Starting phenix.real_space_refine on Tue Mar 3 23:41:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x2l_22011/03_2026/6x2l_22011.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x2l_22011/03_2026/6x2l_22011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x2l_22011/03_2026/6x2l_22011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x2l_22011/03_2026/6x2l_22011.map" model { file = "/net/cci-nas-00/data/ceres_data/6x2l_22011/03_2026/6x2l_22011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x2l_22011/03_2026/6x2l_22011.cif" } resolution = 2.85 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 69 5.16 5 C 6159 2.51 5 N 1491 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9396 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3132 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 2 Restraints were copied for chains: B, C Time building chain proxies: 1.85, per 1000 atoms: 0.20 Number of scatterers: 9396 At special positions: 0 Unit cell: (113.984, 109.824, 82.368, 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 69 16.00 O 1677 8.00 N 1491 7.00 C 6159 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: 0.53 Conformation dependent library (CDL) restraints added in 369.0 milliseconds 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 81.3% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.613A pdb=" N ALA A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.739A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 86 removed outlier: 3.580A pdb=" N LEU A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.761A pdb=" N SER A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 117 removed outlier: 3.565A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.554A pdb=" N MET A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.531A 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 230 removed outlier: 3.517A pdb=" N GLY A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 Proline residue: A 259 - end of helix removed outlier: 3.631A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 299 removed outlier: 3.679A pdb=" N THR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.623A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.608A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 removed outlier: 3.548A pdb=" N THR A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 349 removed outlier: 4.158A pdb=" N ARG A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 363 removed outlier: 4.179A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.595A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.696A pdb=" N THR A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.527A pdb=" N SER A 405 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 removed outlier: 3.592A pdb=" N MET A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.995A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.594A pdb=" N LEU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG A 445 " --> pdb=" O TRP A 441 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.613A pdb=" N ALA B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.739A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 86 removed outlier: 3.580A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix removed outlier: 3.761A pdb=" N SER B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 117 removed outlier: 3.565A pdb=" N VAL B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.554A pdb=" N MET B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.531A 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 230 removed outlier: 3.518A pdb=" N GLY B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 Proline residue: B 259 - end of helix removed outlier: 3.631A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 299 removed outlier: 3.679A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.624A pdb=" N VAL B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 319 removed outlier: 3.608A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 removed outlier: 3.549A pdb=" N THR B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 349 removed outlier: 4.158A pdb=" N ARG B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN B 347 " --> pdb=" O CYS B 343 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 removed outlier: 