Starting phenix.real_space_refine on Wed Feb 4 02:23:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vsd_65301/02_2026/9vsd_65301.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vsd_65301/02_2026/9vsd_65301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vsd_65301/02_2026/9vsd_65301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vsd_65301/02_2026/9vsd_65301.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vsd_65301/02_2026/9vsd_65301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vsd_65301/02_2026/9vsd_65301.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.040 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 39 5.16 5 C 5508 2.51 5 N 1293 2.21 5 O 1434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8274 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2758 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 10, 'TRANS': 350} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 1.49, per 1000 atoms: 0.18 Number of scatterers: 8274 At special positions: 0 Unit cell: (116.6, 122.1, 69.3, 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 39 16.00 O 1434 8.00 N 1293 7.00 C 5508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 298.0 milliseconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 0 sheets defined 76.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.886A pdb=" N GLN A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.678A pdb=" N PHE A 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Proline residue: A 80 - end of helix Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.899A pdb=" N ALA A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 removed outlier: 3.706A pdb=" N ILE A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 101 " --> pdb=" O TRP A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 removed outlier: 4.256A pdb=" N GLU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 114 through 119' Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.952A pdb=" N LEU A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.646A pdb=" N ILE A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 152 removed outlier: 3.774A pdb=" N ASN A 152 " --> pdb=" O LEU A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 152' Processing helix chain 'A' and resid 153 through 171 removed outlier: 3.782A pdb=" N VAL A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 182 removed outlier: 3.503A pdb=" N THR A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.654A pdb=" N LEU A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Proline residue: A 213 - end of helix removed outlier: 4.028A pdb=" N GLY A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 5.552A pdb=" N ASN A 221 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU A 223 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.513A pdb=" N LEU A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.508A pdb=" N SER A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 236 " --> pdb=" O MET A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 236' Processing helix chain 'A' and resid 236 through 257 removed outlier: 3.588A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TYR A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.930A pdb=" N ILE A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.938A pdb=" N LYS A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.601A pdb=" N ILE A 331 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 346 removed outlier: 4.145A pdb=" N PHE A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.695A pdb=" N ALA A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.571A pdb=" N THR A 372 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 406 removed outlier: 3.787A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 433 removed outlier: 3.605A pdb=" N VAL A 418 " --> pdb=" O MET A 414 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP A 433 " --> pdb=" O CYS A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.886A pdb=" N GLN B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 removed outlier: 3.678A pdb=" N PHE B 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Proline residue: B 80 - end of helix Processing helix chain 'B' and resid 81 through 92 removed outlier: 3.899A pdb=" N ALA B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 removed outlier: 3.706A pdb=" N ILE B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 101 " --> pdb=" O TRP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 removed outlier: 4.256A pdb=" N GLU B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 114 through 119' Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.953A pdb=" N LEU B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA B 134 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.646A pdb=" N ILE B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 152 removed outlier: 3.774A pdb=" N ASN B 152 " --> pdb=" O LEU B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 152' Processing helix chain 'B' and resid 153 through 171 removed outlier: 3.782A pdb=" N VAL B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 182 removed outlier: 3.504A pdb=" N THR B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 196 Processing helix