Starting phenix.real_space_refine on Wed Feb 4 21:43:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uu5_64506/02_2026/9uu5_64506.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uu5_64506/02_2026/9uu5_64506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uu5_64506/02_2026/9uu5_64506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uu5_64506/02_2026/9uu5_64506.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uu5_64506/02_2026/9uu5_64506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uu5_64506/02_2026/9uu5_64506.map" } resolution = 3.26 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= 0.002 sd= 0.049 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 74 5.16 5 C 8224 2.51 5 N 2316 2.21 5 O 2368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 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: 12982 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3107 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "B" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3387 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 401} Chain: "D" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3107 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "C" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3381 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 401} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 3.21, per 1000 atoms: 0.25 Number of scatterers: 12982 At special positions: 0 Unit cell: (107.9, 142.76, 147.74, 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 74 16.00 O 2368 8.00 N 2316 7.00 C 8224 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: 0.83 Conformation dependent library (CDL) restraints added in 630.6 milliseconds 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 12 sheets defined 33.0% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 69 through 77 removed outlier: 3.742A pdb=" N ASP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.795A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.585A pdb=" N LEU A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.681A pdb=" N SER A 146 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 removed outlier: 3.570A pdb=" N THR A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP A 184 " --> pdb=" O CYS A 180 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 248 through 253 removed outlier: 4.116A pdb=" N GLN A 252 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A 253 " --> pdb=" O HIS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.700A pdb=" N ILE A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.589A pdb=" N LEU A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.990A pdb=" N ALA A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.803A pdb=" N GLY A 366 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 367 " --> pdb=" O LEU A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 367' Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.765A pdb=" N ALA A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 removed outlier: 3.545A pdb=" N LEU A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.606A pdb=" N TYR B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.578A pdb=" N CYS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG B 102 " --> pdb=" O ALA B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 102' Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.665A pdb=" N ARG B 113 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 116 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 133 removed outlier: 3.509A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 164 removed outlier: 3.777A pdb=" N GLU B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 175 removed outlier: 4.066A pdb=" N ASP B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 197 through 207 Processing helix chain 'B' and resid 220 through 224 removed outlier: 4.264A pdb=" N SER B 223 " --> pdb=" O MET B 220 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 224 " --> pdb=" O GLY B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 224' Processing helix chain 'B' and resid 226 through 239 removed outlier: 3.755A pdb=" N LEU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.940A pdb=" N PHE B 256 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.640A pdb=" N ALA B 287 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG B 288 " --> pdb=" O ARG B 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 284 through 288' Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.189A pdb=" N ARG B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.518A pdb=" N GLY B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 338 " --> pdb=" O ALA B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 350 removed outlier: 3.536A pdb=" N THR B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.791A pdb=" N LEU B 357 " --> pdb=" O GLU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.782A pdb=" N LYS B 366 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 367' Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.786A pdb=" N LEU B 381 " --> pdb=" O ASP B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 402 removed outlier: 3.865A pdb=" N ILE B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 397 