4.179A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.595A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.696A pdb=" N THR B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 removed outlier: 3.528A pdb=" N SER B 405 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 427 removed outlier: 3.592A pdb=" N MET B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.994A pdb=" N ILE B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.595A pdb=" N LEU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG B 445 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 40 removed outlier: 3.613A pdb=" N ALA C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 removed outlier: 3.739A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 86 removed outlier: 3.579A pdb=" N LEU C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix removed outlier: 3.762A pdb=" N SER C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 117 removed outlier: 3.565A pdb=" N VAL C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.555A pdb=" N MET C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.531A 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 230 removed outlier: 3.518A pdb=" N GLY C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 Proline residue: C 259 - end of helix removed outlier: 3.631A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 299 removed outlier: 3.678A pdb=" N THR C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.622A pdb=" N VAL C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 319 removed outlier: 3.608A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 330 removed outlier: 3.548A pdb=" N THR C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 349 removed outlier: 4.158A pdb=" N ARG C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 363 removed outlier: 4.179A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.595A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.696A pdb=" N THR C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 removed outlier: 3.527A pdb=" N SER C 405 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 427 removed outlier: 3.592A pdb=" N MET C 419 " --> pdb=" O GLY C 415 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 432 removed outlier: 3.589A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.594A pdb=" N LEU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG C 445 " --> pdb=" O TRP C 441 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 464 " --> pdb=" O GLY C 460 " (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 167 624 hydrogen bonds defined for protein. 1836 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: 1.59 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1670 1.32 - 1.45: 2168 1.45 - 1.57: 5573 1.57 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 9534 Sorted by residual: bond pdb=" C MET C 419 " pdb=" O MET C 419 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.19e-02 7.06e+03 9.55e+00 bond pdb=" C MET A 419 " pdb=" O MET A 419 " ideal model delta sigma weight residual 1.237 1.200 0.036 1.19e-02 7.06e+03 9.28e+00 bond pdb=" C MET B 419 " pdb=" O MET B 419 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.19e-02 7.06e+03 9.09e+00 bond pdb=" N LEU B 372 " pdb=" CA LEU B 372 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.41e+00 bond pdb=" N LEU A 372 " pdb=" CA LEU A 372 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.20e+00 ... (remaining 9529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12242 1.89 - 3.77: 591 3.77 - 5.66: 73 5.66 - 7.55: 18 7.55 - 9.44: 12 Bond angle restraints: 12936 Sorted by residual: angle pdb=" C ASP C 388 " pdb=" N LEU C 389 " pdb=" CA LEU C 389 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C ASP A 388 " pdb=" N LEU A 389 " pdb=" CA LEU A 389 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C ASP B 388 " pdb=" N LEU B 389 " pdb=" CA LEU B 389 " ideal model delta sigma weight residual 121.54 128.84 -7.30 1.91e+00 2.74e-01 1.46e+01 angle pdb=" CB MET C 473 " pdb=" CG MET C 473 " pdb=" SD MET C 473 " ideal model delta sigma weight residual 112.70 103.26 9.44 3.00e+00 1.11e-01 9.89e+00 angle pdb=" CB MET A 473 " pdb=" CG MET A 473 " pdb=" SD MET A 473 " ideal model delta sigma weight residual 112.70 103.30 9.40 3.00e+00 1.11e-01 9.82e+00 ... (remaining 12931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 