chain 'B' and resid 197 through 217 removed outlier: 3.654A pdb=" N LEU B 202 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 204 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Proline residue: B 213 - end of helix removed outlier: 4.027A pdb=" N GLY B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 223 removed outlier: 5.552A pdb=" N ASN B 221 " --> pdb=" O TYR B 218 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU B 223 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 removed outlier: 3.513A pdb=" N LEU B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 removed outlier: 3.508A pdb=" N SER B 235 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 236 " --> pdb=" O MET B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 231 through 236' Processing helix chain 'B' and resid 236 through 257 removed outlier: 3.588A pdb=" N SER B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE B 242 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR B 248 " --> pdb=" O MET B 244 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TYR B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 293 through 302 removed outlier: 4.931A pdb=" N ILE B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 Processing helix chain 'B' and resid 311 through 316 removed outlier: 3.938A pdb=" N LYS B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 328 through 332 removed outlier: 3.601A pdb=" N ILE B 331 " --> pdb=" O LEU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 346 removed outlier: 4.145A pdb=" N PHE B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 367 removed outlier: 3.695A pdb=" N ALA B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN B 363 " --> pdb=" O GLY B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 380 removed outlier: 3.571A pdb=" N THR B 372 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE B 374 " --> pdb=" O PRO B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 removed outlier: 3.787A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 433 removed outlier: 3.606A pdb=" N VAL B 418 " --> pdb=" O MET B 414 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 426 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP B 433 " --> pdb=" O CYS B 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.886A pdb=" N GLN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.679A pdb=" N PHE C 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Proline residue: C 80 - end of helix Processing helix chain 'C' and resid 81 through 92 removed outlier: 3.899A pdb=" N ALA C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 102 removed outlier: 3.706A pdb=" N ILE C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 101 " --> pdb=" O TRP C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 119 removed outlier: 4.256A pdb=" N GLU C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN C 119 " --> pdb=" O PHE C 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 114 through 119' Processing helix chain 'C' and resid 125 through 137 removed outlier: 3.952A pdb=" N LEU C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA C 134 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 148 removed outlier: 3.646A pdb=" N ILE C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 152 removed outlier: 3.773A pdb=" N ASN C 152 " --> pdb=" O LEU C 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 149 through 152' Processing helix chain 'C' and resid 153 through 171 removed outlier: 3.782A pdb=" N VAL C 157 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 161 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 169 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 182 removed outlier: 3.503A pdb=" N THR C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 196 Processing helix chain 'C' and resid 197 through 217 removed outlier: 3.653A pdb=" N LEU C 202 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 204 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS C 210 " --> pdb=" O GLY C 206 " (cutoff:3.500A) Proline residue: C 213 - end of helix removed outlier: 4.028A pdb=" N GLY C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 223 removed outlier: 5.552A pdb=" N ASN C 221 " --> pdb=" O TYR C 218 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU C 223 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.513A pdb=" N LEU C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.508A pdb=" N SER C 235 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 236 " --> pdb=" O MET C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 236' Processing helix chain 'C' and resid 236 through 257 removed outlier: 3.589A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TYR C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 290 through 292 No H-bonds generated for 'chain 'C' and resid 290 through 292' Processing helix chain 'C' and resid 293 through 302 removed outlier: 4.930A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 308 Processing helix chain 'C' and resid 311 through 316 removed outlier: 3.939A pdb=" N LYS C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 325 Processing helix chain 'C' and resid 328 through 332 removed outlier: 3.601A pdb=" N ILE C 331 " --> pdb=" O