Starting phenix.real_space_refine on Sat Aug 23 03:09:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x3f_22021/08_2025/6x3f_22021.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x3f_22021/08_2025/6x3f_22021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x3f_22021/08_2025/6x3f_22021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x3f_22021/08_2025/6x3f_22021.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x3f_22021/08_2025/6x3f_22021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x3f_22021/08_2025/6x3f_22021.map" } resolution = 3.03 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6144 2.51 5 N 1488 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9366 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3115 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 11, 'TRANS': 397} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C Time building chain proxies: 1.96, per 1000 atoms: 0.21 Number of scatterers: 9366 At special positions: 0 Unit cell: (115.648, 112.32, 77.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1668 8.00 N 1488 7.00 C 6144 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: 0.75 Conformation dependent library (CDL) restraints added in 288.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 72.9% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 18 through 40 removed outlier: 3.711A pdb=" N THR A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 81 removed outlier: 3.679A pdb=" N LEU A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 96 through 116 removed outlier: 4.034A pdb=" N THR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.982A pdb=" N ASP A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 229 removed outlier: 3.699A pdb=" N CYS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 247 removed outlier: 3.669A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 257 through 273 removed outlier: 3.600A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.846A pdb=" N MET A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.774A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.670A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.846A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 348 removed outlier: 3.590A pdb=" N GLU A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 removed outlier: 3.754A pdb=" N THR A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.657A pdb=" N ALA A 371 " --> pdb=" O MET A 367 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 408 removed outlier: 3.728A pdb=" N ILE A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.583A pdb=" N THR A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.876A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 458 removed outlier: 4.615A pdb=" N ARG A 445 " --> pdb=" O TRP A 441 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 40 removed outlier: 3.710A pdb=" N THR B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 81 removed outlier: 3.680A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix Processing helix chain 'B' and resid 96 through 116 removed outlier: 4.034A pdb=" N THR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 104 " --> pdb=" O CYS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.982A pdb=" N ASP B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 229 removed outlier: 3.699A pdb=" N CYS B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.668A pdb=" N VAL B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 257 through 273 removed outlier: 3.600A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 282 through 296 removed outlier: 3.846A pdb=" N MET B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.775A pdb=" N VAL B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.669A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 removed outlier: 3.846A pdb=" N MET B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 348 removed outlier: 3.589A pdb=" N GLU B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 359 removed outlier: 3.754A pdb=" N THR B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.657A pdb=" N ALA B 371 " --> pdb=" O MET B 367 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 408 removed outlier: 3.727A pdb=" N ILE B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 426 removed outlier: 3.584A pdb=" N THR B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.875A pdb=" N THR B 434 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 458 removed outlier: 4.614A pdb=" N ARG B 445 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 