5150 16.78 - 33.56: 430 33.56 - 50.35: 96 50.35 - 67.13: 21 67.13 - 83.91: 9 Dihedral angle restraints: 5706 sinusoidal: 2172 harmonic: 3534 Sorted by residual: dihedral pdb=" CA LEU A 384 " pdb=" C LEU A 384 " pdb=" N ASN A 385 " pdb=" CA ASN A 385 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU C 384 " pdb=" C LEU C 384 " pdb=" N ASN C 385 " pdb=" CA ASN C 385 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU B 384 " pdb=" C LEU B 384 " pdb=" N ASN B 385 " pdb=" CA ASN B 385 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 847 0.039 - 0.077: 565 0.077 - 0.116: 154 0.116 - 0.154: 59 0.154 - 0.193: 19 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB VAL C 433 " pdb=" CA VAL C 433 " pdb=" CG1 VAL C 433 " pdb=" CG2 VAL C 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CB VAL B 433 " pdb=" CA VAL B 433 " pdb=" CG1 VAL B 433 " pdb=" CG2 VAL B 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CB VAL A 433 " pdb=" CA VAL A 433 " pdb=" CG1 VAL A 433 " pdb=" CG2 VAL A 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 1641 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 301 " -0.049 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO C 302 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 302 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 302 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 301 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO B 302 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 302 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 302 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO A 302 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.041 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 60 2.64 - 3.21: 8450 3.21 - 3.77: 14468 3.77 - 4.34: 20729 4.34 - 4.90: 33676 Nonbonded interactions: 77383 Sorted by model distance: nonbonded pdb=" N GLN B 413 " pdb=" OE1 GLN B 413 " model vdw 2.078 3.120 nonbonded pdb=" N GLN A 413 " pdb=" OE1 GLN A 413 " model vdw 2.079 3.120 nonbonded pdb=" N GLN C 413 " pdb=" OE1 GLN C 413 " model vdw 2.079 3.120 nonbonded pdb=" O SER A 331 " pdb=" OG SER A 331 " model vdw 2.339 3.040 nonbonded pdb=" O SER B 331 " pdb=" OG SER B 331 " model vdw 2.339 3.040 ... (remaining 77378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.390 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 : 0.009 0.075 9534 Z= 0.383 Angle : 0.960 9.435 12936 Z= 0.513 Chirality : 0.056 0.193 1644 Planarity : 0.007 0.073 1572 Dihedral : 13.682 83.912 3426 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.46 (0.14), residues: 1215 helix: -4.23 (0.07), residues: 975 sheet: -2.87 (0.80), residues: 54 loop : -2.72 (0.35), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 353 TYR 0.020 0.003 TYR C 373 PHE 0.021 0.003 PHE B 341 TRP 0.004 0.001 TRP C 276 HIS 0.003 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00927 ( 9534) covalent geometry : angle 0.95981 (12936) hydrogen bonds : bond 0.28419 ( 624) hydrogen bonds : angle 9.99473 ( 1836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.348 Fit side-chains REVERT: A 93 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7933 (mtm-85) REVERT: A 200 TYR cc_start: 0.8079 (m-80) cc_final: 0.7821 (m-80) REVERT: A 322 GLN cc_start: 0.8018 (tp40) cc_final: 0.7739 (mm-40) REVERT: A 352 LYS cc_start: 0.8364 (tmtm) cc_final: 0.7721 (mtmt) REVERT: A 393 GLN cc_start: 0.8605 (mt0) cc_final: 0.8184 (mt0) REVERT: B 200 TYR cc_start: 0.8220 (m-80) cc_final: 0.7731 (m-10) REVERT: B 248 MET cc_start: 0.8289 (tpp) cc_final: 0.8083 (tpt) REVERT: B 280 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7807 (tmm160) REVERT: C 200 TYR cc_start: 0.8208 (m-80) cc_final: 0.7746 (m-10) REVERT: C 248 MET cc_start: 0.8260 (tpp) cc_final: 0.8023 (mmt) REVERT: C 316 PHE cc_start: 0.8052 (t80) cc_final: 0.7805 (t80) REVERT: C 322 GLN cc_start: 0.8040 (tp40) cc_final: 0.7667 (mm110) outliers start: 0 outliers final: 2 residues processed: 200 average time/residue: 0.6102 time to fit residues: 129.7047 Evaluate side-chains 148 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain C residue 461 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 117 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 85 ASN C 85 ASN C 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.100320 restraints weight = 