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLU B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 420 removed outlier: 3.664A pdb=" N LEU B 417 " --> pdb=" O SER B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 438 removed outlier: 3.716A pdb=" N TYR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 77 removed outlier: 3.907A pdb=" N ASP D 75 " --> pdb=" O PHE D 71 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP D 76 " --> pdb=" O PRO D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 123 removed outlier: 3.755A pdb=" N ARG D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.557A pdb=" N LEU D 133 " --> pdb=" O ARG D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.794A pdb=" N SER D 146 " --> pdb=" O LEU D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 190 removed outlier: 3.820A pdb=" N THR D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP D 184 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.741A pdb=" N LEU D 246 " --> pdb=" O SER D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 277 Processing helix chain 'D' and resid 320 through 331 removed outlier: 3.504A pdb=" N LEU D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 329 " --> pdb=" O ALA D 325 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 removed outlier: 3.621A pdb=" N ALA D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.918A pdb=" N ARG C 102 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.800A pdb=" N ARG C 113 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 116 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 130 removed outlier: 3.670A pdb=" N ARG C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 164 removed outlier: 3.920A pdb=" N GLU C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.599A pdb=" N ASP C 169 " --> pdb=" O PHE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 197 through 207 Processing helix chain 'C' and resid 220 through 223 removed outlier: 4.150A pdb=" N SER C 223 " --> pdb=" O MET C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 223' Processing helix chain 'C' and resid 224 through 237 removed outlier: 3.599A pdb=" N ILE C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 4.011A pdb=" N PHE C 256 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 3.550A pdb=" N CYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE C 271 " --> pdb=" O PRO C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 271' Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.597A pdb=" N ARG C 310 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.135A pdb=" N ASP C 336 " --> pdb=" O ALA C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 350 removed outlier: 3.551A pdb=" N THR C 343 " --> pdb=" O LYS C 339 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 392 through 404 removed outlier: 3.805A pdb=" N ILE C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 420 removed outlier: 4.006A pdb=" N LEU C 417 " --> pdb=" O SER C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 438 removed outlier: 3.777A pdb=" N TYR C 430 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 24 removed outlier: 5.363A pdb=" N GLY A 18 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG A 113 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR A 376 " --> pdb=" O TYR A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 241 removed outlier: 3.534A pdb=" N VAL A 392 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR A 286 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 287 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 213 through 218 removed outlier: 6.941A pdb=" N ASP B 183 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N PHE B 215 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 185 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU B 217 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL B 187 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE B 182 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU B 245 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 184 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N VAL B 247 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 186 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N THR B 249 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN B 188 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP B 91 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER B 281 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU B 89 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 296 through 298 Processing sheet with id=AA6, first strand: chain 'B' and resid 312 through 316 Processing sheet with id=AA7, first strand: chain 'D' and resid 16 through 24 removed outlier: 5.125A pdb=" N GLY D 18 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG D 113 " --> pdb=" O GLY D 18 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG D 108 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE D 153 " --> pdb=" O ARG D 108 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL D 110 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ASN D 155 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ALA D 112 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR D 154 