Starting phenix.real_space_refine on Thu Mar 13 23:39:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x3f_22021/03_2025/6x3f_22021.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x3f_22021/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6x3f_22021/03_2025/6x3f_22021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x3f_22021/03_2025/6x3f_22021.map" model { file = "/net/cci-nas-00/data/ceres_data/6x3f_22021/03_2025/6x3f_22021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x3f_22021/03_2025/6x3f_22021.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, B Time building chain proxies: 5.99, per 1000 atoms: 0.64 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: 2.31 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.88 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: 2.57 Time building geometry restraints manager: 2.74 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 2.280 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.120 Find NCS groups from input model: 0.160 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.180 ------------------------------------------------------------------------------- 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= 0.385 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP A 441 HIS 0.001 0.001 HIS C 41 PHE 0.011 0.002 PHE C 159 TYR 0.012 0.002 TYR C 162 ARG 0.005 0.001 ARG A 353 *********************** 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 : 0.965 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: 0.2492 time to fit residues: 58.2704 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 : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 108 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.146007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102137 restraints weight = 10046.324| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.91 r_work: 0.2943 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9501 Z= 0.217 Angle : 0.594 6.576 12894 Z= 0.311 Chirality : 0.041 0.142 1638 Planarity : 0.006 0.042 1563 Dihedral : 5.351 19.903 1293 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.92 % Allowed : 15.16 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.49 (0.19), residues: 1209 helix: -2.71 (0.13), residues: 948 sheet: -3.12 (0.65), residues: 54 loop : -2.76 (0.35), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 441 HIS 0.001 0.000 HIS B 41 PHE 0.022 0.002 PHE A 306 TYR 0.006 0.001 TYR A 285 ARG 0.006 0.001 ARG A 353 *********************** 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 185 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.031 Fit side-chains REVERT: A 163 LYS cc_start: 0.8742 (tttm) cc_final: 0.8388 (tmtt) REVERT: A 228 LYS cc_start: 0.7610 (mtpt) cc_final: 0.7367 (mttp) REVERT: A 262 ILE cc_start: 0.8011 (tt) cc_final: 0.7494 (pt) REVERT: B 149 MET cc_start: 0.9003 (mtt) cc_final: 0.8798 (mtp) REVERT: B 228 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7584 (mttp) REVERT: B 280 ARG cc_start: 0.7026 (ttt180) cc_final: 0.6200 (ttp-110) REVERT: B 325 LEU cc_start: 0.6660 (tt) cc_final: 0.5776 (mp) REVERT: C 21 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6709 (tp) REVERT: C 149 MET cc_start: 0.9020 (mtt) cc_final: 0.8808 (mtp) REVERT: C 228 LYS cc_start: 0.7858 (mtpt) cc_final: 0.7621 (mttp) REVERT: C 280 ARG cc_start: 0.7042 (ttt180) cc_final: 0.6300 (ttp-110) REVERT: C 298 ILE cc_start: 0.8578 (mm) cc_final: 0.8316 (mp) REVERT: C 325 LEU cc_start: 0.6674 (tt) cc_final: 0.5995 (mp) REVERT: C 342 ARG cc_start: 0.7030 (ttp80) cc_final: 0.6657 (ttp-170) outliers start: 30 outliers final: 17 residues processed: 175 average time/residue: 0.2396 time to fit residues: 56.6826 Evaluate side-chains 159 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 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 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 8 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.145591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.100585 restraints weight = 10181.125| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.96 r_work: 0.2899 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9501 Z= 0.218 Angle : 0.562 7.999 12894 Z= 0.287 Chirality : 0.040 0.138 1638 Planarity : 0.004 0.031 1563 Dihedral : 4.941 16.864 1293 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.33 % Allowed : 17.59 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.22), residues: 1209 helix: -1.47 (0.16), residues: 945 sheet: -2.72 (0.68), residues: 54 loop : -2.39 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 441 HIS 0.002 0.001 HIS B 41 PHE 0.020 0.001 PHE B 306 TYR 0.007 0.001 TYR C 285 ARG 0.008 0.001 ARG B 353 *********************** 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 161 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.050 Fit side-chains REVERT: A 228 LYS cc_start: 0.7565 (mtpt) cc_final: 0.7355 (mttm) REVERT: A 298 ILE cc_start: 0.8378 (mm) cc_final: 0.8158 (mt) REVERT: B 41 HIS cc_start: 0.7262 (t70) cc_final: 0.6835 (m-70) REVERT: B 228 LYS cc_start: 0.7619 (mtpt) cc_final: 0.7403 (mttp) REVERT: B 342 ARG cc_start: 0.6918 (ttp80) cc_final: 0.6587 (ttp80) REVERT: C 21 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6640 (tp) REVERT: C 149 MET cc_start: 0.8931 (mtt) cc_final: 0.8718 (mtp) REVERT: C 228 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7499 (mttp) REVERT: C 325 LEU cc_start: 0.6331 (tt) cc_final: 0.5700 (mp) REVERT: C 342 ARG cc_start: 0.7034 (ttp80) cc_final: 0.6681 (ttp-170) outliers start: 24 outliers final: 14 residues processed: 154 average time/residue: 0.2031 time to fit residues: 44.6208 Evaluate side-chains 149 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 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 69 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 96 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.146767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102289 restraints weight = 10023.732| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.91 r_work: 0.2931 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2419 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= 0.191 Angle : 0.526 8.485 12894 Z= 0.269 Chirality : 0.040 0.119 1638 Planarity : 0.004 0.030 1563 Dihedral : 4.683 16.714 1293 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.46 % Allowed : 18.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.24), residues: 1209 helix: -0.91 (0.17), residues: 948 sheet: -2.58 (0.69), residues: 54 loop : -2.03 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 441 HIS 0.002 0.001 HIS B 41 PHE 0.017 0.001 PHE C 306 TYR 0.005 0.001 TYR C 285 ARG 0.009 0.000 ARG B 353 *********************** 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 157 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.189 Fit side-chains REVERT: A 41 HIS cc_start: 0.6912 (t70) cc_final: 0.6630 (m-70) REVERT: A 262 ILE cc_start: 0.7731 (tt) cc_final: 0.7279 (tt) REVERT: B 41 HIS cc_start: 0.7383 (t70) cc_final: 0.7095 (m-70) REVERT: B 228 LYS cc_start: 0.7643 (mtpt) cc_final: 0.7279 (mttt) REVERT: B 286 MET cc_start: 0.8326 (mtm) cc_final: 0.8109 (mtt) REVERT: B 342 ARG cc_start: 0.6969 (ttp80) cc_final: 0.6637 (ttp80) REVERT: C 21 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6718 (tp) REVERT: C 41 HIS cc_start: 0.7003 (t70) cc_final: 0.6727 (m-70) REVERT: C 342 ARG cc_start: 0.7016 (ttp80) cc_final: 0.6509 (ttp-170) outliers start: 15 outliers final: 12 residues processed: 154 average time/residue: 0.2221 time to fit residues: 48.7490 Evaluate side-chains 148 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 304 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 406 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.147195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.101922 restraints weight = 10002.457| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.94 r_work: 0.2906 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2588 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= 0.178 Angle : 0.510 7.333 12894 Z= 0.260 Chirality : 0.039 0.120 1638 Planarity : 0.003 0.027 1563 Dihedral : 4.517 17.849 1293 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.65 % Allowed : 19.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.25), residues: 1209 helix: -0.61 (0.17), residues: 960 sheet: -2.37 (0.72), residues: 54 loop : -1.87 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 441 HIS 0.001 0.001 HIS B 41 PHE 0.013 0.001 PHE C 306 TYR 0.005 0.001 TYR C 285 ARG 0.006 0.000 ARG B 353 *********************** 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 153 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.324 Fit side-chains REVERT: A 163 LYS cc_start: 0.8690 (tttm) cc_final: 0.8421 (tptp) REVERT: A 262 ILE cc_start: 0.7788 (tt) cc_final: 0.7360 (tt) REVERT: B 228 LYS cc_start: 0.7565 (mtpt) cc_final: 0.7188 (mttt) REVERT: B 353 ARG cc_start: 0.5219 (mtm-85) cc_final: 0.5010 (mtm180) REVERT: C 21 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6604 (tp) REVERT: C 342 ARG cc_start: 0.6934 (ttp80) cc_final: 0.6432 (ttp-170) outliers start: 17 outliers final: 12 residues processed: 149 average time/residue: 0.2587 time to fit residues: 57.6019 Evaluate side-chains 146 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 2.180 ------------------------------------------------------------------------------- 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 328 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.147523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.101956 restraints weight = 9918.107| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.95 r_work: 0.2924 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2693 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= 0.183 Angle : 0.514 6.485 12894 Z= 0.260 Chirality : 0.039 0.121 1638 Planarity : 0.003 0.026 1563 Dihedral : 4.446 19.653 1293 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1209 helix: -0.39 (0.18), residues: 960 sheet: -2.29 (0.73), residues: 54 loop : -1.70 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 441 HIS 0.001 0.000 HIS C 296 PHE 