LEU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 346 removed outlier: 4.145A pdb=" N PHE C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 367 removed outlier: 3.695A pdb=" N ALA C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN C 363 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 380 removed outlier: 3.571A pdb=" N THR C 372 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE C 374 " --> pdb=" O PRO C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 406 removed outlier: 3.786A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY C 393 " --> pdb=" O PRO C 389 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 400 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 433 removed outlier: 3.606A pdb=" N VAL C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE C 426 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP C 433 " --> pdb=" O CYS C 429 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 954 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: 0.98 Time building geometry restraints manager: 0.85 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: 2143 1.33 - 1.45: 1521 1.45 - 1.57: 4727 1.57 - 1.69: 0 1.69 - 1.80: 54 Bond restraints: 8445 Sorted by residual: bond pdb=" C LEU C 329 " pdb=" N PRO C 330 " ideal model delta sigma weight residual 1.339 1.419 -0.080 3.40e-02 8.65e+02 5.51e+00 bond pdb=" C LEU A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 1.339 1.419 -0.080 3.40e-02 8.65e+02 5.50e+00 bond pdb=" C LEU B 329 " pdb=" N PRO B 330 " ideal model delta sigma weight residual 1.339 1.419 -0.080 3.40e-02 8.65e+02 5.49e+00 bond pdb=" CB PRO A 370 " pdb=" CG PRO A 370 " ideal model delta sigma weight residual 1.492 1.387 0.105 5.00e-02 4.00e+02 4.43e+00 bond pdb=" CB PRO B 370 " pdb=" CG PRO B 370 " ideal model delta sigma weight residual 1.492 1.387 0.105 5.00e-02 4.00e+02 4.38e+00 ... (remaining 8440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 10339 1.72 - 3.43: 906 3.43 - 5.15: 175 5.15 - 6.87: 55 6.87 - 8.58: 27 Bond angle restraints: 11502 Sorted by residual: angle pdb=" N GLN C 95 " pdb=" CA GLN C 95 " pdb=" C GLN C 95 " ideal model delta sigma weight residual 113.57 119.45 -5.88 1.38e+00 5.25e-01 1.82e+01 angle pdb=" N GLN A 95 " pdb=" CA GLN A 95 " pdb=" C GLN A 95 " ideal model delta sigma weight residual 113.57 119.42 -5.85 1.38e+00 5.25e-01 1.80e+01 angle pdb=" N GLN B 95 " pdb=" CA GLN B 95 " pdb=" C GLN B 95 " ideal model delta sigma weight residual 113.57 119.41 -5.84 1.38e+00 5.25e-01 1.79e+01 angle pdb=" N GLY C 137 " pdb=" CA GLY C 137 " pdb=" C GLY C 137 " ideal model delta sigma weight residual 114.66 109.74 4.92 1.24e+00 6.50e-01 1.57e+01 angle pdb=" N GLY A 137 " pdb=" CA GLY A 137 " pdb=" C GLY A 137 " ideal model delta sigma weight residual 114.66 109.76 4.90 1.24e+00 6.50e-01 1.56e+01 ... (remaining 11497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.16: 4180 10.16 - 20.32: 611 20.32 - 30.48: 81 30.48 - 40.64: 18 40.64 - 50.80: 6 Dihedral angle restraints: 4896 sinusoidal: 1800 harmonic: 3096 Sorted by residual: dihedral pdb=" CA MET A 295 " pdb=" C MET A 295 " pdb=" N THR A 296 " pdb=" CA THR A 296 " ideal model delta harmonic sigma weight residual 180.00 152.67 27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA MET B 295 " pdb=" C MET B 295 " pdb=" N THR B 296 " pdb=" CA THR B 296 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA MET C 295 " pdb=" C MET C 295 " pdb=" N THR C 296 " pdb=" CA THR C 296 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 4893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 765 0.047 - 0.095: 525 0.095 - 0.142: 127 0.142 - 0.190: 14 0.190 - 0.237: 3 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CA GLN B 95 " pdb=" N GLN B 95 " pdb=" C GLN B 95 " pdb=" CB GLN B 95 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA GLN C 95 " pdb=" N GLN C 95 " pdb=" C GLN C 95 " pdb=" CB GLN C 95 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA GLN A 95 " pdb=" N GLN A 95 " pdb=" C GLN A 95 " pdb=" CB GLN A 95 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1431 not shown) Planarity restraints: 1389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 329 " -0.047 5.00e-02 4.00e+02 7.36e-02 8.66e+00 pdb=" N PRO B 330 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 329 " 0.047 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO C 330 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 329 " -0.047 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO A 330 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.041 5.00e-02 4.00e+02 ... (remaining 1386 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2597 2.81 - 3.33: 7089 3.33 - 3.85: 12699 3.85 - 4.38: 15452 4.38 - 4.90: 26149 Nonbonded interactions: 63986 Sorted by model distance: nonbonded pdb=" OG SER A 314 " pdb=" O LEU A 319 " model vdw 2.286 3.040 nonbonded pdb=" OG SER C 314 " pdb=" O LEU C 319 " model vdw 2.286 3.040 nonbonded pdb=" OG SER B 314 " pdb=" O LEU B 319 " model vdw 2.287 3.040 nonbonded pdb=" O SER A 398 " pdb=" OG1 THR A 402 " model vdw 2.288 3.040 nonbonded pdb=" O SER C 398 " pdb=" OG1 THR C 402 " model vdw 2.288 3.040 ... (remaining 63981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 