11269.476| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.84 r_work: 0.2924 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9534 Z= 0.125 Angle : 0.561 8.059 12936 Z= 0.293 Chirality : 0.038 0.132 1644 Planarity : 0.005 0.037 1572 Dihedral : 4.543 18.497 1297 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.74 % Allowed : 10.63 % Favored : 87.63 % 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 are not related in a simple way. whole: -2.97 (0.20), residues: 1215 helix: -1.59 (0.14), residues: 960 sheet: -3.05 (0.69), residues: 54 loop : -2.35 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 353 TYR 0.010 0.001 TYR B 373 PHE 0.015 0.002 PHE B 218 TRP 0.008 0.001 TRP A 441 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9534) covalent geometry : angle 0.56107 (12936) hydrogen bonds : bond 0.04190 ( 624) hydrogen bonds : angle 4.55718 ( 1836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.347 Fit side-chains REVERT: A 40 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7822 (tp30) REVERT: A 248 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8882 (mmt) REVERT: A 322 GLN cc_start: 0.7985 (tp40) cc_final: 0.7445 (mm-40) REVERT: A 329 MET cc_start: 0.6414 (mmm) cc_final: 0.5895 (mtt) REVERT: A 431 GLU cc_start: 0.7426 (pm20) cc_final: 0.7108 (mp0) REVERT: B 200 TYR cc_start: 0.8286 (m-80) cc_final: 0.7905 (m-10) REVERT: B 248 MET cc_start: 0.8964 (tpp) cc_final: 0.8729 (mmm) REVERT: B 473 MET cc_start: 0.6736 (ttt) cc_final: 0.6392 (mtp) REVERT: C 248 MET cc_start: 0.9048 (tpp) cc_final: 0.8574 (mmt) REVERT: C 280 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6922 (ttm170) REVERT: C 322 GLN cc_start: 0.7925 (tp40) cc_final: 0.7425 (mm-40) REVERT: C 393 GLN cc_start: 0.8718 (mt0) cc_final: 0.8493 (mt0) outliers start: 18 outliers final: 6 residues processed: 189 average time/residue: 0.5042 time to fit residues: 102.5838 Evaluate side-chains 148 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 373 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 85 ASN B 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.098296 restraints weight = 11080.696| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.82 r_work: 0.2947 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9534 Z= 0.140 Angle : 0.536 7.062 12936 Z= 0.275 Chirality : 0.039 0.125 1644 Planarity : 0.004 0.032 1572 Dihedral : 4.157 17.922 1293 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.71 % Allowed : 13.82 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.23), residues: 1215 helix: -0.20 (0.16), residues: 966 sheet: -2.53 (0.71), residues: 54 loop : -2.35 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 353 TYR 0.006 0.001 TYR B 373 PHE 0.016 0.002 PHE C 218 TRP 0.004 0.001 TRP B 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9534) covalent geometry : angle 0.53595 (12936) hydrogen bonds : bond 0.04010 ( 624) hydrogen bonds : angle 4.10926 ( 1836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.372 Fit side-chains REVERT: A 40 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7816 (tp30) REVERT: A 248 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8905 (mmp) REVERT: A 276 TRP cc_start: 0.7512 (m100) cc_final: 0.7147 (m-90) REVERT: A 393 GLN cc_start: 0.8679 (mt0) cc_final: 0.8217 (mt0) REVERT: A 431 GLU cc_start: 0.7408 (pm20) cc_final: 0.7098 (mp0) REVERT: B 200 TYR cc_start: 0.8331 (m-80) cc_final: 0.7955 (m-10) REVERT: B 248 MET cc_start: 0.8984 (tpp) cc_final: 0.8721 (mmm) REVERT: B 473 MET cc_start: 0.6730 (ttt) cc_final: 0.6412 (mtp) REVERT: C 248 MET cc_start: 0.9073 (tpp) cc_final: 0.8610 (mmt) REVERT: C 280 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.6936 (ttm170) REVERT: C 322 GLN cc_start: 0.7945 (tp40) cc_final: 0.7432 (mm-40) REVERT: C 393 GLN cc_start: 0.8724 (mt0) cc_final: 0.8383 (mt0) outliers start: 28 outliers final: 12 residues processed: 168 average time/residue: 0.5415 time to fit residues: 97.5043 Evaluate side-chains 158 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 114 optimal weight: 0.0060 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 111 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN B 393 GLN C 85 ASN C 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.100377 restraints weight = 11186.598| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.89 r_work: 0.2925 