D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 151 through 170 Processing helix chain 'D' and resid 214 through 226 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 253 through 257 removed outlier: 4.058A pdb=" N GLN D 256 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 308 removed outlier: 3.900A pdb=" N ALA D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 353 Processing helix chain 'D' and resid 358 through 365 Processing helix chain 'D' and resid 371 through 376 removed outlier: 4.071A pdb=" N ALA D 376 " --> pdb=" O ARG D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 Processing sheet with id=AA1, first strand: chain 'E' and resid 8 through 13 Processing sheet with id=AA2, first strand: chain 'E' and resid 68 through 69 removed outlier: 8.874A pdb=" N GLU E 68 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY E 57 " --> pdb=" O GLU E 68 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG E 30 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N VAL E 91 " --> pdb=" O ARG E 30 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU E 32 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE E 134 " --> pdb=" O HIS E 92 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL E 179 " --> pdb=" O PHE E 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 185 through 186 Processing sheet with id=AA4, first strand: chain 'E' and resid 211 through 214 Processing sheet with id=AA5, first strand: chain 'F' and resid 8 through 13 Processing sheet with id=AA6, first strand: chain 'F' and resid 68 through 69 removed outlier: 6.881A pdb=" N VAL F 31 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N CYS F 58 " --> pdb=" O VAL F 31 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL F 33 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL F 89 " --> pdb=" O ARG F 30 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 32 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 91 " --> pdb=" O LEU F 32 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE F 134 " --> pdb=" O HIS F 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA F 178 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL F 179 " --> pdb=" O PHE F 248 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 185 through 186 Processing sheet with id=AA8, first strand: chain 'F' and resid 211 through 214 removed outlier: 3.603A pdb=" N ARG F 277 " --> pdb=" O ALA F 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 17 through 25 removed outlier: 4.753A pdb=" N GLN B 208 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ASP B 179 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER B 206 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS B 181 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 204 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN B 183 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR B 202 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR B 185 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL B 200 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN B 187 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N ILE B 241 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N HIS B 201 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N HIS B 243 " --> pdb=" O HIS B 201 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE B 203 " --> pdb=" O HIS B 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 61 removed outlier: 6.356A pdb=" N ILE B 65 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA B 109 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 67 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLU B 111 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY B 69 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N GLN B 113 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE B 71 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.617A pdb=" N PHE B 99 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 136 through 143 removed outlier: 3.673A pdb=" N SER B 329 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 17 through 25 removed outlier: 5.978A pdb=" N ARG A 177 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N HIS A 209 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASP A 179 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL A 207 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS A 181 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE A 205 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN A 183 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE A 203 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A 185 " --> pdb=" O HIS A 201 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 199 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N MET A 189 " --> pdb=" O PRO A 197 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP A 191 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N ILE A 241 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS A 201 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N HIS A 243 " --> pdb=" O HIS A 201 