450 " --> pdb=" O PHE B 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 40 removed outlier: 3.711A pdb=" N THR C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 81 removed outlier: 3.679A pdb=" N LEU C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix Processing helix chain 'C' and resid 96 through 116 removed outlier: 4.033A pdb=" N THR C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 104 " --> pdb=" O CYS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.982A pdb=" N ASP C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 229 removed outlier: 3.698A pdb=" N CYS C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 247 removed outlier: 3.669A pdb=" N VAL C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 257 through 273 removed outlier: 3.600A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 282 through 296 removed outlier: 3.845A pdb=" N MET C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.774A pdb=" N VAL C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.670A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 removed outlier: 3.845A pdb=" N MET C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 348 removed outlier: 3.590A pdb=" N GLU C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU C 346 " --> pdb=" O ARG C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 359 removed outlier: 3.754A pdb=" N THR C 355 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.657A pdb=" N ALA C 371 " --> pdb=" O MET C 367 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 408 removed outlier: 3.727A pdb=" N ILE C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 426 removed outlier: 3.582A pdb=" N THR C 418 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET C 419 " --> pdb=" O GLY C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.876A pdb=" N THR C 434 " --> pdb=" O GLU C 431 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 435 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 458 removed outlier: 4.614A pdb=" N ARG C 445 " --> pdb=" O TRP C 441 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 167 Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 167 Processing sheet with id=AA5, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 164 through 167 517 hydrogen bonds defined for protein. 1497 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2847 1.34 - 1.46: 1329 1.46 - 1.57: 5208 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 9501 Sorted by residual: bond pdb=" C5 CHT A 601 " pdb=" N1 CHT A 601 " ideal model delta sigma weight residual 1.509 1.456 0.053 2.00e-02 2.50e+03 7.10e+00 bond pdb=" C5 CHT B 601 " pdb=" N1 CHT B 601 " ideal model delta sigma weight residual 1.509 1.456 0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" C5 CHT C 601 " pdb=" N1 CHT C 601 " ideal model delta sigma weight residual 1.509 1.456 0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" C7 CHT C 601 " pdb=" N1 CHT C 601 " ideal model delta sigma weight residual 1.492 1.451 0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C8 CHT B 601 " pdb=" N1 CHT B 601 " ideal model delta sigma weight residual 1.492 1.451 0.041 2.00e-02 2.50e+03 4.11e+00 ... (remaining 9496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 12254 1.84 - 3.67: 525 3.67 - 5.51: 73 5.51 - 7.34: 21 7.34 - 9.18: 21 Bond angle restraints: 12894 Sorted by residual: angle pdb=" C VAL C 120 " pdb=" N THR C 121 " pdb=" CA THR C 121 " ideal model delta sigma weight residual 121.70 127.94 -6.24 1.80e+00 3.09e-01 1.20e+01 angle pdb=" C VAL B 120 " pdb=" N THR B 121 " pdb=" CA THR B 121 " ideal model delta sigma weight residual 121.70 127.91 -6.21 1.80e+00 3.09e-01 1.19e+01 angle pdb=" C VAL A 120 " pdb=" N THR A 121 " pdb=" CA THR A 121 " ideal model delta sigma weight residual 121.70 127.91 -6.21 1.80e+00 3.09e-01 1.19e+01 angle pdb=" C ASP B 388 " pdb=" N LEU B 389 " pdb=" CA LEU B 389 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.59e+00 angle pdb=" C ASP A 388 " pdb=" N LEU A 389 " pdb=" CA LEU A 389 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.53e+00 ... (remaining 12889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5124 17.91 - 35.83: 429 35.83 - 53.74: 96 53.74 - 71.65: 21 71.65 - 89.56: 6 Dihedral angle restraints: 5676 sinusoidal: 2160 harmonic: 3516 Sorted by residual: dihedral pdb=" CA VAL B 462 " pdb=" C VAL B 462 " pdb=" N GLU B 463 " pdb=" CA GLU B 463 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA THR A 247 " pdb=" C THR A 247 " pdb=" N MET A 248 " pdb=" CA MET A 248 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA THR B 247 " pdb=" C THR B 247 " pdb=" N MET B 248 " pdb=" CA MET B 248 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1380 0.071 - 0.143: 210 0.143 - 0.214: 42 0.214 - 0.286: 3 0.286 - 0.357: 3 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CB VAL B 36 " pdb=" CA VAL B 36 " pdb=" CG1 VAL B 36 " pdb=" CG2 VAL B 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CB VAL C 36 " pdb=" CA VAL C 36 " pdb=" CG1 VAL C 36 " pdb=" CG2 VAL C 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB VAL A 36 " pdb=" CA VAL A 36 " pdb=" CG1 VAL A 36 " pdb=" CG2 VAL A 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 1635 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 258 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO B 259 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 258 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO A 259 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 258 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO C 259 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 259 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 259 " 0.037 5.00e-02 4.00e+02 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3219 2.86 - 3.37: 8826 3.37 - 3.88: 14813 3.88 - 4.39: 18117 4.39 - 4.90: 31053 Nonbonded interactions: 76028 Sorted by model distance: nonbonded pdb=" OH TYR B 98 " pdb=" OD1 ASP B 455 " model vdw 2.351 3.040 nonbonded pdb=" OH TYR A 98 " pdb=" OD1 ASP A 455 " model vdw 2.351 3.040 nonbonded pdb=" OH TYR C 98 " pdb=" OD1 ASP C 455 " model vdw 2.352 3.040 nonbonded pdb=" OH TYR C 373 " pdb=" OD1 ASP C 440 " model vdw 2.369 3.040 nonbonded pdb=" OH TYR A 373 " pdb=" OD1 ASP A 440 " model vdw 2.369 3.040 ... (remaining 76023 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 8.460 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.006 0.055 9501 Z= 0.256 Angle : 0.934 9.177 12894 Z= 0.489 Chirality : 0.058 0.357 1638 Planarity : 0.008 0.065 1563 Dihedral : 14.719 89.564 3408 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.78 (0.13), residues: 1209 helix: -4.59 (0.07), residues: 933 sheet: -3.31 (0.65), residues: 54 loop : -2.49 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 353 TYR 0.012 0.002 TYR C 162 PHE 0.011 0.002 PHE C 159 TRP 0.010 0.001 TRP A 441 HIS 0.001 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 9501) covalent geometry : angle 0.93431 (12894) hydrogen bonds : bond 0.31178 ( 517) hydrogen bonds : angle 11.26628 ( 1497) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.346 Fit side-chains REVERT: A 149 MET cc_start: 0.8776 (mtt) cc_final: 0.8543 (mtp) REVERT: A 163 LYS cc_start: 0.8467 (tttm) cc_final: 0.8119 (tptp) REVERT: B 149 MET cc_start: 0.8755 (mtt) cc_final: 0.8534 (mtp) REVERT: B 163 LYS cc_start: 0.8481 (tttm) cc_final: 0.8244 (tmtt) REVERT: B 280 ARG cc_start: 0.6785 (ttt180) cc_final: 0.6295 (ttp-110) REVERT: B 306 PHE cc_start: 0.7504 (t80) cc_final: 0.7286 (t80) REVERT: B 307 ILE cc_start: 0.8214 (mm) cc_final: 0.8013 (mt) REVERT: C 149 MET cc_start: 0.8729 (mtt) cc_final: 0.8483 (mtp) REVERT: C 280 ARG cc_start: 0.6844 (ttt180) cc_final: 0.6472 (ttp-110) REVERT: C 307 ILE cc_start: 0.8236 (mm) cc_final: 0.7984 (mt) REVERT: C 342 ARG cc_start: 0.7488 (ttp80) cc_final: 0.7013 (ttp-170) REVERT: C 445 ARG cc_start: 0.7729 (mpt180) cc_final: 0.7518 (mpt180) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1001 time to fit residues: 23.4413 Evaluate side-chains 143 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 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 347 ASN A 385 ASN A 413 GLN B 347 ASN B 385 ASN B 413 GLN C 347 ASN C 385 ASN C 413 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.147916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103413 restraints weight = 10080.933| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.86 r_work: 0.2964 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9501 Z= 0.117 Angle : 0.572 6.707 12894 Z= 0.301 Chirality : 0.040 0.136 1638 Planarity : 0.006 0.041 1563 Dihedral : 5.252 20.976 1293 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.92 % Allowed : 14.87 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.41 (0.19), residues: 1209 helix: -2.65 (0.13), residues: 948 sheet: -3.08 (0.66), residues: 54 loop : -2.75 (0.35), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 353 TYR 0.006 0.001 TYR A 285 PHE 0.023 0.001 PHE A 306 TRP 0.014 0.001 TRP C 441 HIS 0.001 0.000 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9501) covalent geometry : angle 0.57194 (12894) hydrogen