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D 376 " --> pdb=" O TYR D 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 34 through 36 Processing sheet with id=AA9, first strand: chain 'D' and resid 235 through 241 removed outlier: 3.550A pdb=" N VAL D 392 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR D 286 " --> pdb=" O LEU D 356 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 213 through 217 removed outlier: 7.171A pdb=" N ASP C 183 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N PHE C 215 " --> pdb=" O ASP C 183 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU C 185 " --> pdb=" O PHE C 215 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU C 217 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL C 187 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE C 182 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU C 245 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 184 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL C 247 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 186 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR C 249 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN C 188 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA C 275 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS C 94 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA C 277 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR C 92 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU C 279 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 292 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 296 through 298 removed outlier: 3.525A pdb=" N ILE C 450 " --> pdb=" O CYS C 387 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 312 through 316 removed outlier: 3.504A pdb=" N TYR C 313 " --> pdb=" O SER C 325 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2280 1.32 - 1.44: 3355 1.44 - 1.57: 7522 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 13269 Sorted by residual: bond pdb=" CA SER C 454 " pdb=" CB SER C 454 " ideal model delta sigma weight residual 1.534 1.458 0.076 1.45e-02 4.76e+03 2.76e+01 bond pdb=" N VAL D 138 " pdb=" CA VAL D 138 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.07e-02 8.73e+03 9.93e+00 bond pdb=" C THR B 195 " pdb=" N PRO B 196 " ideal model delta sigma weight residual 1.335 1.362 -0.027 8.70e-03 1.32e+04 9.43e+00 bond pdb=" N LYS D 137 " pdb=" CA LYS D 137 " ideal model delta sigma weight residual 1.455 1.492 -0.036 1.41e-02 5.03e+03 6.63e+00 bond pdb=" N LEU D 139 " pdb=" CA LEU D 139 " ideal model delta sigma weight residual 1.463 1.494 -0.031 1.23e-02 6.61e+03 6.45e+00 ... (remaining 13264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 17520 2.14 - 4.28: 389 4.28 - 6.42: 58 6.42 - 8.56: 28 8.56 - 10.71: 4 Bond angle restraints: 17999 Sorted by residual: angle pdb=" CA VAL D 138 " pdb=" C VAL D 138 " pdb=" O VAL D 138 " ideal model delta sigma weight residual 121.09 116.29 4.80 8.20e-01 1.49e+00 3.43e+01 angle pdb=" CA VAL A 138 " pdb=" C VAL A 138 " pdb=" O VAL A 138 " ideal model delta sigma weight residual 121.49 116.46 5.03 1.01e+00 9.80e-01 2.48e+01 angle pdb=" CA LYS C 457 " pdb=" C LYS C 457 " pdb=" O LYS C 457 " ideal model delta sigma weight residual 121.16 116.10 5.06 1.12e+00 7.97e-01 2.04e+01 angle pdb=" N GLY C 455 " pdb=" CA GLY C 455 " pdb=" C GLY C 455 " ideal model delta sigma weight residual 113.18 102.47 10.71 2.37e+00 1.78e-01 2.04e+01 angle pdb=" C PHE B 456 " pdb=" CA PHE B 456 " pdb=" CB PHE B 456 " ideal model delta sigma weight residual 111.63 117.51 -5.88 1.36e+00 5.41e-01 1.87e+01 ... (remaining 17994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 7248 17.32 - 34.64: 625 34.64 - 51.95: 104 51.95 - 69.27: 17 69.27 - 86.59: 14 Dihedral angle restraints: 8008 sinusoidal: 3184 harmonic: 4824 Sorted by residual: dihedral pdb=" C PHE B 456 " pdb=" N PHE B 456 " pdb=" CA PHE B 456 " pdb=" CB PHE B 456 " ideal model delta harmonic sigma weight residual -122.60 -140.49 17.89 0 2.50e+00 1.60e-01 5.12e+01 dihedral pdb=" N PHE B 456 " pdb=" C PHE B 456 " pdb=" CA PHE B 456 " pdb=" CB PHE B 456 " ideal model delta harmonic sigma weight residual 122.80 139.30 -16.50 0 2.50e+00 1.60e-01 4.36e+01 dihedral pdb=" CA PHE B 456 " pdb=" C PHE B 456 " pdb=" N LYS B 457 " pdb=" CA LYS B 457 " ideal model delta harmonic sigma weight residual 180.00 150.28 29.72 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 8005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 1971 0.150 - 0.300: 23 0.300 - 0.449: 1 0.449 - 0.599: 0 0.599 - 0.749: 1 Chirality restraints: 1996 Sorted by residual: chirality pdb=" CA PHE B 456 " pdb=" N PHE B 456 " pdb=" C PHE B 456 " pdb=" CB PHE B 456 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CB VAL D 138 " pdb=" CA VAL D 138 " pdb=" CG1 VAL D 138 " pdb=" CG2 VAL D 138 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA THR D 199 " pdb=" N THR D 199 " pdb=" C THR D 199 " pdb=" CB THR D 199 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1993 not shown) Planarity restraints: 2347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 266 " 0.043 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO C 267 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 267 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 