Starting phenix.real_space_refine on Thu Mar 13 23:15:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x2l_22011/03_2025/6x2l_22011.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x2l_22011/03_2025/6x2l_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_2025/6x2l_22011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x2l_22011/03_2025/6x2l_22011.map" model { file = "/net/cci-nas-00/data/ceres_data/6x2l_22011/03_2025/6x2l_22011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x2l_22011/03_2025/6x2l_22011.cif" } resolution = 2.85 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 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, B Time building chain proxies: 6.34, per 1000 atoms: 0.67 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.05 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: 2.64 Time building geometry restraints manager: 2.63 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: 0.06 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: 2.400 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.960 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:16.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.980 ------------------------------------------------------------------------------- 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= 0.585 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 : 2.99 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 (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: -6.46 (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 TRP 0.004 0.001 TRP C 276 HIS 0.003 0.001 HIS B 41 PHE 0.021 0.003 PHE B 341 TYR 0.020 0.003 TYR C 373 ARG 0.006 0.001 ARG B 353 *********************** 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 : 1.044 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: 1.2598 time to fit residues: 268.5982 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 : 1.055 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.0170 chunk 111 optimal weight: 0.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.140587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.100582 restraints weight = 11132.857| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.83 r_work: 0.2983 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2101 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= 0.167 Angle : 0.559 8.084 12936 Z= 0.292 Chirality : 0.038 0.130 1644 Planarity : 0.005 0.037 1572 Dihedral : 4.546 18.591 1297 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.74 % Allowed : 10.34 % Favored : 87.92 % 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: -2.96 (0.20), residues: 1215 helix: -1.59 (0.14), residues: 960 sheet: -3.04 (0.69), residues: 54 loop : -2.34 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 441 HIS 0.001 0.000 HIS B 296 PHE 0.015 0.002 PHE B 218 TYR 0.010 0.001 TYR B 373 ARG 0.005 0.000 ARG A 353 *********************** 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 196 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 1.060 Fit side-chains REVERT: A 40 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7836 (tp30) REVERT: A 248 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8861 (mmt) REVERT: A 322 GLN cc_start: 0.7979 (tp40) cc_final: 0.7453 (mm-40) REVERT: A 329 MET cc_start: 0.6421 (mmm) cc_final: 0.5899 (mtt) REVERT: A 431 GLU cc_start: 0.7439 (pm20) cc_final: 0.7122 (mp0) REVERT: B 200 TYR cc_start: 0.8292 (m-80) cc_final: 0.7908 (m-10) REVERT: B 248 MET cc_start: 0.8981 (tpp) cc_final: 0.8738 (mmm) REVERT: B 473 MET cc_start: 0.6738 (ttt) cc_final: 0.6394 (mtp) REVERT: C 248 MET cc_start: 0.9054 (tpp) cc_final: 0.8614 (mmt) REVERT: C 280 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6937 (ttm170) REVERT: C 322 GLN cc_start: 0.7931 (tp40) cc_final: 0.7421 (mm-40) REVERT: C 393 GLN cc_start: 0.8721 (mt0) cc_final: 0.8499 (mt0) outliers start: 18 outliers final: 6 residues processed: 188 average time/residue: 1.0416 time to fit residues: 211.2344 Evaluate side-chains 149 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 37 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 156 GLN B 85 ASN B 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.136682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.095903 restraints weight = 11171.893| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.82 r_work: 0.2836 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9534 Z= 0.312 Angle : 0.584 6.941 12936 Z= 0.300 Chirality : 0.041 0.126 1644 Planarity : 0.004 0.035 1572 Dihedral : 4.342 18.859 1293 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.48 % Allowed : 13.33 % Favored : 83.19 % 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: -1.33 (0.23), residues: 1215 helix: -0.33 (0.16), residues: 963 sheet: -2.57 (0.70), residues: 54 loop : -2.44 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 19 HIS 0.001 0.001 HIS A 41 PHE 0.017 0.002 PHE A 218 TYR 0.007 0.001 TYR B 373 ARG 0.004 0.001 ARG A 353 *********************** 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 188 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.995 Fit side-chains REVERT: A 276 TRP cc_start: 0.7496 (m100) cc_final: 