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 : 0.013 0.105 8445 Z= 0.503 Angle : 1.175 8.584 11502 Z= 0.602 Chirality : 0.060 0.237 1434 Planarity : 0.008 0.074 1389 Dihedral : 9.633 50.805 2904 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.35 (0.13), residues: 1071 helix: -4.89 (0.06), residues: 822 sheet: None (None), residues: 0 loop : -3.53 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 238 TYR 0.033 0.004 TYR A 159 PHE 0.022 0.003 PHE B 346 TRP 0.041 0.005 TRP B 377 HIS 0.007 0.003 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.01250 ( 8445) covalent geometry : angle 1.17508 (11502) hydrogen bonds : bond 0.33436 ( 330) hydrogen bonds : angle 10.55611 ( 954) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.8054 (m-80) cc_final: 0.6767 (t80) REVERT: A 141 GLU cc_start: 0.7600 (mp0) cc_final: 0.7275 (mp0) REVERT: A 176 SER cc_start: 0.8207 (m) cc_final: 0.7917 (p) REVERT: A 234 LEU cc_start: 0.8851 (tp) cc_final: 0.8614 (tt) REVERT: A 316 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7568 (tptp) REVERT: B 141 GLU cc_start: 0.7720 (mp0) cc_final: 0.7477 (mp0) REVERT: B 176 SER cc_start: 0.8285 (m) cc_final: 0.7955 (p) REVERT: B 193 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7688 (ttt180) REVERT: B 230 SER cc_start: 0.9246 (t) cc_final: 0.9012 (p) REVERT: B 234 LEU cc_start: 0.8740 (tp) cc_final: 0.8451 (tt) REVERT: B 257 TRP cc_start: 0.8440 (t60) cc_final: 0.8235 (t-100) REVERT: B 316 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7541 (tptm) REVERT: B 325 SER cc_start: 0.9182 (m) cc_final: 0.8912 (p) REVERT: C 141 GLU cc_start: 0.7612 (mp0) cc_final: 0.7347 (mp0) REVERT: C 176 SER cc_start: 0.8513 (m) cc_final: 0.8214 (p) REVERT: C 194 LYS cc_start: 0.8876 (mttt) cc_final: 0.8580 (mmmt) REVERT: C 312 GLU cc_start: 0.8082 (tt0) cc_final: 0.7831 (mt-10) REVERT: C 316 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7726 (tptp) REVERT: C 325 SER cc_start: 0.9012 (m) cc_final: 0.8803 (p) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0873 time to fit residues: 22.6841 Evaluate side-chains 133 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.0000 chunk 97 optimal weight: 0.0050 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 382 ASN B 119 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN C 189 GLN C 334 ASN C 382 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.154737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122243 restraints weight = 11122.588| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.19 r_work: 0.3176 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8445 Z= 0.124 Angle : 0.613 9.207 11502 Z= 0.319 Chirality : 0.040 0.142 1434 Planarity : 0.005 0.046 1389 Dihedral : 5.886 19.499 1125 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.22 % Allowed : 6.33 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.68 (0.18), residues: 1071 helix: -3.51 (0.12), residues: 825 sheet: None (None), residues: 0 loop : -3.71 (0.33), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 112 TYR 0.016 0.002 TYR C 413 PHE 0.014 0.001 PHE C 178 TRP 0.020 0.001 TRP C 377 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8445) covalent geometry : angle 0.61350 (11502) hydrogen bonds : bond 0.04863 ( 330) hydrogen bonds : angle 4.92494 ( 954) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8181 (mp0) cc_final: 0.7937 (mp0) REVERT: A 142 LEU cc_start: 0.9045 (tp) cc_final: 0.8662 (tt) REVERT: A 193 ARG cc_start: 0.7419 (ttt180) cc_final: 0.7198 (ttt180) REVERT: A 283 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6468 (pt) REVERT: A 292 LEU cc_start: 0.7252 (tt) cc_final: 0.6882 (tt) REVERT: B 194 LYS cc_start: 0.9068 (mttm) cc_final: 0.8718 (mmmt) REVERT: B 230 SER cc_start: 0.9373 (t) cc_final: 0.9059 (p) REVERT: B 231 ASP cc_start: 0.8825 (m-30) cc_final: 0.8221 (t0) REVERT: B 255 GLN cc_start: 0.8183 (tt0) cc_final: 0.7626 (tt0) REVERT: B 283 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6536 (pt) REVERT: B 316 LYS cc_start: 0.7928 (mmtt) cc_final: 0.7443 (tptm) REVERT: C 194 LYS cc_start: 0.9049 (mttt) cc_final: 0.8722 (mmmt) REVERT: C 231 ASP cc_start: 0.8841 (m-30) cc_final: 0.8129 (t0) REVERT: C 283 ILE cc_start: 0.6835 (OUTLIER) cc_final: 0.6357 (pt) REVERT: C 316 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7781 (tptp) outliers start: 20 outliers final: 6 residues processed: 171 average time/residue: 0.0862 time to fit residues: 20.0803 Evaluate side-chains 137 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 411 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 0.0050 chunk 90 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN C 255 GLN C 382 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.152472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.120995 restraints weight = 11212.182| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.16 r_work: 0.3343 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8445 Z= 0.154 Angle : 0.605 8.105 11502 Z= 0.309 Chirality : 0.041 0.138 1434 Planarity : 0.004 0.044 1389 Dihedral : 5.398 17.929 1125 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.78 % Allowed : 7.33 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.49 (0.21), residues: 1071 helix: -2.60 (0.15), residues: 810 sheet: None (None), residues: 0 loop : -3.52 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 238 TYR 0.015 0.002 TYR B 159 PHE 0.016 0.001 PHE A 178 TRP 0.018 0.002 TRP C 377 HIS 0.005 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8445) covalent geometry : angle 0.60505 (11502) hydrogen bonds : bond 0.04257 ( 330) hydrogen bonds : angle 4.34208 ( 954) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.8996 (tp) cc_final: 0.8680 (tt) REVERT: A 194 LYS cc_start: 0.9019 (mttp) cc_final: 0.8717 (mmtt) REVERT: A 329 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8376 (mp) REVERT: B 147 LEU cc_start: 0.8398 (mm) cc_final: 0.8196 (mm) REVERT: B 194 LYS cc_start: 0.9091 (mttm) cc_final: 0.8798 (mmmt) REVERT: B 230 SER cc_start: 0.9359 (t) cc_final: 0.9091 (p) REVERT: B 231 ASP cc_start: 0.8719 (m-30) cc_final: 0.8225 (t0) REVERT: B 255 GLN cc_start: 0.8299 (tt0) cc_final: 0.7772 (tt0) REVERT: B 295 MET cc_start: 0.7740 (mmm) cc_final: 0.7473 (mmp) REVERT: B 311 GLU cc_start: 0.8215 (pm20) cc_final: 0.7639 (pm20) REVERT: B 316 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7595 (tptm) REVERT: C 147 LEU cc_start: 0.8583 (mm) cc_final: 0.8330 (mm) REVERT: C 194 LYS cc_start: 0.9049 (mttt) cc_final: 0.8731 (mmmt) REVERT: C 231 ASP cc_start: 0.8753 (m-30) cc_final: 0.8103 (t0) REVERT: C 283 ILE cc_start: 0.6808 (OUTLIER) cc_final: 0.6256 (pt) REVERT: C 316 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7835 (tptp) outliers start: 34 outliers final: 19 residues processed: 171 average time/residue: 0.0824 time to fit residues: 19.4204 Evaluate side-chains 157 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 432 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 0.0770 chunk 71 optimal weight: 0.0270 chunk 40 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.156217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124219 restraints weight = 11251.681| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.19 r_work: 0.3409 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8445 Z= 0.110 Angle : 0.548 7.280 11502 Z= 0.278 Chirality : 0.039 0.142 1434 Planarity : 0.003 0.037 1389 Dihedral : 4.718 16.273 1125 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.67 % Allowed : 8.56 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.23), residues: 1071 helix: -1.94 (0.16), residues: 828 sheet: None (None), residues: 0 loop : -3.36 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.011 0.001 TYR A 413 PHE 0.013 0.001 PHE C 178 TRP 0.018 0.001 TRP C 257 HIS 0.003 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8445) covalent geometry : angle 0.54846 (11502) hydrogen bonds : bond 0.03096 ( 330) hydrogen bonds : angle 3.79904 ( 954) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7550 (ttt180) cc_final: 0.6258 (ttt180) REVERT: A 194 LYS cc_start: 0.8950 (mttp) cc_final: 0.8482 (mmtt) REVERT: A 231 ASP cc_start: 0.8729 (m-30) cc_final: 0.8172 (t0) REVERT: A 283 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6284 (pt) REVERT: A 292 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6549 (tt) REVERT: A 329 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 407 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7367 (tm-30) REVERT: B 147 LEU cc_start: 0.8463 (mm) cc_final: 0.8225 (mm) REVERT: B 189 GLN cc_start: 0.7702 (mp10) cc_final: 0.7404 (mp10) REVERT: B 194 LYS cc_start: 0.8993 (mttm) cc_final: 0.8642 (mmmt) REVERT: B 230 SER cc_start: 0.9343 (t) cc_final: 0.9082 (p) REVERT: B 231 ASP cc_start: 0.8629 (m-30) cc_final: 0.8214 (t0) REVERT: B 255 GLN cc_start: 0.8186 (tt0) cc_final: 0.7594 (tt0) REVERT: B 311 GLU cc_start: 0.8186 (pm20) cc_final: 0.7959 (pm20) REVERT: B 316 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7557 (tptm) REVERT: B 407 GLN cc_start: 0.7652 (pt0) cc_final: 0.7005 (tm-30) REVERT: C 147 LEU cc_start: 0.8530 (mm) cc_final: 0.8306 (mm) REVERT: C 194 LYS cc_start: 0.8921 (mttt) cc_final: 0.8668 (mmmt) REVERT: C 231 ASP cc_start: 0.8604 (m-30) cc_final: 0.8079 (t0) REVERT: C 297 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6857 (tt) REVERT: C 316 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7833 (tptp) REVERT: C 408 ASP cc_start: 0.7532 (p0) cc_final: 0.7295 (p0) outliers start: 24 outliers final: 16 residues processed: 166 average time/residue: 0.0841 time to fit residues: 19.1546 Evaluate side-chains 159 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 411 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 0.3980 chunk 107 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.152911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.120934 restraints weight = 11306.327| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.18 r_work: 0.3358 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8445 Z= 0.149 Angle : 0.584 7.682 11502 Z= 0.293 Chirality : 0.040 0.136 1434 Planarity : 0.004 0.042 1389 Dihedral : 4.792 16.941 1125 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.56 % Allowed : 9.33 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.24), residues: 1071 helix: -1.61 (0.17), residues: 831 sheet: None (None), residues: 0 loop : -3.30 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 193 TYR 0.011 0.001 