267 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 266 " 0.043 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO B 267 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 267 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 267 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 346 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO B 347 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 347 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 347 " -0.034 5.00e-02 4.00e+02 ... (remaining 2344 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4006 2.83 - 3.34: 10496 3.34 - 3.86: 20688 3.86 - 4.38: 24152 4.38 - 4.90: 42878 Nonbonded interactions: 102220 Sorted by model distance: nonbonded pdb=" OH TYR D 53 " pdb=" OH TYR D 379 " model vdw 2.307 3.040 nonbonded pdb=" OH TYR A 55 " pdb=" O LEU A 367 " model vdw 2.315 3.040 nonbonded pdb=" O VAL B 73 " pdb=" OG1 THR B 77 " model vdw 2.317 3.040 nonbonded pdb=" OE2 GLU C 354 " pdb=" OH TYR C 375 " model vdw 2.331 3.040 nonbonded pdb=" O SER D 315 " pdb=" OG1 THR D 319 " model vdw 2.333 3.040 ... (remaining 102215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 68 through 455 or (resid 456 and (name N or name CA or nam \ e C or name O or name CB )) or resid 457 through 494)) 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: 6.650 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.840 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 13269 Z= 0.222 Angle : 0.805 10.705 17999 Z= 0.458 Chirality : 0.055 0.749 1996 Planarity : 0.007 0.064 2347 Dihedral : 13.621 86.588 4912 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.13 % 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: -4.93 (0.15), residues: 1668 helix: -4.52 (0.11), residues: 504 sheet: -2.02 (0.23), residues: 384 loop : -2.95 (0.17), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 157 TYR 0.018 0.002 TYR D 150 PHE 0.029 0.002 PHE B 456 TRP 0.016 0.001 TRP A 167 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00480 (13269) covalent geometry : angle 0.80504 (17999) hydrogen bonds : bond 0.25101 ( 369) hydrogen bonds : angle 9.35672 ( 1002) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.516 Fit side-chains REVERT: A 41 ASP cc_start: 0.8651 (m-30) cc_final: 0.8239 (m-30) REVERT: A 105 CYS cc_start: 0.8580 (t) cc_final: 0.8318 (t) REVERT: A 118 MET cc_start: 0.8583 (ttp) cc_final: 0.8362 (ttt) REVERT: A 144 PHE cc_start: 0.9195 (m-10) cc_final: 0.8974 (m-10) REVERT: A 333 VAL cc_start: 0.8640 (t) cc_final: 0.8271 (m) REVERT: B 123 ARG cc_start: 0.8047 (mtp-110) cc_final: 0.7786 (ttp80) REVERT: B 188 ASN cc_start: 0.8780 (p0) cc_final: 0.8548 (p0) REVERT: B 201 MET cc_start: 0.8408 (ttp) cc_final: 0.8109 (ttm) REVERT: B 233 ARG cc_start: 0.7526 (tmt170) cc_final: 0.7296 (ttt180) REVERT: B 235 MET cc_start: 0.9057 (mmm) cc_final: 0.8695 (mmt) REVERT: B 319 GLN cc_start: 0.8634 (mp10) cc_final: 0.8405 (mp10) REVERT: B 331 MET cc_start: 0.8192 (mmt) cc_final: 0.7949 (tpp) REVERT: B 356 LEU cc_start: 0.7950 (mp) cc_final: 0.7726 (mp) REVERT: B 398 GLU cc_start: 0.7419 (mp0) cc_final: 0.7157 (mp0) REVERT: B 399 LEU cc_start: 0.8948 (tp) cc_final: 0.8730 (tt) REVERT: D 117 ASP cc_start: 0.8421 (t0) cc_final: 0.8213 (t0) REVERT: C 328 LYS cc_start: 0.7324 (mmtt) cc_final: 0.7078 (mmtt) REVERT: C 442 ARG cc_start: 0.8192 (mmp-170) cc_final: 0.7961 (mmt180) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1791 time to fit residues: 39.3388 Evaluate side-chains 119 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS B 188 ASN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 HIS ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 HIS D 302 ASN D 372 GLN C 188 ASN C 459 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.092894 restraints weight = 18403.185| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.13 r_work: 0.2962 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13269 Z= 0.136 Angle : 0.569 10.999 17999 Z= 0.294 Chirality : 0.044 0.217 1996 Planarity : 0.005 0.049 2347 Dihedral : 4.922 30.705 1852 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.58 % Allowed : 9.18 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.95 (0.17), residues: 1668 helix: -3.56 (0.16), residues: 526 sheet: -1.52 (0.24), residues: 376 loop : -2.38 (0.19), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 131 TYR 0.015 0.001 TYR D 55 PHE 0.028 0.001 PHE B 456 TRP 0.017 0.002 TRP B 429 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00327 (13269) covalent geometry : angle 0.56885 (17999) hydrogen bonds : bond 0.03972 ( 369) hydrogen bonds : angle 5.89321 ( 1002) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.497 Fit side-chains REVERT: A 64 LYS cc_start: 0.7816 (tptt) cc_final: 0.7608 (tppt) REVERT: A 118 MET cc_start: 0.8359 (ttp) cc_final: 0.8083 (ttt) REVERT: A 252 GLN cc_start: 0.7649 (pm20) cc_final: 0.7434 (pm20) REVERT: B 123 ARG cc_start: 0.8087 (mtp-110) cc_final: 0.7112 (tpt170) REVERT: B 201 MET cc_start: 0.8044 (ttp) cc_final: 0.7834 (ttm) REVERT: B 235 MET cc_start: 0.9006 (mmm) cc_final: 0.8566 (mmt) REVERT: B 331 MET cc_start: 0.8327 (mmt) cc_final: 0.8016 (tpp) REVERT: B 356 LEU cc_start: 0.7681 (mp) cc_final: 0.7475 (mp) REVERT: B 399 LEU cc_start: 0.8633 (tp) cc_final: 