0.7135 (m-90) REVERT: A 393 GLN cc_start: 0.8672 (mt0) cc_final: 0.8192 (mt0) REVERT: A 431 GLU cc_start: 0.7417 (pm20) cc_final: 0.7068 (mp0) REVERT: B 75 MET cc_start: 0.9250 (mmm) cc_final: 0.8920 (tpp) REVERT: B 200 TYR cc_start: 0.8349 (m-80) cc_final: 0.7959 (m-10) REVERT: B 248 MET cc_start: 0.9009 (tpp) cc_final: 0.8747 (mmm) REVERT: B 473 MET cc_start: 0.6685 (ttt) cc_final: 0.6370 (mtp) REVERT: C 248 MET cc_start: 0.9084 (tpp) cc_final: 0.8624 (mmt) REVERT: C 322 GLN cc_start: 0.8006 (tp40) cc_final: 0.7515 (mm-40) outliers start: 36 outliers final: 14 residues processed: 170 average time/residue: 1.1456 time to fit residues: 209.3655 Evaluate side-chains 153 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 207 SER 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 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 78 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.139442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.099274 restraints weight = 11168.906| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.81 r_work: 0.2886 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9534 Z= 0.173 Angle : 0.504 6.503 12936 Z= 0.258 Chirality : 0.038 0.127 1644 Planarity : 0.003 0.031 1572 Dihedral : 3.989 17.412 1293 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.90 % Allowed : 15.17 % Favored : 81.93 % 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: -0.29 (0.24), residues: 1215 helix: 0.43 (0.17), residues: 969 sheet: -2.44 (0.70), residues: 54 loop : -2.25 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 19 HIS 0.000 0.000 HIS C 296 PHE 0.014 0.001 PHE C 316 TYR 0.008 0.001 TYR A 373 ARG 0.003 0.000 ARG A 315 *********************** 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 181 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.080 Fit side-chains REVERT: A 248 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8905 (mmp) REVERT: A 342 ARG cc_start: 0.7087 (ppt170) cc_final: 0.6847 (ppt90) REVERT: A 393 GLN cc_start: 0.8662 (mt0) cc_final: 0.8181 (mt0) REVERT: A 431 GLU cc_start: 0.7433 (pm20) cc_final: 0.7108 (mp0) REVERT: B 75 MET cc_start: 0.9177 (mmm) cc_final: 0.8829 (tpp) REVERT: B 200 TYR cc_start: 0.8361 (m-80) cc_final: 0.8009 (m-10) REVERT: B 248 MET cc_start: 0.9005 (tpp) cc_final: 0.8765 (mmm) REVERT: B 303 LEU cc_start: 0.8256 (tp) cc_final: 0.7844 (tt) REVERT: B 366 ASN cc_start: 0.8144 (t0) cc_final: 0.7913 (t0) REVERT: B 473 MET cc_start: 0.6717 (ttt) cc_final: 0.6421 (mtp) REVERT: C 248 MET cc_start: 0.9062 (tpp) cc_final: 0.8600 (mmt) REVERT: C 280 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6857 (ttm170) REVERT: C 322 GLN cc_start: 0.7921 (tp40) cc_final: 0.7388 (mm-40) REVERT: C 342 ARG cc_start: 0.7374 (ppt170) cc_final: 0.7088 (ppt90) REVERT: C 351 ASP cc_start: 0.7019 (t0) cc_final: 0.6731 (t0) REVERT: C 463 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7538 (tm-30) outliers start: 30 outliers final: 13 residues processed: 165 average time/residue: 1.1407 time to fit residues: 202.1756 Evaluate side-chains 158 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 164 THR 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 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 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 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 12 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3605 r_free = 0.3605 target = 0.138637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.099886 restraints weight = 11146.787| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.92 r_work: 0.2868 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9534 Z= 0.227 Angle : 0.521 6.087 12936 Z= 0.266 Chirality : 0.039 0.125 1644 Planarity : 0.003 0.030 1572 Dihedral : 3.992 17.686 1293 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.09 % Allowed : 15.56 % Favored : 81.35 % 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: 0.13 (0.25), residues: 1215 helix: 0.66 (0.17), residues: 987 sheet: -2.20 (0.72), residues: 54 loop : -2.00 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS C 296 PHE 0.015 0.002 PHE A 218 TYR 0.008 0.001 TYR C 373 ARG 0.003 0.000 ARG A 315 *********************** 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 179 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 1.159 Fit side-chains REVERT: A 276 TRP cc_start: 0.7450 (m100) cc_final: 0.7112 (m-90) REVERT: A 322 GLN cc_start: 0.7853 (tp40) cc_final: 0.7330 (mm-40) REVERT: A 342 ARG cc_start: 0.7151 (ppt170) cc_final: 0.6866 (ppt90) REVERT: A 393 GLN cc_start: 0.8608 (mt0) cc_final: 0.8094 (mt0) REVERT: A 431 GLU cc_start: 0.7382 (pm20) cc_final: 0.7090 (mp0) REVERT: A 463 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7436 (tm-30) REVERT: B 75 MET cc_start: 0.9128 (mmm) cc_final: 0.8782 (tpp) REVERT: B 200 TYR cc_start: 0.8361 (m-80) cc_final: 0.7986 (m-10) REVERT: B 248 MET cc_start: 0.8977 (tpp) cc_final: 0.8714 (mmm) REVERT: B 320 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7459 (mmt) REVERT: B 463 GLU cc_start: 0.7842 (tt0) cc_final: 0.7306 (tm-30) REVERT: B 473 MET cc_start: 0.6689 (ttt) cc_final: 0.6372 (mtp) REVERT: C 248 MET