TYR C 251 PHE 0.021 0.001 PHE A 115 TRP 0.014 0.001 TRP C 257 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8445) covalent geometry : angle 0.58431 (11502) hydrogen bonds : bond 0.03580 ( 330) hydrogen bonds : angle 3.87582 ( 954) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 LYS cc_start: 0.9013 (mttp) cc_final: 0.8566 (mmtt) REVERT: A 231 ASP cc_start: 0.8710 (m-30) cc_final: 0.8186 (t0) REVERT: A 329 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8397 (mp) REVERT: A 407 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7259 (tm-30) REVERT: B 147 LEU cc_start: 0.8648 (mm) cc_final: 0.8374 (mm) REVERT: B 194 LYS cc_start: 0.9015 (mttm) cc_final: 0.8686 (mmmt) REVERT: B 230 SER cc_start: 0.9365 (t) cc_final: 0.9089 (p) REVERT: B 231 ASP cc_start: 0.8669 (m-30) cc_final: 0.8270 (t0) REVERT: B 255 GLN cc_start: 0.8327 (tt0) cc_final: 0.7656 (tt0) REVERT: B 311 GLU cc_start: 0.8179 (pm20) cc_final: 0.7948 (pm20) REVERT: B 316 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7625 (tptm) REVERT: B 407 GLN cc_start: 0.7651 (pt0) cc_final: 0.7190 (tm-30) REVERT: C 194 LYS cc_start: 0.9002 (mttt) cc_final: 0.8710 (mmmt) REVERT: C 231 ASP cc_start: 0.8657 (m-30) cc_final: 0.8123 (t0) REVERT: C 283 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6325 (pt) REVERT: C 297 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6952 (tt) REVERT: C 311 GLU cc_start: 0.8175 (pm20) cc_final: 0.7728 (pm20) REVERT: C 316 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7946 (tptp) REVERT: C 408 ASP cc_start: 0.7632 (p0) cc_final: 0.7410 (p0) outliers start: 23 outliers final: 14 residues processed: 156 average time/residue: 0.0805 time to fit residues: 16.9574 Evaluate side-chains 150 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 411 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 58 optimal weight: 0.0070 chunk 80 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122188 restraints weight = 11208.675| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.21 r_work: 0.3344 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8445 Z= 0.122 Angle : 0.553 6.946 11502 Z= 0.278 Chirality : 0.040 0.139 1434 Planarity : 0.003 0.037 1389 Dihedral : 4.525 15.755 1125 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.89 % Allowed : 9.78 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.25), residues: 1071 helix: -1.25 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -3.20 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 193 TYR 0.009 0.001 TYR A 413 PHE 0.022 0.001 PHE A 115 TRP 0.017 0.001 TRP C 257 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8445) covalent geometry : angle 0.55287 (11502) hydrogen bonds : bond 0.03187 ( 330) hydrogen bonds : angle 3.71327 ( 954) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.220 Fit side-chains REVERT: A 194 LYS cc_start: 0.9006 (mttp) cc_final: 0.8547 (mmtt) REVERT: A 231 ASP cc_start: 0.8702 (m-30) cc_final: 0.8248 (t0) REVERT: A 329 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8352 (mp) REVERT: B 67 GLN cc_start: 0.5643 (tt0) cc_final: 0.5420 (tt0) REVERT: B 102 SER cc_start: 0.8504 (m) cc_final: 0.8133 (t) REVERT: B 147 LEU cc_start: 0.8676 (mm) cc_final: 0.8404 (mm) REVERT: B 194 LYS cc_start: 0.9007 (mttm) cc_final: 0.8614 (mmmt) REVERT: B 230 SER cc_start: 0.9357 (t) cc_final: 0.9077 (p) REVERT: B 231 ASP cc_start: 0.8637 (m-30) cc_final: 0.8274 (t0) REVERT: B 255 GLN cc_start: 0.8309 (tt0) cc_final: 0.7612 (tt0) REVERT: B 311 GLU cc_start: 0.8231 (pm20) cc_final: 0.8019 (pm20) REVERT: B 316 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7670 (tptm) REVERT: B 407 GLN cc_start: 0.7567 (pt0) cc_final: 0.6975 (tm-30) REVERT: C 102 SER cc_start: 0.8581 (m) cc_final: 0.8158 (t) REVERT: C 187 ARG cc_start: 0.8029 (mtm180) cc_final: 0.7619 (mtm180) REVERT: C 194 LYS cc_start: 0.9007 (mttt) cc_final: 0.8745 (mmmt) REVERT: C 231 ASP cc_start: 0.8640 (m-30) cc_final: 0.8082 (t0) REVERT: C 297 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6955 (tt) REVERT: C 311 GLU cc_start: 0.8238 (pm20) cc_final: 0.7788 (pm20) REVERT: C 316 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7920 (tptp) REVERT: C 408 ASP cc_start: 0.7542 (p0) cc_final: 0.7250 (p0) outliers start: 26 outliers final: 17 residues processed: 157 average time/residue: 0.0969 time to fit residues: 20.1447 Evaluate side-chains 149 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 411 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 80 optimal weight: 0.0670 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 0.0070 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.155685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123765 restraints weight = 11227.277| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.16 r_work: 0.3399 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8445 Z= 0.109 Angle : 0.540 6.702 11502 Z= 0.273 Chirality : 0.039 0.141 1434 Planarity : 0.003 0.037 1389 Dihedral : 4.304 14.799 1125 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.67 % Allowed : 10.89 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.25), residues: 1071 helix: -0.98 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -3.06 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 