0.8296 (tt) REVERT: D 105 CYS cc_start: 0.8540 (t) cc_final: 0.7907 (t) REVERT: D 224 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7981 (t0) REVERT: C 154 GLU cc_start: 0.7953 (tp30) cc_final: 0.7651 (tp30) REVERT: C 442 ARG cc_start: 0.8084 (mmp-170) cc_final: 0.7825 (mmt180) outliers start: 8 outliers final: 4 residues processed: 133 average time/residue: 0.1371 time to fit residues: 25.0180 Evaluate side-chains 126 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain C residue 471 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 19 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 123 optimal weight: 0.1980 chunk 157 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 393 GLN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN D 250 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.129060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.093045 restraints weight = 18462.883| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.15 r_work: 0.2963 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13269 Z= 0.126 Angle : 0.541 8.923 17999 Z= 0.276 Chirality : 0.043 0.191 1996 Planarity : 0.004 0.051 2347 Dihedral : 4.601 29.154 1852 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.80 % Allowed : 11.21 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -3.12 (0.19), residues: 1668 helix: -2.83 (0.19), residues: 516 sheet: -1.06 (0.26), residues: 360 loop : -1.92 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 443 TYR 0.010 0.001 TYR D 53 PHE 0.023 0.001 PHE B 456 TRP 0.015 0.001 TRP B 429 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00304 (13269) covalent geometry : angle 0.54088 (17999) hydrogen bonds : bond 0.03298 ( 369) hydrogen bonds : angle 5.33000 ( 1002) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.379 Fit side-chains REVERT: A 64 LYS cc_start: 0.7963 (tptt) cc_final: 0.7720 (tppt) REVERT: A 105 CYS cc_start: 0.8963 (t) cc_final: 0.8587 (t) REVERT: A 118 MET cc_start: 0.8428 (ttp) cc_final: 0.8113 (ttt) REVERT: A 252 GLN cc_start: 0.7701 (pm20) cc_final: 0.7348 (pm20) REVERT: B 123 ARG cc_start: 0.8016 (mtp-110) cc_final: 0.7069 (tpt170) REVERT: B 235 MET cc_start: 0.8958 (mmm) cc_final: 0.8658 (mmt) REVERT: B 319 GLN cc_start: 0.8407 (mp10) cc_final: 0.8157 (mp10) REVERT: B 331 MET cc_start: 0.8294 (mmt) cc_final: 0.8030 (tpp) REVERT: B 399 LEU cc_start: 0.8679 (tp) cc_final: 0.8357 (tt) REVERT: D 105 CYS cc_start: 0.8523 (t) cc_final: 0.7848 (t) REVERT: D 282 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7886 (m) REVERT: C 154 GLU cc_start: 0.7972 (tp30) cc_final: 0.7704 (tp30) REVERT: C 442 ARG cc_start: 0.8107 (mmp-170) cc_final: 0.7864 (mmt180) outliers start: 11 outliers final: 8 residues processed: 134 average time/residue: 0.1221 time to fit residues: 22.6935 Evaluate side-chains 131 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 471 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 58 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 97 optimal weight: 0.0980 chunk 155 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.091072 restraints weight = 18615.420| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.15 r_work: 0.2930 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13269 Z= 0.178 Angle : 0.563 7.976 17999 Z= 0.288 Chirality : 0.044 0.219 1996 Planarity : 0.004 0.043 2347 Dihedral : 4.628 31.381 1852 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.88 % Allowed : 11.79 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.74 (0.19), residues: 1668 helix: -2.42 (0.21), residues: 522 sheet: -0.92 (0.27), residues: 360 loop : -1.70 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 443 TYR 0.012 0.001 TYR A 349 PHE 0.031 0.001 PHE B 456 TRP 0.017 0.002 TRP A 167 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00436 (13269) covalent geometry : angle 0.56311 (17999) hydrogen bonds : bond 0.03462 ( 369) hydrogen bonds : angle 5.17876 ( 1002) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.324 Fit side-chains REVERT: A 64 LYS cc_start: 0.7975 (tptt) cc_final: 0.7672 (tppt) REVERT: A 105 CYS cc_start: 0.9026 (t) cc_final: 0.8484 (t) REVERT: A 118 MET cc_start: 0.8419 (ttp) cc_final: 0.8077 (ttt) REVERT: A 252 GLN cc_start: 0.7684 (pm20) cc_final: 0.7296 (pm20) REVERT: B 123 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.6956 (tpt170) REVERT: B 235 MET cc_start: 0.8951 (mmm) cc_final: 0.8630 (mmt) REVERT: B 257 TYR cc_start: 0.8897 (t80) cc_final: 0.8456 (t80) REVERT: B 319 GLN cc_start: 0.8312 (mp10) cc_final: 0.7993 (mp10) REVERT: B 331 MET cc_start: 0.8281 (mmt) cc_final: 0.7905 (tpp) REVERT: B 356 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7496 (mp) REVERT: D 105 CYS cc_start: 0.8623 (t) cc_final: 0.7832 (t) REVERT: D 282 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7822 (m) REVERT: C 442 ARG cc_start: 0.8074 (mmp-170) cc_final: 0.7832 (mmt180) outliers start: 26 outliers final: 13 residues processed: 136 average time/residue: 0.1310 time to fit residues: 24.3174 Evaluate side-chains 132 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 494 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 145 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 70 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 