bonds : bond 0.03776 ( 517) hydrogen bonds : angle 4.99434 ( 1497) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.222 Fit side-chains REVERT: A 163 LYS cc_start: 0.8713 (tttm) cc_final: 0.8380 (tmtt) REVERT: A 228 LYS cc_start: 0.7546 (mtpt) cc_final: 0.7307 (mttp) REVERT: A 262 ILE cc_start: 0.8042 (tt) cc_final: 0.7554 (pt) REVERT: A 328 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.5990 (mp) REVERT: B 228 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7561 (mttp) REVERT: B 280 ARG cc_start: 0.7040 (ttt180) cc_final: 0.6217 (ttp-110) REVERT: B 306 PHE cc_start: 0.7476 (t80) cc_final: 0.7244 (t80) REVERT: B 325 LEU cc_start: 0.6599 (tt) cc_final: 0.5735 (mp) REVERT: C 21 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6678 (tp) REVERT: C 149 MET cc_start: 0.9042 (mtt) cc_final: 0.8813 (mtp) REVERT: C 228 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7605 (mttp) REVERT: C 280 ARG cc_start: 0.7029 (ttt180) cc_final: 0.6290 (ttp-110) REVERT: C 298 ILE cc_start: 0.8532 (mm) cc_final: 0.8271 (mp) REVERT: C 325 LEU cc_start: 0.6609 (tt) cc_final: 0.5951 (mp) REVERT: C 342 ARG cc_start: 0.7059 (ttp80) cc_final: 0.6696 (ttp-170) outliers start: 30 outliers final: 18 residues processed: 176 average time/residue: 0.0894 time to fit residues: 21.3419 Evaluate side-chains 163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 461 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 36 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.147976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.103298 restraints weight = 10036.813| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.01 r_work: 0.2942 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9501 Z= 0.115 Angle : 0.533 7.429 12894 Z= 0.273 Chirality : 0.040 0.132 1638 Planarity : 0.004 0.031 1563 Dihedral : 4.778 17.086 1293 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.04 % Allowed : 16.33 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.73 (0.23), residues: 1209 helix: -1.41 (0.16), residues: 957 sheet: -2.62 (0.71), residues: 54 loop : -2.44 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 353 TYR 0.008 0.001 TYR C 285 PHE 0.014 0.001 PHE A 306 TRP 0.006 0.001 TRP C 441 HIS 0.001 0.000 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9501) covalent geometry : angle 0.53327 (12894) hydrogen bonds : bond 0.03536 ( 517) hydrogen bonds : angle 4.40553 ( 1497) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.328 Fit side-chains REVERT: A 163 LYS cc_start: 0.8754 (tttm) cc_final: 0.8453 (tptp) REVERT: A 228 LYS cc_start: 0.7576 (mtpt) cc_final: 0.7358 (mttm) REVERT: A 260 LEU cc_start: 0.8060 (tp) cc_final: 0.7835 (tp) REVERT: B 41 HIS cc_start: 0.7333 (t70) cc_final: 0.6916 (m-70) REVERT: B 228 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7362 (mttt) REVERT: B 262 ILE cc_start: 0.7773 (tt) cc_final: 0.7536 (tt) REVERT: B 280 ARG cc_start: 0.7029 (ttt180) cc_final: 0.6243 (ttp-110) REVERT: C 21 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6671 (tp) REVERT: C 41 HIS cc_start: 0.7148 (t70) cc_final: 0.6722 (m-70) REVERT: C 149 MET cc_start: 0.8939 (mtt) cc_final: 0.8722 (mtp) REVERT: C 228 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7553 (mttp) REVERT: C 325 LEU cc_start: 0.6349 (tt) cc_final: 0.5731 (mp) REVERT: C 342 ARG cc_start: 0.7015 (ttp80) cc_final: 0.6669 (ttp-170) REVERT: C 353 ARG cc_start: 0.5226 (mtm-85) cc_final: 0.4973 (mtm-85) outliers start: 21 outliers final: 12 residues processed: 155 average time/residue: 0.0850 time to fit residues: 18.5240 Evaluate side-chains 153 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 462 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 47 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN C 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.146162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.101223 restraints weight = 10111.033| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.91 r_work: 0.2926 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9501 Z= 0.140 Angle : 0.541 8.242 12894 Z= 0.275 Chirality : 0.040 0.120 1638 Planarity : 0.004 0.028 1563 Dihedral : 4.696 16.532 1293 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.04 % Allowed : 18.17 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.24), residues: 1209 helix: -0.88 (0.17), residues: 945 sheet: -2.55 (0.70), residues: 54 loop : -2.03 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 353 TYR 0.007 0.001 TYR B 285 PHE 0.024 0.002 PHE B 306 TRP 0.005 0.001 TRP C 441 HIS 0.002 