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE A 203 " --> pdb=" O HIS A 243 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 53 through 54 removed outlier: 6.366A pdb=" N ILE A 65 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ALA A 109 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 67 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU A 111 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY A 69 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLN A 113 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A 71 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.521A pdb=" N ASP A 94 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 99 " --> pdb=" O ASP A 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 136 through 143 removed outlier: 3.531A pdb=" N GLY A 136 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 329 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 17 through 25 removed outlier: 3.515A pdb=" N PHE C 18 " --> pdb=" O TYR C 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 17 through 25 removed outlier: 3.515A pdb=" N PHE C 18 " --> pdb=" O TYR C 188 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS C 181 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE C 205 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLN C 183 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE C 203 " --> pdb=" O GLN C 183 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR C 185 " --> pdb=" O HIS C 201 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 199 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 105 through 113 removed outlier: 6.257A pdb=" N ILE C 65 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ALA C 109 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU C 67 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLU C 111 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY C 69 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLN C 113 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 71 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.952A pdb=" N PHE C 99 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 143 Processing sheet with id=AC5, first strand: chain 'D' and resid 17 through 25 removed outlier: 5.958A pdb=" N ARG D 177 " --> pdb=" O HIS D 209 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N HIS D 209 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASP D 179 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL D 207 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS D 181 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE D 205 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN D 183 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE D 203 " --> pdb=" O GLN D 183 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR D 185 " --> pdb=" O HIS D 201 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG D 199 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N MET D 189 " --> pdb=" O PRO D 197 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP D 191 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N ILE D 241 " --> pdb=" O ARG D 199 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N HIS D 201 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N HIS D 243 " --> pdb=" O HIS D 201 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE D 203 " --> pdb=" O HIS D 243 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.383A pdb=" N ILE D 65 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA D 109 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU D 67 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU D 111 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY D 69 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'D' and resid 93 through 94 removed outlier: 3.542A pdb=" N PHE D 99 " --> pdb=" O ASP D 94 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 136 through 143 removed outlier: 3.504A pdb=" N ALA D 142 " --> pdb=" O VAL D 314 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D 314 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER D 329 " --> pdb=" O SER D 319 " (cutoff:3.500A) 733 hydrogen bonds defined for protein. 2013 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4401 1.33 - 1.45: 3054 1.45 - 1.57: 9725 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 17276 Sorted by residual: bond pdb=" N VAL C 195 " pdb=" CA VAL C 195 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.14e-02 7.69e+03 8.92e+00 bond pdb=" CA SER D 304 " pdb=" CB SER D 304 " ideal model delta sigma weight residual 1.529 1.484 0.045 1.55e-02 4.16e+03 8.43e+00 bond pdb=" N LEU D 305 " pdb=" CA LEU D 305 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.00e+00 bond pdb=" N GLN E 233 " pdb=" CA GLN E 233 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.44e+00 bond pdb=" N LEU E 120 " pdb=" CA LEU E 120 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.22e+00 ... (remaining 17271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 22991 2.34 - 4.68: 356 4.68 - 7.03: 36 7.03 - 9.37: 6 9.37 - 11.71: 2 Bond angle restraints: 23391 Sorted