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9534 Z= 0.097 Angle : 0.475 6.308 12936 Z= 0.244 Chirality : 0.037 0.124 1644 Planarity : 0.003 0.029 1572 Dihedral : 3.802 17.846 1293 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.80 % Allowed : 14.98 % 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 are not related in a simple way. whole: 0.20 (0.24), residues: 1215 helix: 0.74 (0.17), residues: 963 sheet: -2.32 (0.72), residues: 54 loop : -1.74 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 315 TYR 0.008 0.001 TYR C 373 PHE 0.014 0.001 PHE C 316 TRP 0.004 0.001 TRP A 441 HIS 0.001 0.000 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 9534) covalent geometry : angle 0.47510 (12936) hydrogen bonds : bond 0.03174 ( 624) hydrogen bonds : angle 3.78868 ( 1836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.354 Fit side-chains REVERT: A 248 MET cc_start: 0.9076 (tpt) cc_final: 0.8856 (mmp) REVERT: A 393 GLN cc_start: 0.8608 (mt0) cc_final: 0.8126 (mt0) REVERT: A 431 GLU cc_start: 0.7346 (pm20) cc_final: 0.7081 (mp0) REVERT: B 75 MET cc_start: 0.9153 (mmm) cc_final: 0.8769 (tpp) REVERT: B 200 TYR cc_start: 0.8329 (m-80) cc_final: 0.7931 (m-10) REVERT: B 248 MET cc_start: 0.8982 (tpp) cc_final: 0.8739 (mmm) REVERT: B 303 LEU cc_start: 0.8169 (tp) cc_final: 0.7746 (tt) REVERT: B 473 MET cc_start: 0.6730 (ttt) cc_final: 0.6412 (mtp) REVERT: C 248 MET cc_start: 0.9040 (tpp) cc_final: 0.8745 (mmt) REVERT: C 303 LEU cc_start: 0.8200 (tp) cc_final: 0.7823 (tt) REVERT: C 322 GLN cc_start: 0.7912 (tp40) cc_final: 0.7380 (mm-40) REVERT: C 351 ASP cc_start: 0.6964 (t0) cc_final: 0.6633 (t0) REVERT: C 393 GLN cc_start: 0.8675 (mt0) cc_final: 0.8309 (mt0) REVERT: C 463 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7479 (tm-30) outliers start: 29 outliers final: 11 residues processed: 184 average time/residue: 0.5176 time to fit residues: 102.2482 Evaluate side-chains 155 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 0.0010 chunk 104 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.142106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102598 restraints weight = 11196.208| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.76 r_work: 0.2919 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9534 Z= 0.106 Angle : 0.489 5.833 12936 Z= 0.249 Chirality : 0.037 0.122 1644 Planarity : 0.003 0.026 1572 Dihedral : 3.722 18.438 1293 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.80 % Allowed : 17.29 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.25), residues: 1215 helix: 1.15 (0.17), residues: 963 sheet: -2.00 (0.77), residues: 54 loop : -1.64 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.008 0.001 TYR C 373 PHE 0.012 0.001 PHE A 218 TRP 0.003 0.000 TRP A 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9534) covalent geometry : angle 0.48933 (12936) hydrogen bonds : bond 0.03230 ( 624) hydrogen bonds : angle 3.72508 ( 1836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.403 Fit side-chains REVERT: A 276 TRP cc_start: 0.7430 (m100) cc_final: 0.7070 (m-90) REVERT: A 393 GLN cc_start: 0.8621 (mt0) cc_final: 0.8131 (mt0) REVERT: A 431 GLU cc_start: 0.7426 (pm20) cc_final: 0.7097 (mp0) REVERT: A 463 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7188 (tt0) REVERT: B 75 MET cc_start: 0.9137 (mmm) cc_final: 0.8791 (tpp) REVERT: B 200 TYR cc_start: 0.8356 (m-80) cc_final: 0.7974 (m-10) REVERT: B 248 MET cc_start: 0.9011 (tpp) cc_final: 0.8760 (mmm) REVERT: B 303 LEU cc_start: 0.8218 (tp) cc_final: 0.7805 (tt) REVERT: B 320 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7343 (mmt) REVERT: B 473 MET cc_start: 0.6788 (ttt) cc_final: 0.6451 (mtp) REVERT: C 248 MET cc_start: 0.9069 (tpp) cc_final: 0.8759 (mmt) REVERT: C 303 LEU cc_start: 0.8221 (tp) cc_final: 0.7849 (tt) REVERT: C 322 GLN cc_start: 0.7829 (tp40) cc_final: 0.7191 (mm-40) REVERT: C 342 ARG cc_start: 0.7321 (ppt170) cc_final: 0.7078 (ppt90) REVERT: C 351 ASP cc_start: 0.7063 (t0) cc_final: 0.6755 (t0) REVERT: C 463 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7568 (tm-30) outliers start: 29 outliers final: 12 residues processed: 162 average time/residue: 0.5087 time to fit residues: 88.6765 Evaluate side-chains 159 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 29 optimal weight: 0.0670 chunk 95 optimal weight: 0.0020 