0.011 0.001 PHE C 306 TYR 0.015 0.001 TYR B 285 ARG 0.005 0.000 ARG B 353 *********************** 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 162 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.099 Fit side-chains REVERT: A 163 LYS cc_start: 0.8681 (tttm) cc_final: 0.8408 (tptp) REVERT: A 262 ILE cc_start: 0.7820 (tt) cc_final: 0.7350 (tt) REVERT: B 228 LYS cc_start: 0.7535 (mtpt) cc_final: 0.7186 (mttt) REVERT: B 307 ILE cc_start: 0.7903 (mm) cc_final: 0.7694 (mt) REVERT: B 353 ARG cc_start: 0.5289 (mtm-85) cc_final: 0.5017 (mtm-85) REVERT: B 442 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8255 (tt) REVERT: B 446 PHE cc_start: 0.7855 (m-80) cc_final: 0.7589 (m-80) REVERT: C 21 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6570 (tp) REVERT: C 342 ARG cc_start: 0.7067 (ttp80) cc_final: 0.6541 (ttp-170) outliers start: 22 outliers final: 17 residues processed: 155 average time/residue: 0.1923 time to fit residues: 43.2295 Evaluate side-chains 155 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 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 442 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 115 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 14 optimal weight: 0.0070 chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 52 optimal weight: 0.0770 chunk 104 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 68 optimal weight: 10.0000 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.150524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105183 restraints weight = 10051.545| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.95 r_work: 0.2941 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9501 Z= 0.126 Angle : 0.479 6.071 12894 Z= 0.246 Chirality : 0.038 0.117 1638 Planarity : 0.003 0.025 1563 Dihedral : 4.199 19.310 1293 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.43 % Allowed : 19.63 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 1209 helix: -0.12 (0.18), residues: 978 sheet: -2.26 (0.74), residues: 54 loop : -1.61 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 441 HIS 0.001 0.000 HIS B 41 PHE 0.009 0.001 PHE B 306 TYR 0.018 0.001 TYR B 285 ARG 0.005 0.000 ARG B 353 *********************** 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 164 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.037 Fit side-chains REVERT: A 163 LYS cc_start: 0.8718 (tttm) cc_final: 0.8447 (tptp) REVERT: A 260 LEU cc_start: 0.8127 (tp) cc_final: 0.7923 (tp) REVERT: A 262 ILE cc_start: 0.7757 (tt) cc_final: 0.7286 (tt) REVERT: A 286 MET cc_start: 0.8277 (mtm) cc_final: 0.8059 (mtt) REVERT: A 367 MET cc_start: 0.6948 (mtm) cc_final: 0.6720 (mtm) REVERT: B 228 LYS cc_start: 0.7541 (mtpt) cc_final: 0.7170 (mtmt) REVERT: B 258 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7635 (tmm) REVERT: B 307 ILE cc_start: 0.7946 (mm) cc_final: 0.7737 (mt) REVERT: B 437 ILE cc_start: 0.8103 (tp) cc_final: 0.7896 (tp) REVERT: C 21 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6516 (tp) outliers start: 25 outliers final: 19 residues processed: 158 average time/residue: 0.1913 time to fit residues: 43.6529 Evaluate side-chains 159 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 258 MET 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 273 VAL 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 69 optimal weight: 0.0570 chunk 52 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 43 optimal weight: 0.0980 chunk 116 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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 = 0.149872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104258 restraints weight = 10078.651| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.95 r_work: 0.2934 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2929 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= 0.144 Angle : 0.491 7.260 12894 Z= 0.248 Chirality : 0.039 0.133 1638 Planarity : 0.003 0.027 1563 Dihedral : 4.146 19.582 1293 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.04 % Allowed : 20.31 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.26), residues: 1209 helix: 0.01 (0.18), residues: 981 sheet: -2.21 (0.75), residues: 54 loop : -1.57 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 441 HIS 0.001 0.000 HIS B 41 PHE 0.009 0.001 PHE C 306 TYR 0.011 0.001 TYR B 285 ARG 0.007 0.000 ARG B 353 *********************** 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: 21 poor density : 136 time to evaluate : 1.088 Fit side-chains REVERT: A 163 LYS cc_start: 0.8727 (tttm) cc_final: 0.8450 (tptp) REVERT: A 262 ILE cc_start: 0.7788 (tt) cc_final: 0.7323 (tt) REVERT: A 286 MET cc_start: 0.8290 (mtm) cc_final: 0.8076 (mtt) REVERT: B 228 LYS cc_start: 0.7499 (mtpt) cc_final: 0.7142 (mtmt) REVERT: B 258 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7634 (tmm) REVERT: B 432 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8236 (m-30) REVERT: C 21 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6519 (tp) outliers start: 21 outliers final: 18 residues processed: 152 average