238 TYR 0.008 0.001 TYR A 413 PHE 0.022 0.001 PHE A 115 TRP 0.016 0.001 TRP C 257 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8445) covalent geometry : angle 0.53971 (11502) hydrogen bonds : bond 0.02966 ( 330) hydrogen bonds : angle 3.59260 ( 954) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.243 Fit side-chains REVERT: A 102 SER cc_start: 0.8346 (m) cc_final: 0.8081 (t) REVERT: A 194 LYS cc_start: 0.9056 (mttp) cc_final: 0.8620 (mmtt) REVERT: A 231 ASP cc_start: 0.8645 (m-30) cc_final: 0.8182 (t0) REVERT: A 255 GLN cc_start: 0.8013 (tt0) cc_final: 0.7715 (tt0) REVERT: A 329 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8341 (mp) REVERT: A 407 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8004 (tp40) REVERT: B 67 GLN cc_start: 0.5653 (tt0) cc_final: 0.5425 (tt0) REVERT: B 102 SER cc_start: 0.8509 (m) cc_final: 0.8196 (t) REVERT: B 147 LEU cc_start: 0.8650 (mm) cc_final: 0.8396 (mm) REVERT: B 194 LYS cc_start: 0.8998 (mttm) cc_final: 0.8666 (mmmt) REVERT: B 230 SER cc_start: 0.9372 (t) cc_final: 0.9068 (p) REVERT: B 231 ASP cc_start: 0.8552 (m-30) cc_final: 0.8254 (t0) REVERT: B 255 GLN cc_start: 0.8275 (tt0) cc_final: 0.7591 (tt0) REVERT: B 311 GLU cc_start: 0.8203 (pm20) cc_final: 0.8000 (pm20) REVERT: B 316 LYS cc_start: 0.8023 (mmtt) cc_final: 0.7681 (tptm) REVERT: B 407 GLN cc_start: 0.7572 (pt0) cc_final: 0.7095 (tm-30) REVERT: C 102 SER cc_start: 0.8604 (m) cc_final: 0.8267 (t) REVERT: C 187 ARG cc_start: 0.8105 (mtm180) cc_final: 0.7674 (mtm110) REVERT: C 231 ASP cc_start: 0.8594 (m-30) cc_final: 0.8023 (t0) REVERT: C 297 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6994 (tt) REVERT: C 311 GLU cc_start: 0.8162 (pm20) cc_final: 0.7700 (pm20) REVERT: C 316 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7950 (tptp) REVERT: C 408 ASP cc_start: 0.7374 (p0) cc_final: 0.7154 (p0) outliers start: 24 outliers final: 19 residues processed: 160 average time/residue: 0.0867 time to fit residues: 18.7023 Evaluate side-chains 153 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 435 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122658 restraints weight = 11164.904| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.10 r_work: 0.3384 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8445 Z= 0.126 Angle : 0.560 7.292 11502 Z= 0.281 Chirality : 0.040 0.135 1434 Planarity : 0.003 0.036 1389 Dihedral : 4.314 14.808 1125 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.67 % Allowed : 11.44 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.26), residues: 1071 helix: -0.87 (0.19), residues: 819 sheet: None (None), residues: 0 loop : -3.05 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 238 TYR 0.010 0.001 TYR C 251 PHE 0.024 0.001 PHE A 115 TRP 0.018 0.001 TRP B 377 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8445) covalent geometry : angle 0.55988 (11502) hydrogen bonds : bond 0.03224 ( 330) hydrogen bonds : angle 3.65594 ( 954) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.247 Fit side-chains REVERT: A 102 SER cc_start: 0.8329 (m) cc_final: 0.8066 (t) REVERT: A 231 ASP cc_start: 0.8598 (m-30) cc_final: 0.8172 (t0) REVERT: A 255 GLN cc_start: 0.7990 (tt0) cc_final: 0.7746 (tt0) REVERT: A 329 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8328 (mp) REVERT: A 407 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8061 (tp40) REVERT: B 102 SER cc_start: 0.8442 (m) cc_final: 0.8142 (t) REVERT: B 147 LEU cc_start: 0.8751 (mm) cc_final: 0.8458 (mm) REVERT: B 175 THR cc_start: 0.8739 (m) cc_final: 0.8298 (p) REVERT: B 194 LYS cc_start: 0.9035 (mttm) cc_final: 0.8670 (mmmt) REVERT: B 230 SER cc_start: 0.9295 (t) cc_final: 0.9017 (p) REVERT: B 231 ASP cc_start: 0.8518 (m-30) cc_final: 0.8216 (t0) REVERT: B 255 GLN cc_start: 0.8348 (tt0) cc_final: 0.7631 (tt0) REVERT: B 316 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7761 (tptm) REVERT: B 407 GLN cc_start: 0.7678 (pt0) cc_final: 0.7160 (tm-30) REVERT: C 102 SER cc_start: 0.8606 (m) cc_final: 0.8276 (t) REVERT: C 187 ARG cc_start: 0.8059 (mtm180) cc_final: 0.7635 (mtm110) REVERT: C 231 ASP cc_start: 0.8565 (m-30) cc_final: 0.8003 (t0) REVERT: C 297 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7012 (tt) REVERT: C 311 GLU cc_start: 0.8144 (pm20) cc_final: 0.7674 (pm20) REVERT: C 316 LYS cc_start: 0.8324 (mmtt) cc_final: 0.8021 (tptp) outliers start: 24 outliers final: 20 residues processed: 152 average time/residue: 0.1006 time to fit residues: 20.2828 Evaluate side-chains 154 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 435 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 0.7980 chunk 75 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122747 restraints weight = 11228.148| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.11 r_work: 0.3367 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8445 Z= 0.129 Angle : 0.569 8.672 11502 Z= 0.285 Chirality : 0.040 0.151 1434 Planarity : 0.003 0.036 1389 Dihedral : 4.289 14.940 1125 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.33 % Allowed : 11.78 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.26), residues: 1071 helix: -0.79 (0.19), residues: 819 sheet: None (None), residues: 0 loop : -3.07 