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 overall best weight: 0.6128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN C 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.142701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.103205 restraints weight = 11188.216| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.76 r_work: 0.2928 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9534 Z= 0.103 Angle : 0.481 5.558 12936 Z= 0.245 Chirality : 0.037 0.122 1644 Planarity : 0.003 0.026 1572 Dihedral : 3.662 18.434 1293 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.48 % Allowed : 16.52 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1215 helix: 1.47 (0.17), residues: 963 sheet: -1.86 (0.79), residues: 54 loop : -1.57 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.009 0.001 TYR C 373 PHE 0.014 0.001 PHE C 316 TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9534) covalent geometry : angle 0.48136 (12936) hydrogen bonds : bond 0.03157 ( 624) hydrogen bonds : angle 3.67117 ( 1836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.249 Fit side-chains REVERT: A 276 TRP cc_start: 0.7438 (m100) cc_final: 0.7136 (m-90) REVERT: A 393 GLN cc_start: 0.8606 (mt0) cc_final: 0.8099 (mt0) REVERT: A 431 GLU cc_start: 0.7390 (pm20) cc_final: 0.7071 (mp0) REVERT: B 75 MET cc_start: 0.9151 (mmm) cc_final: 0.8801 (tpp) REVERT: B 200 TYR cc_start: 0.8316 (m-80) cc_final: 0.7960 (m-10) REVERT: B 248 MET cc_start: 0.9015 (tpp) cc_final: 0.8754 (mmm) REVERT: B 303 LEU cc_start: 0.8204 (tp) cc_final: 0.7808 (tt) REVERT: B 463 GLU cc_start: 0.7897 (tt0) cc_final: 0.7419 (tm-30) REVERT: B 473 MET cc_start: 0.6780 (ttt) cc_final: 0.6427 (mtp) REVERT: C 206 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7322 (t80) REVERT: C 248 MET cc_start: 0.9082 (tpp) cc_final: 0.8765 (mmt) REVERT: C 303 LEU cc_start: 0.8209 (tp) cc_final: 0.7835 (tt) REVERT: C 322 GLN cc_start: 0.7855 (tp40) cc_final: 0.7298 (mm-40) REVERT: C 342 ARG cc_start: 0.7370 (ppt170) cc_final: 0.7113 (ppt90) REVERT: C 351 ASP cc_start: 0.7121 (t0) cc_final: 0.6782 (t0) REVERT: C 393 GLN cc_start: 0.8658 (mt0) cc_final: 0.8396 (mt0) REVERT: C 463 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7554 (tm-30) outliers start: 36 outliers final: 14 residues processed: 170 average time/residue: 0.5029 time to fit residues: 91.8558 Evaluate side-chains 164 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 85 ASN B 85 ASN C 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.138766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.097405 restraints weight = 11241.350| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.86 r_work: 0.2878 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9534 Z= 0.121 Angle : 0.508 6.544 12936 Z= 0.256 Chirality : 0.038 0.123 1644 Planarity : 0.003 0.027 1572 Dihedral : 3.714 18.106 1293 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.71 % Allowed : 17.78 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1215 helix: 1.51 (0.17), residues: 969 sheet: -1.88 (0.78), residues: 54 loop : -1.48 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.012 0.001 TYR C 373 PHE 0.013 0.001 PHE A 218 TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9534) covalent geometry : angle 0.50768 (12936) hydrogen bonds : bond 0.03370 ( 624) hydrogen bonds : angle 3.72273 ( 1836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.346 Fit side-chains REVERT: A 276 TRP cc_start: 0.7397 (m100) cc_final: 0.7068 (m-90) REVERT: A 393 GLN cc_start: 0.8658 (mt0) cc_final: 0.8146 (mt0) REVERT: A 431 GLU cc_start: 0.7366 (pm20) cc_final: 0.7119 (mp0) REVERT: A 463 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7164 (tt0) REVERT: B 200 TYR cc_start: 0.8331 (m-80) cc_final: 0.7991 (m-10) REVERT: B 248 MET cc_start: 0.9046 (tpp) cc_final: 0.8788 (mmm) REVERT: B 303 LEU cc_start: 0.8244 (tp) cc_final: 0.7835 (tt) REVERT: B 322 GLN cc_start: 0.7899 (tp40) cc_final: 0.7320 (mm-40) REVERT: B 463 GLU cc_start: 0.7918 (tt0) cc_final: 0.7425 (tm-30) REVERT: B 473 MET cc_start: 0.6672 (ttt) cc_final: 0.6319 (mtp) REVERT: C 248 MET cc_start: 0.9124 (tpp) cc_final: 0.8672 (mmt) REVERT: C 303 LEU cc_start: 0.8195 (tp) cc_final: 0.7831 (tt) REVERT: C 322 GLN cc_start: 0.7779 (tp40) cc_final: 0.7229 (mm-40) REVERT: C 342 ARG cc_start: 0.7335 (ppt170) cc_final: 