time/residue: 0.1968 time to fit residues: 43.6290 Evaluate side-chains 153 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 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 A residue 406 ILE 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 258 MET Chi-restraints excluded: chain B residue 328 LEU 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 Chi-restraints excluded: chain C residue 432 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 7 optimal weight: 0.0770 chunk 27 optimal weight: 7.9990 chunk 114 optimal weight: 0.0170 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.151188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105426 restraints weight = 9954.594| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.94 r_work: 0.2948 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9501 Z= 0.132 Angle : 0.486 7.100 12894 Z= 0.246 Chirality : 0.038 0.117 1638 Planarity : 0.003 0.027 1563 Dihedral : 4.064 19.340 1293 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.04 % Allowed : 20.41 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1209 helix: 0.22 (0.18), residues: 981 sheet: -2.20 (0.75), residues: 54 loop : -1.56 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 441 HIS 0.001 0.000 HIS C 296 PHE 0.018 0.001 PHE A 341 TYR 0.014 0.001 TYR B 285 ARG 0.007 0.000 ARG B 353 *********************** 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 158 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.951 Fit side-chains REVERT: A 163 LYS cc_start: 0.8701 (tttm) cc_final: 0.8366 (tptp) REVERT: A 262 ILE cc_start: 0.7678 (tt) cc_final: 0.7221 (tt) REVERT: A 286 MET cc_start: 0.8261 (mtm) cc_final: 0.8042 (mtt) REVERT: B 228 LYS cc_start: 0.7397 (mtpt) cc_final: 0.7061 (mtmt) REVERT: B 329 MET cc_start: 0.5424 (mmm) cc_final: 0.5215 (mmm) REVERT: B 432 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8238 (m-30) REVERT: C 21 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6477 (tp) outliers start: 21 outliers final: 18 residues processed: 155 average time/residue: 0.1828 time to fit residues: 41.3346 Evaluate side-chains 152 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 113 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 83 optimal weight: 0.0060 chunk 56 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.150863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.105133 restraints weight = 10088.571| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.94 r_work: 0.2944 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3053 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= 0.143 Angle : 0.494 7.630 12894 Z= 0.248 Chirality : 0.039 0.117 1638 Planarity : 0.003 0.032 1563 Dihedral : 4.064 19.509 1293 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.94 % Allowed : 20.51 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1209 helix: 0.32 (0.18), residues: 984 sheet: -2.21 (0.75), residues: 54 loop : -1.46 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 441 HIS 0.001 0.000 HIS C 296 PHE 0.015 0.001 PHE A 341 TYR 0.013 0.001 TYR B 285 ARG 0.007 0.000 ARG B 353 ********************** 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: 20 poor density : 131 time to evaluate : 1.043 Fit side-chains REVERT: A 163 LYS cc_start: 0.8666 (tttm) cc_final: 0.8401 (tptp) REVERT: A 262 ILE cc_start: 0.7745 (tt) cc_final: 0.7291 (tt) REVERT: A 286 MET cc_start: 0.8295 (mtm) cc_final: 0.8069 (mtt) REVERT: A 329 MET cc_start: 0.6206 (mmp) cc_final: 0.5800 (mmm) REVERT: B 228 LYS cc_start: 0.7398 (mtpt) cc_final: 0.7072 (mtmt) REVERT: B 258 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7616 (tmm) REVERT: B 329 MET cc_start: 0.5433 (mmm) cc_final: 0.5233 (mmm) REVERT: B 432 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8245 (m-30) REVERT: C 21 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6486 (tp) outliers start: 20 outliers final: 16 residues processed: 147 average time/residue: 0.1931 time to fit residues: 41.4634 Evaluate side-chains 151 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 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 258 MET Chi-restraints excluded: chain B residue 328 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.145960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.100823 restraints weight = 9987.509| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.97 r_work: 0.2866 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9501 Z= 0.260 Angle : 0.563 7.368 12894 Z= 0.279 Chirality : 0.042 0.151 1638 Planarity : 0.003 0.027 1563 Dihedral : 4.407 22.079 1293 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.14 % Allowed : 20.31 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1209 helix: 0.18 (0.18), residues: 963 sheet: -2.17 (0.74), residues: 54 loop : -1.17 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 19 HIS 0.001 0.000 HIS C 296 PHE 0.039 0.002 PHE A 341 TYR 0.007 0.001 TYR C 305 ARG 0.007 0.001 ARG B 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5432.37 seconds wall clock time: 95 minutes 23.31 seconds (5723.31 seconds total)