HIS ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN D 250 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.090828 restraints weight = 18619.911| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.01 r_work: 0.2935 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13269 Z= 0.193 Angle : 0.567 7.552 17999 Z= 0.291 Chirality : 0.045 0.224 1996 Planarity : 0.004 0.040 2347 Dihedral : 4.649 30.847 1852 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.59 % Allowed : 12.87 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.47 (0.20), residues: 1668 helix: -2.10 (0.22), residues: 518 sheet: -0.86 (0.27), residues: 360 loop : -1.58 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.012 0.001 TYR B 206 PHE 0.030 0.001 PHE B 456 TRP 0.017 0.002 TRP A 167 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00474 (13269) covalent geometry : angle 0.56679 (17999) hydrogen bonds : bond 0.03371 ( 369) hydrogen bonds : angle 5.11025 ( 1002) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.514 Fit side-chains REVERT: A 64 LYS cc_start: 0.8062 (tptt) cc_final: 0.7700 (tppt) REVERT: A 105 CYS cc_start: 0.9064 (t) cc_final: 0.8476 (t) REVERT: A 118 MET cc_start: 0.8431 (ttp) cc_final: 0.8084 (ttt) REVERT: A 222 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.6058 (mtp) REVERT: A 252 GLN cc_start: 0.7696 (pm20) cc_final: 0.7321 (pm20) REVERT: B 123 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7153 (tpt170) REVERT: B 235 MET cc_start: 0.8958 (mmm) cc_final: 0.8639 (mmt) REVERT: B 257 TYR cc_start: 0.8871 (t80) cc_final: 0.8477 (t80) REVERT: B 331 MET cc_start: 0.8299 (mmt) cc_final: 0.7959 (tpp) REVERT: B 356 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7529 (mp) REVERT: D 56 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7588 (ttp-110) REVERT: D 105 CYS cc_start: 0.8657 (t) cc_final: 0.7809 (t) REVERT: D 282 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7815 (m) REVERT: C 154 GLU cc_start: 0.7988 (tp30) cc_final: 0.7684 (tp30) REVERT: C 442 ARG cc_start: 0.8052 (mmp-170) cc_final: 0.7686 (mmt-90) outliers start: 22 outliers final: 13 residues processed: 133 average time/residue: 0.1528 time to fit residues: 27.9584 Evaluate side-chains 135 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 494 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 8 optimal weight: 0.0770 chunk 44 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.093573 restraints weight = 18284.968| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.98 r_work: 0.2975 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13269 Z= 0.116 Angle : 0.516 7.112 17999 Z= 0.263 Chirality : 0.043 0.180 1996 Planarity : 0.004 0.038 2347 Dihedral : 4.320 25.644 1852 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.23 % Allowed : 13.59 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -2.10 (0.20), residues: 1668 helix: -1.68 (0.22), residues: 516 sheet: -0.73 (0.27), residues: 360 loop : -1.40 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 443 TYR 0.010 0.001 TYR D 150 PHE 0.021 0.001 PHE B 456 TRP 0.014 0.001 TRP B 429 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00283 (13269) covalent geometry : angle 0.51624 (17999) hydrogen bonds : bond 0.02785 ( 369) hydrogen bonds : angle 4.87593 ( 1002) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.336 Fit side-chains REVERT: A 64 LYS cc_start: 0.8081 (tptt) cc_final: 0.7786 (tppt) REVERT: A 105 CYS cc_start: 0.9042 (t) cc_final: 0.8414 (t) REVERT: A 118 MET cc_start: 0.8350 (ttp) cc_final: 0.7953 (ttt) REVERT: A 222 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.5941 (mtp) REVERT: A 252 GLN cc_start: 0.7662 (pm20) cc_final: 0.7255 (pm20) REVERT: B 123 ARG cc_start: 0.7926 (mtp-110) cc_final: 0.6971 (tpt170) REVERT: B 235 MET cc_start: 0.8998 (mmm) cc_final: 0.8734 (mmt) REVERT: B 257 TYR cc_start: 0.8846 (t80) cc_final: 0.8441 (t80) REVERT: B 319 GLN cc_start: 0.8212 (mp10) cc_final: 0.7946 (mp10) REVERT: B 331 MET cc_start: 0.8235 (mmt) cc_final: 0.7919 (tpp) REVERT: B 352 MET cc_start: 0.8042 (mmt) cc_final: 0.7521 (mmt) REVERT: B 356 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7505 (mp) REVERT: D 56 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7632 (ttp-110) REVERT: D 105 CYS cc_start: 0.8605 (t) cc_final: 0.7776 (t) REVERT: D 282 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7789 (m) REVERT: C 154 GLU cc_start: 0.7957 (tp30) cc_final: 0.7587 (tp30) REVERT: C 442 ARG cc_start: 0.8100 (mmp-170) cc_final: 0.7740 (mmt-90) outliers start: 17 outliers final: 11 residues processed: 139 average time/residue: 0.1374 time to fit residues: 26.4149 Evaluate side-chains 131 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 494 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 15 optimal weight: 0.9980 chunk 138 optimal weight: 0.0670 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.093704 restraints weight = 18301.980| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.97 r_work: 0.2980 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13269 Z= 0.120 Angle : 0.515 6.536 17999 Z= 0.262 Chirality : 0.043 0.178 1996 Planarity : 0.004 0.040 2347 Dihedral : 4.228 25.601 1852 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.59 % Allowed : 13.59 