0.7058 (ppt90) REVERT: C 351 ASP cc_start: 0.7116 (t0) cc_final: 0.6739 (t0) REVERT: C 393 GLN cc_start: 0.8693 (mt0) cc_final: 0.8392 (mt0) REVERT: C 463 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7545 (tm-30) outliers start: 28 outliers final: 17 residues processed: 167 average time/residue: 0.5035 time to fit residues: 90.4509 Evaluate side-chains 167 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 114 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.142052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.102357 restraints weight = 11214.121| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.76 r_work: 0.2908 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9534 Z= 0.113 Angle : 0.503 6.087 12936 Z= 0.254 Chirality : 0.038 0.121 1644 Planarity : 0.003 0.026 1572 Dihedral : 3.688 17.671 1293 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.00 % Allowed : 17.87 % Favored : 79.13 % 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 are not related in a simple way. whole: 1.43 (0.25), residues: 1215 helix: 1.60 (0.17), residues: 972 sheet: -1.83 (0.77), residues: 54 loop : -1.52 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.015 0.001 TYR C 373 PHE 0.015 0.001 PHE C 316 TRP 0.003 0.000 TRP A 19 HIS 0.001 0.000 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9534) covalent geometry : angle 0.50263 (12936) hydrogen bonds : bond 0.03279 ( 624) hydrogen bonds : angle 3.70028 ( 1836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.373 Fit side-chains REVERT: A 276 TRP cc_start: 0.7318 (m100) cc_final: 0.7096 (m-90) REVERT: A 393 GLN cc_start: 0.8625 (mt0) cc_final: 0.8120 (mt0) REVERT: A 431 GLU cc_start: 0.7278 (pm20) cc_final: 0.7064 (mp0) REVERT: B 75 MET cc_start: 0.9206 (mmm) cc_final: 0.8850 (tpp) REVERT: B 142 MET cc_start: 0.8975 (mmm) cc_final: 0.8743 (mmm) REVERT: B 200 TYR cc_start: 0.8285 (m-80) cc_final: 0.7942 (m-10) REVERT: B 248 MET cc_start: 0.9019 (tpp) cc_final: 0.8756 (mmm) REVERT: B 322 GLN cc_start: 0.7869 (tp40) cc_final: 0.7355 (mm-40) REVERT: B 463 GLU cc_start: 0.7866 (tt0) cc_final: 0.7409 (tm-30) REVERT: B 473 MET cc_start: 0.6749 (ttt) cc_final: 0.6389 (mtp) REVERT: C 248 MET cc_start: 0.9087 (tpp) cc_final: 0.8621 (mmt) REVERT: C 303 LEU cc_start: 0.8204 (tp) cc_final: 0.7815 (tt) REVERT: C 322 GLN cc_start: 0.7767 (tp40) cc_final: 0.7255 (mm-40) REVERT: C 342 ARG cc_start: 0.7345 (ppt170) cc_final: 0.7072 (ppt90) REVERT: C 351 ASP cc_start: 0.7108 (t0) cc_final: 0.6765 (t0) REVERT: C 393 GLN cc_start: 0.8665 (mt0) cc_final: 0.8354 (mt0) REVERT: C 463 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7498 (tm-30) outliers start: 31 outliers final: 20 residues processed: 163 average time/residue: 0.5212 time to fit residues: 91.1285 Evaluate side-chains 170 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 120 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN C 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.101329 restraints weight = 11150.348| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.76 r_work: 0.2899 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9534 Z= 0.114 Angle : 0.506 7.531 12936 Z= 0.255 Chirality : 0.038 0.121 1644 Planarity : 0.003 0.026 1572 Dihedral : 3.699 17.389 1293 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.42 % Allowed : 18.74 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.25), residues: 1215 helix: 1.67 (0.17), residues: 969 sheet: -1.83 (0.76), residues: 54 loop : -1.49 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.015 0.001 TYR C 373 PHE 0.019 0.001 PHE C 316 TRP 0.002 0.000 TRP A 19 HIS 0.001 0.000 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9534) covalent geometry : angle 0.50631 (12936) hydrogen bonds : bond 0.03293 ( 624) hydrogen bonds : angle 3.71345 ( 1836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.376 Fit side-chains REVERT: A 276 TRP cc_start: 0.7301 (m100) cc_final: 0.7084 (m-90) REVERT: A 393 GLN cc_start: 0.8652 (mt0) cc_final: 0.8143 (mt0) REVERT: B 75 MET cc_start: 0.9229 (mmm) cc_final: 0.8889 (tpp) REVERT: B 142 MET cc_start: 0.8999 (mmm) cc_final: 0.8781 (mmm) REVERT: B 200 TYR cc_start: 0.8269 (m-80) cc_final: 0.7918 (m-10) REVERT: B 248 MET cc_start: 0.9039 (tpp) cc_final: 0.8777 (mmm) REVERT: B 322 GLN cc_start: 0.7934 (tp40) cc_final: 0.7383 (mm-40) REVERT: B 463 