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9501) covalent geometry : angle 0.54061 (12894) hydrogen bonds : bond 0.03553 ( 517) hydrogen bonds : angle 4.28638 ( 1497) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.220 Fit side-chains REVERT: A 41 HIS cc_start: 0.6898 (t70) cc_final: 0.6629 (m-70) REVERT: A 163 LYS cc_start: 0.8730 (tttm) cc_final: 0.8461 (tptp) REVERT: A 228 LYS cc_start: 0.7583 (mtpt) cc_final: 0.7199 (mttt) REVERT: A 262 ILE cc_start: 0.7737 (tt) cc_final: 0.7292 (tt) REVERT: B 41 HIS cc_start: 0.7333 (t70) cc_final: 0.7080 (m-70) REVERT: B 228 LYS cc_start: 0.7699 (mtpt) cc_final: 0.7328 (mttt) REVERT: B 262 ILE cc_start: 0.7836 (tt) cc_final: 0.7544 (tt) REVERT: B 353 ARG cc_start: 0.5421 (mtm-85) cc_final: 0.5126 (mtm-85) REVERT: C 21 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6710 (tp) REVERT: C 41 HIS cc_start: 0.6972 (t70) cc_final: 0.6756 (m-70) REVERT: C 149 MET cc_start: 0.8928 (mtt) cc_final: 0.8715 (mtp) REVERT: C 342 ARG cc_start: 0.7022 (ttp80) cc_final: 0.6515 (ttp-170) REVERT: C 353 ARG cc_start: 0.5365 (mtm-85) cc_final: 0.5100 (mtm-85) outliers start: 21 outliers final: 12 residues processed: 153 average time/residue: 0.0739 time to fit residues: 16.0126 Evaluate side-chains 145 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.147368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.102541 restraints weight = 10061.744| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.98 r_work: 0.2893 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9501 Z= 0.122 Angle : 0.513 7.216 12894 Z= 0.262 Chirality : 0.039 0.120 1638 Planarity : 0.003 0.026 1563 Dihedral : 4.510 17.827 1293 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.75 % Allowed : 18.66 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.25), residues: 1209 helix: -0.55 (0.17), residues: 948 sheet: -2.37 (0.72), residues: 54 loop : -1.69 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 353 TYR 0.005 0.001 TYR C 305 PHE 0.016 0.001 PHE B 306 TRP 0.005 0.001 TRP C 441 HIS 0.001 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9501) covalent geometry : angle 0.51267 (12894) hydrogen bonds : bond 0.03360 ( 517) hydrogen bonds : angle 4.15879 ( 1497) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.259 Fit side-chains REVERT: A 228 LYS cc_start: 0.7570 (mtpt) cc_final: 0.7173 (mttt) REVERT: A 262 ILE cc_start: 0.7835 (tt) cc_final: 0.7405 (tt) REVERT: B 228 LYS cc_start: 0.7596 (mtpt) cc_final: 0.7229 (mttt) REVERT: B 262 ILE cc_start: 0.7888 (tt) cc_final: 0.7567 (tt) REVERT: B 307 ILE cc_start: 0.7918 (mm) cc_final: 0.7691 (mt) REVERT: B 367 MET cc_start: 0.7270 (mtm) cc_final: 0.7065 (mtm) REVERT: C 21 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6640 (tp) REVERT: C 342 ARG cc_start: 0.6925 (ttp80) cc_final: 0.6421 (ttp-170) REVERT: C 353 ARG cc_start: 0.5333 (mtm-85) cc_final: 0.5084 (mtm-85) outliers start: 18 outliers final: 12 residues processed: 147 average time/residue: 0.0696 time to fit residues: 15.0943 Evaluate side-chains 144 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 461 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 74 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 HIS C 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.147179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.101769 restraints weight = 10140.617| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.95 r_work: 0.2904 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9501 Z= 0.124 Angle : 0.521 8.820 12894 Z= 0.262 Chirality : 0.040 0.121 1638 Planarity : 0.003 0.026 1563 Dihedral : 4.461 19.605 1293 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.75 % Allowed : 18.46 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.25), residues: 1209 helix: -0.35 (0.18), residues: 948 sheet: -2.29 (0.73), residues: 54 loop : -1.55 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 353 TYR 0.010 0.001 TYR B 285 PHE 0.013 0.001 PHE B 306 TRP 0.004 0.001 TRP C 19 HIS 0.001 0.000 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9501) covalent geometry : angle 0.52117 (12894) hydrogen bonds : bond 0.03339 ( 517) hydrogen bonds : angle 4.11832 ( 1497) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.265 Fit side-chains REVERT: A 228 LYS cc_start: 0.7552 (mtpt) cc_final: 0.7157 (mttt) REVERT: A 262 ILE cc_start: 0.7840 (tt) cc_final: 0.7373 (tt) REVERT: B 228 LYS cc_start: 0.7578 (mtpt) cc_final: 0.7221 (mttt) REVERT: B 262 ILE cc_start: 0.7835 (tt) cc_final: 0.7495 (tt) REVERT: B 307 ILE cc_start: 0.7910 (mm) cc_final: 0.7687 (mt) REVERT: B 353 