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.87 (0.20), residues: 1668 helix: -1.47 (0.23), residues: 528 sheet: -0.63 (0.27), residues: 360 loop : -1.24 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 443 TYR 0.010 0.001 TYR D 150 PHE 0.021 0.001 PHE B 456 TRP 0.014 0.001 TRP B 429 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00294 (13269) covalent geometry : angle 0.51453 (17999) hydrogen bonds : bond 0.02785 ( 369) hydrogen bonds : angle 4.78138 ( 1002) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.354 Fit side-chains REVERT: A 64 LYS cc_start: 0.8125 (tptt) cc_final: 0.7855 (tppt) REVERT: A 105 CYS cc_start: 0.9055 (t) cc_final: 0.8383 (t) REVERT: A 222 MET cc_start: 0.6376 (OUTLIER) cc_final: 0.6066 (mtp) REVERT: A 224 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.6947 (t0) REVERT: A 252 GLN cc_start: 0.7700 (pm20) cc_final: 0.7294 (pm20) REVERT: A 310 GLU cc_start: 0.6709 (pm20) cc_final: 0.6330 (pm20) REVERT: B 123 ARG cc_start: 0.7979 (mtp-110) cc_final: 0.7555 (ttm-80) REVERT: B 235 MET cc_start: 0.8996 (mmm) cc_final: 0.8736 (mmt) REVERT: B 257 TYR cc_start: 0.8866 (t80) cc_final: 0.8494 (t80) REVERT: B 331 MET cc_start: 0.8209 (mmt) cc_final: 0.7866 (tpp) REVERT: B 352 MET cc_start: 0.8078 (mmt) cc_final: 0.7608 (mmt) REVERT: B 356 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7499 (mp) REVERT: D 56 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7647 (ttp80) REVERT: D 105 CYS cc_start: 0.8643 (t) cc_final: 0.7818 (t) REVERT: D 282 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7776 (m) REVERT: C 154 GLU cc_start: 0.7950 (tp30) cc_final: 0.7668 (tp30) REVERT: C 442 ARG cc_start: 0.8071 (mmp-170) cc_final: 0.7719 (mmt-90) outliers start: 22 outliers final: 17 residues processed: 135 average time/residue: 0.1252 time to fit residues: 23.2380 Evaluate side-chains 141 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 494 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 139 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 133 optimal weight: 0.0870 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.095243 restraints weight = 18064.947| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.96 r_work: 0.3006 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13269 Z= 0.098 Angle : 0.501 7.791 17999 Z= 0.254 Chirality : 0.042 0.177 1996 Planarity : 0.004 0.038 2347 Dihedral : 4.035 22.068 1852 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.45 % Allowed : 14.17 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.61 (0.20), residues: 1668 helix: -1.22 (0.23), residues: 530 sheet: -0.50 (0.27), residues: 360 loop : -1.11 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 443 TYR 0.009 0.001 TYR D 150 PHE 0.015 0.001 PHE B 456 TRP 0.013 0.001 TRP B 429 HIS 0.003 0.000 HIS C 385 Details of bonding type rmsd covalent geometry : bond 0.00238 (13269) covalent geometry : angle 0.50091 (17999) hydrogen bonds : bond 0.02541 ( 369) hydrogen bonds : angle 4.64125 ( 1002) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.358 Fit side-chains REVERT: A 64 LYS cc_start: 0.8140 (tptt) cc_final: 0.7782 (tppt) REVERT: A 105 CYS cc_start: 0.9044 (t) cc_final: 0.8344 (t) REVERT: A 222 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5943 (mtp) REVERT: A 224 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.6940 (t0) REVERT: A 252 GLN cc_start: 0.7695 (pm20) cc_final: 0.7284 (pm20) REVERT: A 310 GLU cc_start: 0.6686 (pm20) cc_final: 0.6308 (pm20) REVERT: A 399 ARG cc_start: 0.8719 (mtm180) cc_final: 0.8435 (mtm-85) REVERT: B 123 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7512 (ttm-80) REVERT: B 235 MET cc_start: 0.8993 (mmm) cc_final: 0.8763 (mmt) REVERT: B 257 TYR cc_start: 0.8790 (t80) cc_final: 0.8524 (t80) REVERT: B 319 GLN cc_start: 0.8129 (mp10) cc_final: 0.7905 (mp10) REVERT: B 331 MET cc_start: 0.8135 (mmt) cc_final: 0.7838 (tpp) REVERT: B 352 MET cc_start: 0.8113 (mmt) cc_final: 0.7676 (mmt) REVERT: B 398 GLU cc_start: 0.7584 (mp0) cc_final: 0.7224 (mp0) REVERT: D 56 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7694 (ttp80) REVERT: D 105 CYS cc_start: 0.8623 (t) cc_final: 0.7786 (t) REVERT: D 282 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7763 (m) REVERT: C 154 GLU cc_start: 0.7952 (tp30) cc_final: 0.7697 (tp30) REVERT: C 289 ARG cc_start: 0.8816 (ttp-170) cc_final: 0.8517 (ttp-170) outliers start: 20 outliers final: 13 residues processed: 135 average time/residue: 0.1385 time to fit residues: 25.1911 Evaluate side-chains 134 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 494 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN C 389 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.088436 restraints weight = 18437.032| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.05 r_work: 0.2929 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13269 Z= 0.224 Angle : 0.588 11.539 17999 Z= 0.298 Chirality : 0.046 0.243 1996 Planarity : 0.004 0.041 2347 Dihedral : 4.459 29.238 1852 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.37 % Allowed : 14.39 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.73 (0.20), residues: 1668 helix: -1.21 (0.23), residues: 516 sheet: -0.60 (0.27), residues: 360 loop : -1.25 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 