GLU cc_start: 0.7892 (tt0) cc_final: 0.7435 (tm-30) REVERT: B 473 MET cc_start: 0.6752 (ttt) cc_final: 0.6396 (mtp) REVERT: C 248 MET cc_start: 0.9101 (tpp) cc_final: 0.8644 (mmt) REVERT: C 303 LEU cc_start: 0.8218 (tp) cc_final: 0.7838 (tt) REVERT: C 322 GLN cc_start: 0.7655 (tp40) cc_final: 0.7197 (mm-40) REVERT: C 342 ARG cc_start: 0.7347 (ppt170) cc_final: 0.7058 (ppt90) REVERT: C 351 ASP cc_start: 0.7187 (t0) cc_final: 0.6821 (t0) REVERT: C 393 GLN cc_start: 0.8672 (mt0) cc_final: 0.8352 (mt0) REVERT: C 463 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7504 (tm-30) outliers start: 25 outliers final: 20 residues processed: 161 average time/residue: 0.4913 time to fit residues: 85.1500 Evaluate side-chains 167 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN C 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.098651 restraints weight = 11314.507| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.84 r_work: 0.2904 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9534 Z= 0.121 Angle : 0.521 9.622 12936 Z= 0.261 Chirality : 0.038 0.131 1644 Planarity : 0.003 0.027 1572 Dihedral : 3.733 17.121 1293 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.22 % Allowed : 18.94 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.25), residues: 1215 helix: 1.67 (0.18), residues: 969 sheet: -1.78 (0.76), residues: 54 loop : -1.46 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 61 TYR 0.015 0.001 TYR C 373 PHE 0.013 0.001 PHE A 218 TRP 0.003 0.000 TRP C 276 HIS 0.001 0.000 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9534) covalent geometry : angle 0.52113 (12936) hydrogen bonds : bond 0.03362 ( 624) hydrogen bonds : angle 3.73824 ( 1836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.297 Fit side-chains REVERT: A 276 TRP cc_start: 0.7290 (m100) cc_final: 0.7020 (m-90) REVERT: A 279 PHE cc_start: 0.8080 (m-80) cc_final: 0.7861 (m-80) REVERT: A 393 GLN cc_start: 0.8671 (mt0) cc_final: 0.8166 (mt0) REVERT: B 75 MET cc_start: 0.9226 (mmm) cc_final: 0.8884 (tpp) REVERT: B 142 MET cc_start: 0.8998 (mmm) cc_final: 0.8774 (mmm) REVERT: B 200 TYR cc_start: 0.8301 (m-80) cc_final: 0.7959 (m-10) REVERT: B 248 MET cc_start: 0.9058 (tpp) cc_final: 0.8828 (mmm) REVERT: B 322 GLN cc_start: 0.7832 (tp40) cc_final: 0.7292 (mm-40) REVERT: B 329 MET cc_start: 0.6436 (mmm) cc_final: 0.6036 (mmt) REVERT: B 463 GLU cc_start: 0.7918 (tt0) cc_final: 0.7468 (tm-30) REVERT: B 473 MET cc_start: 0.6708 (ttt) cc_final: 0.6384 (mtp) REVERT: C 248 MET cc_start: 0.9116 (tpp) cc_final: 0.8665 (mmt) REVERT: C 303 LEU cc_start: 0.8214 (tp) cc_final: 0.7823 (tt) REVERT: C 322 GLN cc_start: 0.7716 (tp40) cc_final: 0.7263 (mm-40) REVERT: C 342 ARG cc_start: 0.7350 (ppt170) cc_final: 0.7051 (ppt90) REVERT: C 351 ASP cc_start: 0.7225 (t0) cc_final: 0.6832 (t0) REVERT: C 393 GLN cc_start: 0.8693 (mt0) cc_final: 0.8361 (mt0) REVERT: C 463 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7541 (tm-30) outliers start: 23 outliers final: 19 residues processed: 164 average time/residue: 0.5140 time to fit residues: 90.5090 Evaluate side-chains 169 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 96 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 98 optimal weight: 0.0770 chunk 37 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN C 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.101856 restraints weight = 11278.138| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.86 r_work: 0.2932 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9534 Z= 0.100 Angle : 0.509 8.852 12936 Z= 0.254 Chirality : 0.037 0.122 1644 Planarity : 0.003 0.034 1572 Dihedral : 3.586 16.006 1293 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.64 % Allowed : 19.71 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.26), residues: 1215 helix: 1.88 (0.18), residues: 969 sheet: -1.79 (0.77), residues: 54 loop : -1.32 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 61 TYR 0.014 0.001 TYR C 373 PHE 0.011 0.001 PHE A 218 TRP 0.003 0.001 TRP A 441 HIS 0.001 0.000 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 9534) covalent geometry : angle 0.50896 (12936) hydrogen bonds : bond 0.02977 ( 624) hydrogen bonds : angle 3.63279 ( 1836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3503.43 seconds wall clock time: 60 minutes 6.76 seconds (3606.76 seconds total)