ARG cc_start: 0.5441 (mtm-85) cc_final: 0.5117 (mtm-85) REVERT: C 21 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6639 (tp) REVERT: C 342 ARG cc_start: 0.7101 (ttp80) cc_final: 0.6571 (ttp-170) REVERT: C 353 ARG cc_start: 0.5287 (mtm-85) cc_final: 0.4949 (mtm-85) outliers start: 18 outliers final: 15 residues processed: 145 average time/residue: 0.0660 time to fit residues: 14.1017 Evaluate side-chains 148 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 461 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 80 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 95 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.149374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104043 restraints weight = 10009.834| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.94 r_work: 0.2931 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9501 Z= 0.100 Angle : 0.485 6.010 12894 Z= 0.247 Chirality : 0.039 0.118 1638 Planarity : 0.003 0.025 1563 Dihedral : 4.262 19.912 1293 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.94 % Allowed : 19.14 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.25), residues: 1209 helix: -0.16 (0.18), residues: 978 sheet: -2.25 (0.74), residues: 54 loop : -1.69 (0.43), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 353 TYR 0.008 0.001 TYR B 285 PHE 0.012 0.001 PHE B 306 TRP 0.005 0.001 TRP C 441 HIS 0.001 0.000 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9501) covalent geometry : angle 0.48476 (12894) hydrogen bonds : bond 0.03102 ( 517) hydrogen bonds : angle 3.98909 ( 1497) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.384 Fit side-chains REVERT: A 228 LYS cc_start: 0.7545 (mtpt) cc_final: 0.7155 (mtmt) REVERT: A 260 LEU cc_start: 0.8168 (tp) cc_final: 0.7932 (tp) REVERT: A 262 ILE cc_start: 0.7794 (tt) cc_final: 0.7328 (tt) REVERT: A 286 MET cc_start: 0.8289 (mtm) cc_final: 0.8080 (mtt) REVERT: A 367 MET cc_start: 0.7014 (mtm) cc_final: 0.6773 (mtm) REVERT: B 228 LYS cc_start: 0.7542 (mtpt) cc_final: 0.7197 (mttt) REVERT: B 262 ILE cc_start: 0.7721 (tt) cc_final: 0.7408 (tt) REVERT: B 307 ILE cc_start: 0.7901 (mm) cc_final: 0.7694 (mt) REVERT: B 341 PHE cc_start: 0.5910 (OUTLIER) cc_final: 0.5696 (m-80) REVERT: C 21 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6556 (tp) REVERT: C 353 ARG cc_start: 0.5282 (mtm-85) cc_final: 0.4996 (mtm-85) outliers start: 20 outliers final: 15 residues processed: 151 average time/residue: 0.0737 time to fit residues: 16.4169 Evaluate side-chains 150 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 97 optimal weight: 0.0060 chunk 89 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.149826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104203 restraints weight = 9964.605| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.95 r_work: 0.2934 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9501 Z= 0.100 Angle : 0.491 5.947 12894 Z= 0.248 Chirality : 0.039 0.119 1638 Planarity : 0.003 0.027 1563 Dihedral : 4.192 20.075 1293 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.14 % Allowed : 19.73 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.25), residues: 1209 helix: -0.04 (0.18), residues: 981 sheet: -2.22 (0.74), residues: 54 loop : -1.64 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 353 TYR 0.010 0.001 TYR B 285 PHE 0.011 0.001 PHE B 306 TRP 0.004 0.001 TRP C 441 HIS 0.001 0.000 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9501) covalent geometry : angle 0.49128 (12894) hydrogen bonds : bond 0.03088 ( 517) hydrogen bonds : angle 3.97055 ( 1497) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.308 Fit side-chains REVERT: A 228 LYS cc_start: 0.7540 (mtpt) cc_final: 0.7155 (mtmt) REVERT: A 260 LEU cc_start: 0.8112 (tp) cc_final: 0.7887 (tp) REVERT: A 262 ILE cc_start: 0.7799 (tt) cc_final: 0.7331 (tt) REVERT: A 286 MET cc_start: 0.8291 (mtm) cc_final: 0.8079 (mtt) REVERT: B 228 LYS cc_start: 0.7551 (mtpt) cc_final: 0.7214 (mttt) REVERT: B 262 ILE cc_start: 0.7726 (tt) cc_final: 0.7421 (tt) REVERT: B 307 ILE cc_start: 0.7972 (mm) cc_final: 0.7752 (mt) REVERT: B 432 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: C 21 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6531 (tp) REVERT: C 353 ARG cc_start: 0.5253 (mtm-85) cc_final: 0.4960 (mtm-85) outliers start: 22 outliers final: 18 residues processed: 153 average time/residue: 0.0755 time to fit residues: 17.1549 Evaluate side-chains 153 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 32 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.144867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.099407 