by residual: angle pdb=" CA LYS E 161 " pdb=" CB LYS E 161 " pdb=" CG LYS E 161 " ideal model delta sigma weight residual 114.10 123.20 -9.10 2.00e+00 2.50e-01 2.07e+01 angle pdb=" N GLY B 69 " pdb=" CA GLY B 69 " pdb=" C GLY B 69 " ideal model delta sigma weight residual 110.38 115.95 -5.57 1.42e+00 4.96e-01 1.54e+01 angle pdb=" CB MET E 213 " pdb=" CG MET E 213 " pdb=" SD MET E 213 " ideal model delta sigma weight residual 112.70 124.41 -11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CA MET F 239 " pdb=" CB MET F 239 " pdb=" CG MET F 239 " ideal model delta sigma weight residual 114.10 121.54 -7.44 2.00e+00 2.50e-01 1.39e+01 angle pdb=" C GLN E 49 " pdb=" N GLN E 50 " pdb=" CA GLN E 50 " ideal model delta sigma weight residual 121.94 114.90 7.04 2.00e+00 2.50e-01 1.24e+01 ... (remaining 23386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 9282 17.89 - 35.77: 873 35.77 - 53.66: 179 53.66 - 71.54: 41 71.54 - 89.43: 30 Dihedral angle restraints: 10405 sinusoidal: 4200 harmonic: 6205 Sorted by residual: dihedral pdb=" CA PRO F 87 " pdb=" C PRO F 87 " pdb=" N HIS F 88 " pdb=" CA HIS F 88 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET D 64 " pdb=" C MET D 64 " pdb=" N ILE D 65 " pdb=" CA ILE D 65 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA MET E 239 " pdb=" C MET E 239 " pdb=" N LEU E 240 " pdb=" CA LEU E 240 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 10402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1822 0.044 - 0.089: 572 0.089 - 0.133: 177 0.133 - 0.178: 10 0.178 - 0.222: 4 Chirality restraints: 2585 Sorted by residual: chirality pdb=" CG LEU B 137 " pdb=" CB LEU B 137 " pdb=" CD1 LEU B 137 " pdb=" CD2 LEU B 137 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU D 164 " pdb=" CB LEU D 164 " pdb=" CD1 LEU D 164 " pdb=" CD2 LEU D 164 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LEU E 234 " pdb=" N LEU E 234 " pdb=" C LEU E 234 " pdb=" CB LEU E 234 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 2582 not shown) Planarity restraints: 3054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 48 " 0.015 2.00e-02 2.50e+03 1.61e-02 4.54e+00 pdb=" CG PHE E 48 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE E 48 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE E 48 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE E 48 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 48 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 48 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 85 " -0.011 2.00e-02 2.50e+03 1.61e-02 4.53e+00 pdb=" CG PHE F 85 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE F 85 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE F 85 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE F 85 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE F 85 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE F 85 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 26 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO F 27 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO F 27 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 27 " -0.029 5.00e-02 4.00e+02 ... (remaining 3051 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1017 2.72 - 3.27: 17611 3.27 - 3.81: 28823 3.81 - 4.36: 35463 4.36 - 4.90: 59757 Nonbonded interactions: 142671 Sorted by model distance: nonbonded pdb=" N GLU B 211 " pdb=" OE1 GLU B 211 " model vdw 2.175 3.120 nonbonded pdb=" NZ LYS C 303 " pdb=" OE1 GLU C 388 " model vdw 2.208 3.120 nonbonded pdb=" OG1 THR C 21 " pdb=" OG1 THR C 185 " model vdw 2.238 3.040 nonbonded pdb=" O ASN D 352 " pdb=" NZ LYS D 391 " model vdw 2.241 3.120 nonbonded pdb=" OG1 THR B 146 " pdb=" O MET B 150 " model vdw 2.242 3.040 ... (remaining 142666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 13 through 116 or resid 125 through 395)) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.580 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 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 : 0.005 0.075 17276 Z= 0.244 Angle : 0.721 11.712 23391 Z= 0.409 Chirality : 0.047 0.222 2585 Planarity : 0.005 0.053 3054 Dihedral : 15.452 89.428 6423 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.13 % Favored : 96.73 % Rotamer: Outliers : 1.88 % Allowed : 18.53 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.18), residues: 2141 helix: 0.55 (0.18), residues: 722 sheet: 0.36 (0.25), residues: 420 loop : -0.56 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 192 TYR 0.029 0.002 TYR F 259 PHE 0.037 0.002 PHE E 48 TRP 0.013 0.001 TRP F 328 HIS 0.014 0.001 HIS E 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.24 (17276) covalent geometry : angle 0.72121 / 0.41 (23391) hydrogen bonds : bond 0.18228 / 12.92 ( 722) hydrogen bonds : angle 6.53009 / 4.46 ( 2013) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 132 ILE cc_start: 0.6364 (mm) cc_final: 0.5990 (mp) REVERT: E 141 ASP cc_start: 0.8882 (t0) cc_final: 0.8053 (p0) REVERT: E 155 PRO cc_start: 0.6168 (Cg_endo) cc_final: 0.5792 (Cg_exo) REVERT: E 233 GLN cc_start: 0.8387 (pt0) cc_final: 0.8174 (tp-100) REVERT: F 141 ASP cc_start: 0.6831 (OUTLIER) cc_final: 0.6576 (m-30) REVERT: F 213 MET cc_start: 0.5421 (pmm) cc_final: 0.5098 (pmm) REVERT: B 137 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7114 (pp) REVERT: A 343 ARG cc_start: 0.9363 (mmm160) cc_final: 0.8516 (tpm-80) REVERT: C 57 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: C 134 ASP cc_start: 0.8543 (t0) cc_final: 0.8326 (t0) REVERT: D 137 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7994 (pp) outliers start: 34 outliers final: 13 residues processed: 181 average time/residue: 0.4719 time to fit residues: 98.7495 Evaluate side-chains 173 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 346 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS ** E 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS B 339 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 36 GLN D 113 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.153616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.104774 restraints weight = 35838.468| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 4.26 r_work: 0.3326 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17276 Z= 0.222 Angle : 0.632 13.218 23391 Z= 0.333 Chirality : 0.046 0.174 2585 Planarity : 0.004 0.045 3054 Dihedral : 5.659 50.391 2383 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.76 % Favored : 97.10 % Rotamer: Outliers : 3.42 % Allowed : 15.44 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.18), residues: 2141 helix: 0.80 (0.19), residues: 726 sheet: 0.39 (0.26), residues: 398 loop : -0.57 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 18 TYR 0.016 0.001 TYR B 141 PHE 0.032 0.002 PHE E 130 TRP 0.008 0.001 TRP E 53 HIS 0.010 0.001 HIS E 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (17276) covalent geometry : angle 0.63202 / 0.33 (23391) hydrogen bonds : bond 0.04822 / 3.42 ( 722) hydrogen bonds : angle 5.06053 / 3.47 ( 2013) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 177 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 88 HIS cc_start: 0.6404 (m-70) cc_final: 0.6082 (m-70) REVERT: E 141 ASP cc_start: 0.8891 (t0) cc_final: 0.8155 (p0) REVERT: E 155 PRO cc_start: 0.5844 (Cg_endo) cc_final: 0.5467 (Cg_exo) REVERT: E 209 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6677 (pptt) REVERT: F 191 LYS cc_start: 0.8035 (ptpp) cc_final: 0.7465 (ptpp) REVERT: F 213 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5522 (pmm) REVERT: F 317 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 137 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.6623 (pp) REVERT: A 57 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: A 249 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7013 (tpt170) REVERT: C 57 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.7858 (mm-30) REVERT: C 70 GLU cc_start: 0.8249 (mp0) cc_final: 0.7980 (mp0) REVERT: C 134 ASP cc_start: 0.8492 (t0) cc_final: 0.8280 (t0) REVERT: D 189 MET cc_start: 0.8408 (mmm) cc_final: 0.8143 (mpp) REVERT: D 313 ARG cc_start: 0.7436 (mtm180) cc_final: 0.6944 (mtm180) outliers start: 62 outliers final: 25 residues processed: 220 average time/residue: 0.4992 time to fit residues: 125.6467 Evaluate side-chains 178 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 209 LYS Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 346 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 42 optimal weight: 30.0000 chunk 176 optimal weight: 0.9980 chunk 103 optimal weight: 0.0770 chunk 16 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 181 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS ** E 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN B 135 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.154777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.106050 restraints weight = 36422.139| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 4.23 r_work: 0.3334 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17276 Z= 0.161 Angle : 0.593 11.195 23391 Z= 0.309 Chirality : 0.044 0.151 2585 Planarity : 0.004 0.042 3054 Dihedral : 5.363 55.447 2371 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.34 % Rotamer: Outliers : 3.03 % Allowed : 15.83 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 2141 helix: 0.88 (0.19), residues: 726 sheet: 0.40 (0.26), residues: 398 loop : -0.56 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 18 TYR 0.013 0.001 TYR B 141 PHE 0.028 0.001 PHE E 206 TRP 0.010 0.001 TRP E 320 HIS 0.011 0.001 HIS E 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (17276) covalent geometry : angle 0.59264 / 0.31 (23391) hydrogen bonds : bond 0.04216 / 2.98 ( 722) hydrogen bonds : angle 4.76753 / 3.27 ( 2013) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 88 HIS cc_start: 0.6444 (m-70) cc_final: 0.6119 (m-70) REVERT: E 141 ASP cc_start: 0.8876 (t0) cc_final: 0.8137 (p0) REVERT: E 155 PRO cc_start: 0.5920 (Cg_endo) cc_final: 0.5535 (Cg_exo) REVERT: E 188 GLU cc_start: 0.5263 (OUTLIER) cc_final: 0.4688 (pp20) REVERT: E 209 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6741 (pptt) REVERT: F 213 MET cc_start: 0.5979 (OUTLIER) cc_final: 0.5443 (pmm) REVERT: F 317 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7749 (mm-30) REVERT: B 249 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8244 (ttt90) REVERT: A 57 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: A 249 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7031 (tpt170) REVERT: C 57 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: C 70 GLU cc_start: 0.8209 (mp0) cc_final: 0.7941 (mp0) REVERT: D 313 ARG cc_start: 0.7440 (mtm180) cc_final: 0.6835 (mtm180) outliers start: 55 outliers final: 26 residues processed: 208 average time/residue: 0.4762 time to fit residues: 114.4737 Evaluate side-chains 180 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 209 LYS Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 68 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 126 optimal weight: 0.0770 chunk 72 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 50 GLN E 54 HIS ** E 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS F 54 HIS ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN B 339 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.153943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.105825 restraints weight = 35782.458| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 4.16 r_work: 0.3331 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17276 Z= 0.180 Angle : 0.591 13.850 23391 Z= 0.306 Chirality : 0.044 0.150 2585 Planarity : 0.004 0.045 3054 Dihedral : 5.200 53.392 2369 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.82 % Rotamer: Outliers : 3.36 % Allowed : 16.77 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 2141 helix: 0.90 (0.19), residues: 726 sheet: 0.39 (0.26), residues: 397 loop : -0.57 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 18 TYR 0.019 0.001 TYR D 287 PHE 0.030 0.001 PHE E 130 TRP 0.011 0.001 TRP E 320 HIS 0.011 0.001 HIS E 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (17276) covalent geometry : angle 0.59119 / 0.31 (23391) hydrogen bonds : bond 0.04065 / 2.88 ( 722) hydrogen bonds : angle 4.69487 / 3.23 ( 2013) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 166 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 88 HIS cc_start: 0.6390 (m-70) cc_final: 0.6111 (m-70) REVERT: E 141 ASP cc_start: 0.8853 (t0) cc_final: 0.8111 (p0) REVERT: E 155 PRO cc_start: 0.5906 (Cg_endo) cc_final: 0.5530 (Cg_exo) REVERT: E 188 GLU cc_start: 0.5204 (OUTLIER) cc_final: 0.4693 (pp20) REVERT: E 206 PHE cc_start: 0.8744 (m-80) cc_final: 0.8508 (m-80) REVERT: F 182 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7605 (mp) REVERT: F 191 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7456 (ptpp) REVERT: F 213 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.5750 (pmm) REVERT: F 317 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7726 (mm-30) REVERT: A 57 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: A 249 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7050 (tpt170) REVERT: C 57 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.7962 (mm-30) REVERT: C 70 GLU cc_start: 0.8129 (mp0) cc_final: 0.7882 (mp0) REVERT: D 181 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8566 (tttt) REVERT: D 313 ARG cc_start: 0.7474 (mtm180) cc_final: 0.7181 (mtm180) outliers start: 61 outliers final: 28 residues processed: 211 average time/residue: 0.4628 time to fit residues: 113.3084 Evaluate side-chains 185 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 126 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 196 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS E 76 ASN ** E 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 GLN B 126 ASN B 339 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.154767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.106398 restraints weight = 35822.221| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 4.11 r_work: 0.3354 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17276 Z= 0.155 Angle : 0.579 12.610 23391 Z= 0.299 Chirality : 0.044 0.162 2585 Planarity : 0.004 0.044 3054 Dihedral : 5.090 49.226 2368 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.01 % Rotamer: Outliers : 3.42 % Allowed : 17.32 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2141 helix: 0.96 (0.19), residues: 726 sheet: 0.41 (0.26), residues: 397 loop : -0.55 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 18 TYR 0.018 0.001 TYR D 287 PHE 0.025 0.001 PHE E 48 TRP 0.009 0.001 TRP E 320 HIS 0.012 0.001 HIS E 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (17276) covalent geometry : angle 0.57940 / 0.30 (23391) hydrogen bonds : bond 0.03880 / 2.75 ( 722) hydrogen bonds : angle 4.57837 / 3.15 ( 2013) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 164 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 141 ASP cc_start: 0.8857 (t0) cc_final: 0.8089 (p0) REVERT: E 155 PRO cc_start: 0.6131 (Cg_endo) cc_final: 0.5770 (Cg_exo) REVERT: E 261 MET cc_start: 0.7915 (mtt) cc_final: 0.7454 (mtt) REVERT: F 85 PHE cc_start: 0.7150 (t80) cc_final: 0.6780 (t80) REVERT: F 182 ILE cc_start: 0.7789 (mm) cc_final: 0.7576 (mp) REVERT: F 213 MET cc_start: 0.6449 (OUTLIER) cc_final: 0.5812 (pmm) REVERT: F 317 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7733 (mm-30) REVERT: B 22 SER cc_start: 0.8476 (OUTLIER) cc_final: 0.8055 (p) REVERT: B 88 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9200 (ttmm) REVERT: B 287 TYR cc_start: 0.8913 (p90) cc_final: 0.8630 (p90) REVERT: A 57 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: A 249 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7046 (tpt170) REVERT: A 343 ARG cc_start: 0.9158 (mmm160) cc_final: 0.8252 (tpm-80) REVERT: C 57 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.7987 (mm-30) REVERT: D 181 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8623 (tttt) REVERT: D 313 ARG cc_start: 0.7497 (mtm180) cc_final: 0.7144 (mmm160) outliers start: 62 outliers final: 27 residues processed: 211 average time/residue: 0.4479 time to fit residues: 110.0916 Evaluate side-chains 183 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 40.0000 chunk 74 optimal weight: 4.9990 chunk 207 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** E 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.153696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.104511 restraints weight = 35886.893| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 4.41 r_work: 0.3315 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 17276 Z= 0.220 Angle : 0.630 16.071 23391 Z= 0.324 Chirality : 0.046 0.240 2585 Planarity : 0.004 0.044 3054 Dihedral : 5.226 45.210 2368 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 3.20 % Allowed : 18.26 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.18), residues: 2141 helix: 0.85 (0.19), residues: 734 sheet: 0.31 (0.26), residues: 397 loop : -0.64 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 18 TYR 0.017 0.001 TYR B 141 PHE 0.033 0.002 PHE E 130 TRP 0.014 0.001 TRP E 320 HIS 0.014 0.001 HIS F 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (17276) covalent geometry : angle 0.63041 / 0.32 (23391) hydrogen bonds : bond 0.04190 / 2.97 ( 722) hydrogen bonds : angle 4.70509 / 3.23 ( 2013) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 152 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 141 ASP cc_start: 0.8869 (t0) cc_final: 0.8161 (p0) REVERT: E 155 PRO cc_start: 0.5832 (Cg_endo) cc_final: 0.5454 (Cg_exo) REVERT: F 182 ILE cc_start: 0.7783 (mm) cc_final: 0.7512 (mm) REVERT: F 213 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.6304 (pmm) REVERT: F 317 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7776 (mm-30) REVERT: B 22 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8067 (p) REVERT: A 57 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: A 249 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7035 (tpt170) REVERT: C 57 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8090 (mm-30) REVERT: D 181 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8528 (tttt) REVERT: D 360 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7761 (mp) outliers start: 58 outliers final: 32 residues processed: 194 average time/residue: 0.4429 time to fit residues: 99.7679 Evaluate side-chains 182 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 173 ASN Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 163 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 60 optimal weight: 30.0000 chunk 147 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 198 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN E 174 ASN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.156299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.107813 restraints weight = 36000.142| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 4.22 r_work: 0.3366 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 17276 Z= 0.112 Angle : 0.591 13.519 23391 Z= 0.300 Chirality : 0.044 0.370 2585 Planarity : 0.004 0.075 3054 Dihedral : 4.997 44.835 2368 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 2.65 % Allowed : 19.08 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 2141 helix: 0.98 (0.19), residues: 734 sheet: 0.42 (0.26), residues: 397 loop : -0.48 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 18 TYR 0.019 0.001 TYR D 287 PHE 0.038 0.001 PHE E 206 TRP 0.015 0.001 TRP E 320 HIS 0.009 0.001 HIS E 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (17276) covalent geometry : angle 0.59064 / 0.30 (23391) hydrogen bonds : bond 0.03538 / 2.51 ( 722) hydrogen bonds : angle 4.49650 / 3.09 ( 2013) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 123 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7913 (tp30) REVERT: E 141 ASP cc_start: 0.8862 (t0) cc_final: 0.8161 (p0) REVERT: E 155 PRO cc_start: 0.6079 (Cg_endo) cc_final: 0.5708 (Cg_exo) REVERT: E 261 MET cc_start: 0.8039 (mtt) cc_final: 0.7508 (mtt) REVERT: F 182 ILE cc_start: 0.7706 (mm) cc_final: 0.7459 (mm) REVERT: F 213 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6049 (pmm) REVERT: F 215 HIS cc_start: 0.5306 (m170) cc_final: 0.4938 (m-70) REVERT: F 317 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7772 (mm-30) REVERT: B 88 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9149 (ttmm) REVERT: B 137 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7466 (pt) REVERT: B 287 TYR cc_start: 0.8934 (p90) cc_final: 0.8635 (p90) REVERT: B 352 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7527 (m-40) REVERT: A 249 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7066 (tpt170) REVERT: C 57 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.7686 (mm-30) REVERT: D 39 ASP cc_start: 0.9012 (m-30) cc_final: 0.8766 (m-30) REVERT: D 313 ARG cc_start: 0.7298 (mmm160) cc_final: 0.6090 (mmm-85) REVERT: D 360 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7651 (pp) outliers start: 48 outliers final: 22 residues processed: 192 average time/residue: 0.4857 time to fit residues: 107.2532 Evaluate side-chains 176 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 39 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 174 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 212 optimal weight: 0.7980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN B 135 GLN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.153421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.104658 restraints weight = 36460.405| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 4.21 r_work: 0.3318 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17276 Z= 0.225 Angle : 0.651 13.861 23391 Z= 0.332 Chirality : 0.046 0.351 2585 Planarity : 0.004 0.056 3054 Dihedral : 5.183 44.299 2368 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 3.14 % Allowed : 18.81 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.18), residues: 2141 helix: 0.90 (0.19), residues: 734 sheet: 0.33 (0.26), residues: 397 loop : -0.57 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 343 TYR 0.019 0.001 TYR B 141 PHE 0.033 0.002 PHE E 130 TRP 0.020 0.001 TRP E 320 HIS 0.009 0.001 HIS E 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (17276) covalent geometry : angle 0.65083 / 0.33 (23391) hydrogen bonds : bond 0.04109 / 2.92 ( 722) hydrogen bonds : angle 4.68061 / 3.23 ( 2013) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 135 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 123 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7970 (tp30) REVERT: E 155 PRO cc_start: 0.6123 (Cg_endo) cc_final: 0.5895 (Cg_exo) REVERT: E 261 MET cc_start: 0.7931 (mtt) cc_final: 0.7534 (mtt) REVERT: F 182 ILE cc_start: 0.7755 (mm) cc_final: 0.7504 (mm) REVERT: F 213 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6029 (pmm) REVERT: F 215 HIS cc_start: 0.5511 (m170) cc_final: 0.5026 (m-70) REVERT: F 317 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7741 (mm-30) REVERT: B 88 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9207 (ttmt) REVERT: B 287 TYR cc_start: 0.8929 (p90) cc_final: 0.8646 (p90) REVERT: B 352 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7481 (m-40) REVERT: A 57 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: A 249 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7090 (tpt170) REVERT: C 57 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8049 (mm-30) REVERT: D 313 ARG cc_start: 0.7378 (mmm160) cc_final: 0.6162 (mmm-85) REVERT: D 360 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7739 (mp) outliers start: 57 outliers final: 29 residues processed: 185 average time/residue: 0.4534 time to fit residues: 97.3625 Evaluate side-chains 173 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 173 ASN Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 182 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 0.0070 chunk 206 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 64 optimal weight: 7.9990 overall best weight: 0.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.157598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.109061 restraints weight = 35880.449| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 4.16 r_work: 0.3379 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17276 Z= 0.110 Angle : 0.621 14.518 23391 Z= 0.311 Chirality : 0.045 0.337 2585 Planarity : 0.004 0.047 3054 Dihedral : 4.981 46.051 2368 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.20 % Rotamer: Outliers : 1.99 % Allowed : 20.08 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 2141 helix: 1.02 (0.19), residues: 734 sheet: 0.35 (0.25), residues: 414 loop : -0.43 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 18 TYR 0.019 0.001 TYR D 287 PHE 0.034 0.001 PHE E 206 TRP 0.018 0.001 TRP E 320 HIS 0.008 0.001 HIS E 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (17276) covalent geometry : angle 0.62114 / 0.31 (23391) hydrogen bonds : bond 0.03423 / 2.42 ( 722) hydrogen bonds : angle 4.50714 / 3.10 ( 2013) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 123 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: E 155 PRO cc_start: 0.6298 (Cg_endo) cc_final: 0.6054 (Cg_exo) REVERT: E 261 MET cc_start: 0.7951 (mtt) cc_final: 0.7269 (mtt) REVERT: E 307 GLN cc_start: 0.5039 (tp-100) cc_final: 0.4195 (mp10) REVERT: F 182 ILE cc_start: 0.7634 (mm) cc_final: 0.7373 (mm) REVERT: F 213 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6232 (pmm) REVERT: F 215 HIS cc_start: 0.5614 (m170) cc_final: 0.5120 (m-70) REVERT: F 256 MET cc_start: 0.7675 (tmm) cc_final: 0.7358 (tmm) REVERT: F 261 MET cc_start: 0.9192 (ptp) cc_final: 0.8778 (mpp) REVERT: F 317 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 81 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8728 (tptp) REVERT: B 88 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9151 (ttmm) REVERT: B 287 TYR cc_start: 0.8917 (p90) cc_final: 0.8563 (p90) REVERT: B 352 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7441 (m-40) REVERT: A 249 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7113 (tpt170) REVERT: C 57 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: C 85 GLU cc_start: 0.9131 (tp30) cc_final: 0.8908 (tp30) REVERT: C 250 PHE cc_start: 0.6781 (t80) cc_final: 0.6092 (t80) REVERT: D 39 ASP cc_start: 0.8985 (m-30) cc_final: 0.8730 (m-30) REVERT: D 313 ARG cc_start: 0.7302 (mmm160) cc_final: 0.6154 (mmm-85) REVERT: D 360 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7664 (pp) outliers start: 36 outliers final: 19 residues processed: 181 average time/residue: 0.4576 time to fit residues: 96.1936 Evaluate side-chains 168 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 173 ASN Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 198 optimal weight: 0.1980 chunk 187 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.154625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.105692 restraints weight = 36307.874| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 4.22 r_work: 0.3328 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17276 Z= 0.217 Angle : 0.664 14.429 23391 Z= 0.338 Chirality : 0.046 0.347 2585 Planarity : 0.004 0.045 3054 Dihedral : 5.091 52.401 2366 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 2.04 % Allowed : 20.46 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.18), residues: 2141 helix: 0.95 (0.19), residues: 731 sheet: 0.35 (0.26), residues: 398 loop : -0.54 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 343 TYR 0.019 0.001 TYR B 141 PHE 0.033 0.002 PHE E 130 TRP 0.018 0.001 TRP E 320 HIS 0.008 0.001 HIS E 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (17276) covalent geometry : angle 0.66447 / 0.34 (23391) hydrogen bonds : bond 0.04079 / 2.89 ( 722) hydrogen bonds : angle 4.67542 / 3.22 ( 2013) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 123 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8023 (tp30) REVERT: E 155 PRO cc_start: 0.6130 (Cg_endo) cc_final: 0.5697 (Cg_exo) REVERT: E 261 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7310 (mtt) REVERT: F 182 ILE cc_start: 0.7658 (mm) cc_final: 0.7400 (mm) REVERT: F 213 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6485 (pmm) REVERT: F 317 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7761 (mm-30) REVERT: B 88 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9171 (ttmt) REVERT: B 138 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7171 (mmt) REVERT: B 287 TYR cc_start: 0.8933 (p90) cc_final: 0.8626 (p90) REVERT: B 352 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7565 (m-40) REVERT: A 249 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7055 (tpt170) REVERT: C 57 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.7997 (mm-30) REVERT: C 85 GLU cc_start: 0.9146 (tp30) cc_final: 0.8927 (tp30) REVERT: C 250 PHE cc_start: 0.6956 (t80) cc_final: 0.6319 (t80) REVERT: D 360 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7770 (mp) outliers start: 37 outliers final: 19 residues processed: 171 average time/residue: 0.4751 time to fit residues: 93.8680 Evaluate side-chains 165 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 173 ASN Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 170 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 210 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 GLN ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.155276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.107292 restraints weight = 36125.154| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 4.12 r_work: 0.3370 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17276 Z= 0.146 Angle : 0.644 14.525 23391 Z= 0.326 Chirality : 0.046 0.347 2585 Planarity : 0.004 0.085 3054 Dihedral : 5.053 56.957 2366 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.15 % Allowed : 20.35 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 2141 helix: 0.92 (0.19), residues: 731 sheet: 0.39 (0.26), residues: 398 loop : -0.49 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A 343 TYR 0.017 0.001 TYR D 287 PHE 0.040 0.001 PHE E 48 TRP 0.021 0.001 TRP E 320 HIS 0.008 0.001 HIS E 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (17276) covalent geometry : angle 0.64367 / 0.33 (23391) hydrogen bonds : bond 0.03721 / 2.61 ( 722) hydrogen bonds : angle 4.63194 / 3.19 ( 2013) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6647.68 seconds wall clock time: 114 minutes 5.57 seconds (6845.57 seconds total)