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 238 TYR 0.010 0.001 TYR C 251 PHE 0.024 0.001 PHE A 115 TRP 0.018 0.001 TRP B 377 HIS 0.004 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8445) covalent geometry : angle 0.56928 (11502) hydrogen bonds : bond 0.03239 ( 330) hydrogen bonds : angle 3.68628 ( 954) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.332 Fit side-chains REVERT: A 102 SER cc_start: 0.8282 (m) cc_final: 0.8077 (t) REVERT: A 231 ASP cc_start: 0.8658 (m-30) cc_final: 0.8260 (t0) REVERT: A 329 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 102 SER cc_start: 0.8458 (m) cc_final: 0.8181 (t) REVERT: B 147 LEU cc_start: 0.8755 (mm) cc_final: 0.8476 (mm) REVERT: B 175 THR cc_start: 0.8691 (m) cc_final: 0.8264 (p) REVERT: B 230 SER cc_start: 0.9260 (t) cc_final: 0.9017 (p) REVERT: B 231 ASP cc_start: 0.8516 (m-30) cc_final: 0.8247 (t0) REVERT: B 255 GLN cc_start: 0.8308 (tt0) cc_final: 0.7649 (tt0) REVERT: B 316 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7797 (tptm) REVERT: B 407 GLN cc_start: 0.7632 (pt0) cc_final: 0.7059 (tm-30) REVERT: C 86 ILE cc_start: 0.7986 (mt) cc_final: 0.7740 (tt) REVERT: C 102 SER cc_start: 0.8553 (m) cc_final: 0.8276 (t) REVERT: C 187 ARG cc_start: 0.8081 (mtm180) cc_final: 0.7642 (mtm180) REVERT: C 231 ASP cc_start: 0.8566 (m-30) cc_final: 0.8021 (t0) REVERT: C 297 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7022 (tt) REVERT: C 311 GLU cc_start: 0.8154 (pm20) cc_final: 0.7723 (pm20) REVERT: C 316 LYS cc_start: 0.8315 (mmtt) cc_final: 0.8003 (tptp) outliers start: 21 outliers final: 16 residues processed: 150 average time/residue: 0.1160 time to fit residues: 22.9345 Evaluate side-chains 147 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 435 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 0.0170 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 63 optimal weight: 0.1980 chunk 36 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123655 restraints weight = 11136.868| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.14 r_work: 0.3366 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8445 Z= 0.115 Angle : 0.564 8.403 11502 Z= 0.282 Chirality : 0.040 0.156 1434 Planarity : 0.003 0.037 1389 Dihedral : 4.143 14.395 1125 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.33 % Allowed : 12.00 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.26), residues: 1071 helix: -0.68 (0.19), residues: 819 sheet: None (None), residues: 0 loop : -3.04 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 238 TYR 0.008 0.001 TYR C 251 PHE 0.024 0.001 PHE A 115 TRP 0.018 0.001 TRP C 257 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8445) covalent geometry : angle 0.56358 (11502) hydrogen bonds : bond 0.03110 ( 330) hydrogen bonds : angle 3.66843 ( 954) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 194 LYS cc_start: 0.9019 (mttp) cc_final: 0.8636 (mmtt) REVERT: A 231 ASP cc_start: 0.8635 (m-30) cc_final: 0.8263 (t0) REVERT: A 329 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8318 (mp) REVERT: B 102 SER cc_start: 0.8454 (m) cc_final: 0.8194 (t) REVERT: B 147 LEU cc_start: 0.8731 (mm) cc_final: 0.8463 (mm) REVERT: B 175 THR cc_start: 0.8728 (m) cc_final: 0.8332 (p) REVERT: B 230 SER cc_start: 0.9255 (t) cc_final: 0.9025 (p) REVERT: B 231 ASP cc_start: 0.8483 (m-30) cc_final: 0.8230 (t0) REVERT: B 255 GLN cc_start: 0.8303 (tt0) cc_final: 0.7650 (tt0) REVERT: B 316 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7835 (tptm) REVERT: B 407 GLN cc_start: 0.7625 (pt0) cc_final: 0.7081 (tm-30) REVERT: C 86 ILE cc_start: 0.7977 (mt) cc_final: 0.7745 (tt) REVERT: C 187 ARG cc_start: 0.8035 (mtm180) cc_final: 0.7592 (mtm180) REVERT: C 231 ASP cc_start: 0.8582 (m-30) cc_final: 0.8051 (t0) REVERT: C 297 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7017 (tt) REVERT: C 316 LYS cc_start: 0.8274 (mmtt) cc_final: 0.7993 (tptp) outliers start: 21 outliers final: 18 residues processed: 155 average time/residue: 0.1117 time to fit residues: 22.8352 Evaluate side-chains 150 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 435 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 0.0970 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.156169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124406 restraints weight = 11144.201| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.14 r_work: 0.3375 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8445 Z= 0.112 Angle : 0.578 13.989 11502 Z= 0.283 Chirality : 0.040 0.144 1434 Planarity : 0.003 0.037 1389 Dihedral : 4.076 14.155 1125 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.22 % Allowed : 12.33 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.26), residues: 1071 helix: -0.57 (0.19), residues: 816 sheet: None (None), residues: 0 loop : -2.96 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 238 TYR 0.008 0.001 TYR C 251 PHE 0.023 0.001 PHE A 115 TRP 0.019 0.001 TRP C 257 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8445) covalent geometry : angle 0.57832 (11502) hydrogen bonds : bond 0.02980 ( 330) hydrogen bonds : angle 3.63088 ( 954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1916.94 seconds wall clock time: 33 minutes 28.31 seconds (2008.31 seconds total)