restraints weight = 10035.311| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.93 r_work: 0.2870 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9501 Z= 0.182 Angle : 0.565 7.227 12894 Z= 0.282 Chirality : 0.042 0.127 1638 Planarity : 0.004 0.030 1563 Dihedral : 4.531 22.051 1293 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.24 % Allowed : 18.85 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.25), residues: 1209 helix: -0.25 (0.17), residues: 984 sheet: -2.19 (0.73), residues: 54 loop : -1.59 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 353 TYR 0.016 0.001 TYR B 285 PHE 0.016 0.002 PHE B 240 TRP 0.004 0.001 TRP C 19 HIS 0.001 0.000 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 9501) covalent geometry : angle 0.56501 (12894) hydrogen bonds : bond 0.03655 ( 517) hydrogen bonds : angle 4.18289 ( 1497) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.237 Fit side-chains REVERT: A 262 ILE cc_start: 0.7864 (tt) cc_final: 0.7391 (tt) REVERT: B 262 ILE cc_start: 0.7842 (tt) cc_final: 0.7535 (tt) REVERT: B 280 ARG cc_start: 0.7046 (ttt180) cc_final: 0.6258 (ttp-110) REVERT: B 307 ILE cc_start: 0.7932 (mm) cc_final: 0.7703 (mt) REVERT: C 21 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6620 (tp) REVERT: C 41 HIS cc_start: 0.7868 (m90) cc_final: 0.7632 (m90) REVERT: C 353 ARG cc_start: 0.5266 (mtm-85) cc_final: 0.4931 (mtm-85) outliers start: 23 outliers final: 17 residues processed: 151 average time/residue: 0.0792 time to fit residues: 16.9530 Evaluate side-chains 149 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 98 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 100 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.149484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.103934 restraints weight = 9963.552| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.95 r_work: 0.2924 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9501 Z= 0.102 Angle : 0.495 5.731 12894 Z= 0.251 Chirality : 0.039 0.118 1638 Planarity : 0.003 0.029 1563 Dihedral : 4.252 20.810 1293 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.65 % Allowed : 19.73 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.26), residues: 1209 helix: 0.07 (0.18), residues: 981 sheet: -2.15 (0.73), residues: 54 loop : -1.60 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 353 TYR 0.014 0.001 TYR B 285 PHE 0.010 0.001 PHE B 306 TRP 0.004 0.001 TRP C 441 HIS 0.001 0.000 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9501) covalent geometry : angle 0.49505 (12894) hydrogen bonds : bond 0.03136 ( 517) hydrogen bonds : angle 4.01603 ( 1497) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.318 Fit side-chains REVERT: A 163 LYS cc_start: 0.8739 (tttm) cc_final: 0.8482 (tptp) REVERT: A 260 LEU cc_start: 0.8092 (tp) cc_final: 0.7880 (tp) REVERT: A 262 ILE cc_start: 0.7762 (tt) cc_final: 0.7306 (tt) REVERT: B 262 ILE cc_start: 0.7660 (tt) cc_final: 0.7379 (tt) REVERT: B 307 ILE cc_start: 0.7933 (mm) cc_final: 0.7704 (mt) REVERT: C 21 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6524 (tp) REVERT: C 41 HIS cc_start: 0.7889 (m90) cc_final: 0.7681 (m90) REVERT: C 353 ARG cc_start: 0.5285 (mtm-85) cc_final: 0.4984 (mtm-85) outliers start: 17 outliers final: 16 residues processed: 147 average time/residue: 0.0763 time to fit residues: 16.5705 Evaluate side-chains 147 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 74 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.148711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.103117 restraints weight = 9898.742| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.92 r_work: 0.2919 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9501 Z= 0.114 Angle : 0.513 7.546 12894 Z= 0.257 Chirality : 0.039 0.120 1638 Planarity : 0.003 0.028 1563 Dihedral : 4.247 21.075 1293 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.55 % Allowed : 20.21 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.26), residues: 1209 helix: 0.12 (0.18), residues: 981 sheet: -2.16 (0.73), residues: 54 loop : -1.60 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 353 TYR 0.012 0.001 TYR B 285 PHE 0.010 0.001 PHE A 240 TRP 0.004 0.001 TRP C 441 HIS 0.001 0.000 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9501) covalent geometry : angle 0.51293 (12894) hydrogen bonds : bond 0.03255 ( 517) hydrogen bonds : angle 4.02733 ( 1497) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2219.77 seconds wall clock time: 38 minutes 30.89 seconds (2310.89 seconds total)