443 TYR 0.012 0.002 TYR A 150 PHE 0.036 0.001 PHE B 456 TRP 0.018 0.002 TRP A 167 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00553 (13269) covalent geometry : angle 0.58790 (17999) hydrogen bonds : bond 0.03405 ( 369) hydrogen bonds : angle 4.90409 ( 1002) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.543 Fit side-chains REVERT: A 64 LYS cc_start: 0.8223 (tptt) cc_final: 0.7859 (tppt) REVERT: A 105 CYS cc_start: 0.9113 (t) cc_final: 0.8448 (t) REVERT: A 222 MET cc_start: 0.6335 (OUTLIER) cc_final: 0.6006 (mtp) REVERT: A 399 ARG cc_start: 0.8725 (mtm180) cc_final: 0.8392 (mtm-85) REVERT: B 123 ARG cc_start: 0.8072 (mtp-110) cc_final: 0.7650 (ttm-80) REVERT: B 235 MET cc_start: 0.8997 (mmm) cc_final: 0.8703 (mmt) REVERT: B 257 TYR cc_start: 0.8922 (t80) cc_final: 0.8505 (t80) REVERT: B 319 GLN cc_start: 0.8221 (mp10) cc_final: 0.7962 (mp10) REVERT: B 331 MET cc_start: 0.8146 (mmt) cc_final: 0.7840 (tpp) REVERT: B 352 MET cc_start: 0.8026 (mmt) cc_final: 0.7615 (mmt) REVERT: B 398 GLU cc_start: 0.7703 (mp0) cc_final: 0.7342 (mp0) REVERT: D 56 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7722 (ttp80) REVERT: D 105 CYS cc_start: 0.8720 (t) cc_final: 0.7802 (t) REVERT: D 282 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7753 (m) REVERT: D 399 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7686 (mtm-85) outliers start: 19 outliers final: 16 residues processed: 129 average time/residue: 0.1397 time to fit residues: 25.0055 Evaluate side-chains 135 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 50 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 113 optimal weight: 0.0020 chunk 5 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.091042 restraints weight = 18401.348| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.08 r_work: 0.2968 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13269 Z= 0.120 Angle : 0.535 10.945 17999 Z= 0.269 Chirality : 0.043 0.180 1996 Planarity : 0.004 0.040 2347 Dihedral : 4.235 24.881 1852 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.30 % Allowed : 14.82 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.57 (0.20), residues: 1668 helix: -1.11 (0.23), residues: 528 sheet: -0.60 (0.27), residues: 362 loop : -1.07 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 443 TYR 0.010 0.001 TYR B 206 PHE 0.021 0.001 PHE B 456 TRP 0.013 0.001 TRP B 429 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00294 (13269) covalent geometry : angle 0.53469 (17999) hydrogen bonds : bond 0.02783 ( 369) hydrogen bonds : angle 4.73414 ( 1002) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.532 Fit side-chains REVERT: A 64 LYS cc_start: 0.8141 (tptt) cc_final: 0.7794 (tppt) REVERT: A 105 CYS cc_start: 0.9086 (t) cc_final: 0.8374 (t) REVERT: A 222 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.6017 (mtp) REVERT: A 224 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.6938 (t0) REVERT: A 310 GLU cc_start: 0.6714 (pm20) cc_final: 0.6335 (pm20) REVERT: A 399 ARG cc_start: 0.8719 (mtm180) cc_final: 0.8486 (mtm-85) REVERT: B 123 ARG cc_start: 0.7825 (mtp-110) cc_final: 0.7425 (ttm-80) REVERT: B 235 MET cc_start: 0.8994 (mmm) cc_final: 0.8760 (mmt) REVERT: B 257 TYR cc_start: 0.8827 (t80) cc_final: 0.8434 (t80) REVERT: B 319 GLN cc_start: 0.8192 (mp10) cc_final: 0.7952 (mp10) REVERT: B 331 MET cc_start: 0.8088 (mmt) cc_final: 0.7773 (tpp) REVERT: B 352 MET cc_start: 0.8142 (mmt) cc_final: 0.7860 (mmt) REVERT: B 398 GLU cc_start: 0.7616 (mp0) cc_final: 0.7254 (mp0) REVERT: D 56 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7717 (ttp80) REVERT: D 105 CYS cc_start: 0.8682 (t) cc_final: 0.7813 (t) REVERT: D 282 VAL cc_start: 0.7957 (OUTLIER) cc_final: 0.7676 (m) REVERT: D 399 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7655 (mtm-85) outliers start: 18 outliers final: 14 residues processed: 127 average time/residue: 0.1333 time to fit residues: 23.4786 Evaluate side-chains 131 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 1.9990 chunk 82 optimal weight: 0.0770 chunk 75 optimal weight: 0.3980 chunk 143 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 153 optimal weight: 0.0170 chunk 129 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.093169 restraints weight = 18108.271| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.06 r_work: 0.3003 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13269 Z= 0.097 Angle : 0.515 11.777 17999 Z= 0.257 Chirality : 0.042 0.176 1996 Planarity : 0.004 0.041 2347 Dihedral : 3.973 20.952 1852 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.30 % Allowed : 14.82 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -1.35 (0.21), residues: 1668 helix: -0.88 (0.24), residues: 528 sheet: -0.52 (0.27), residues: 362 loop : -0.95 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 443 TYR 0.009 0.001 TYR D 150 PHE 0.013 0.001 PHE B 456 TRP 0.013 0.001 TRP B 429 HIS 0.004 0.001 HIS C 385 Details of bonding type rmsd covalent geometry : bond 0.00234 (13269) covalent geometry : angle 0.51523 (17999) hydrogen bonds : bond 0.02510 ( 369) hydrogen bonds : angle 4.57328 ( 1002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2469.06 seconds wall clock time: 43 minutes 12.48 seconds (2592.48 seconds total)