cc_start: 0.9059 (tpp) cc_final: 0.8572 (mmt) REVERT: C 280 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6803 (ttm170) REVERT: C 322 GLN cc_start: 0.7872 (tp40) cc_final: 0.7378 (mm-40) REVERT: C 342 ARG cc_start: 0.7378 (ppt170) cc_final: 0.7070 (ppt90) REVERT: C 351 ASP cc_start: 0.7049 (t0) cc_final: 0.6723 (t0) REVERT: C 393 GLN cc_start: 0.8715 (mt0) cc_final: 0.8383 (mt0) REVERT: C 463 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7540 (tm-30) outliers start: 32 outliers final: 17 residues processed: 163 average time/residue: 1.4672 time to fit residues: 255.9713 Evaluate side-chains 163 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 SER 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 B residue 433 VAL Chi-restraints excluded: chain C residue 30 LEU 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 280 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN B 393 GLN C 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.100866 restraints weight = 11024.802| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.73 r_work: 0.2891 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9534 Z= 0.183 Angle : 0.500 5.732 12936 Z= 0.255 Chirality : 0.038 0.126 1644 Planarity : 0.003 0.028 1572 Dihedral : 3.868 17.885 1293 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.19 % Allowed : 15.94 % Favored : 80.87 % 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: 0.77 (0.25), residues: 1215 helix: 1.13 (0.17), residues: 969 sheet: -1.98 (0.74), residues: 54 loop : -1.62 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS C 41 PHE 0.013 0.001 PHE A 218 TYR 0.010 0.001 TYR A 373 ARG 0.002 0.000 ARG A 353 *********************** 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 184 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 1.264 Fit side-chains REVERT: A 276 TRP cc_start: 0.7457 (m100) cc_final: 0.7131 (m-90) REVERT: A 322 GLN cc_start: 0.7866 (tp40) cc_final: 0.7344 (mm-40) REVERT: A 342 ARG cc_start: 0.7104 (ppt170) cc_final: 0.6887 (ppt90) REVERT: A 393 GLN cc_start: 0.8672 (mt0) cc_final: 0.8172 (mt0) REVERT: A 431 GLU cc_start: 0.7454 (pm20) cc_final: 0.7221 (mp0) REVERT: A 463 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7482 (tm-30) REVERT: B 200 TYR cc_start: 0.8327 (m-80) cc_final: 0.7961 (m-10) REVERT: B 248 MET cc_start: 0.8987 (tpp) cc_final: 0.8735 (mmm) REVERT: B 303 LEU cc_start: 0.8263 (tp) cc_final: 0.7862 (tt) REVERT: B 342 ARG cc_start: 0.7485 (ppt170) cc_final: 0.7123 (ppt90) REVERT: B 366 ASN cc_start: 0.8214 (t0) cc_final: 0.7964 (t0) REVERT: B 463 GLU cc_start: 0.7872 (tt0) cc_final: 0.7358 (tm-30) REVERT: B 473 MET cc_start: 0.6696 (ttt) cc_final: 0.6377 (mtp) REVERT: C 248 MET cc_start: 0.9061 (tpp) cc_final: 0.8583 (mmt) REVERT: C 280 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.6825 (ttm170) REVERT: C 320 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7268 (mmt) REVERT: C 322 GLN cc_start: 0.7842 (tp40) cc_final: 0.7359 (mm-40) REVERT: C 342 ARG cc_start: 0.7396 (ppt170) cc_final: 0.7069 (ppt90) REVERT: C 351 ASP cc_start: 0.7091 (t0) cc_final: 0.6756 (t0) REVERT: C 393 GLN cc_start: 0.8714 (mt0) cc_final: 0.8396 (mt0) REVERT: C 463 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7524 (tm-30) outliers start: 33 outliers final: 17 residues processed: 164 average time/residue: 1.3380 time to fit residues: 235.6787 Evaluate side-chains 166 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL 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 B residue 433 VAL 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 280 ARG Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 320 MET 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 114 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.139641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.098539 restraints weight = 11225.601| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.86 r_work: 0.2896 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9534 Z= 0.151 Angle : 0.489 5.505 12936 Z= 0.249 Chirality : 0.037 0.123 1644 Planarity : 0.003 0.027 1572 Dihedral : 3.722 18.104 1293 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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 (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: 1.22 (0.25), residues: 1215 helix: 1.46 (0.17), residues: 966 sheet: -1.92 (0.77), residues: 54 loop : -1.52 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS C 41 PHE 0.012 0.001 PHE A 218 TYR 0.010 0.001 TYR A 373 ARG 0.002 0.000 ARG A 61 *********************** 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 191 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 1.067 Fit side-chains REVERT: A 276 TRP cc_start: 0.7412 (m100) cc_final: 0.7089 (m-90) REVERT: A 322 GLN cc_start: 0.7811 (tp40) cc_final: 0.7281 (mm-40) REVERT: A 342 ARG cc_start: 0.7035 (ppt170) cc_final: 0.6808 (ppt90) REVERT: A 393 GLN cc_start: 0.8669 (mt0) cc_final: 0.8175 (mt0) REVERT: A 431 GLU cc_start: 0.7456 (pm20) cc_final: 0.7187 (mp0) REVERT: A 463 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 75 MET cc_start: 0.9230 (mmm) cc_final: 0.8895 (tpp) REVERT: B 200 TYR cc_start: 0.8316 (m-80) cc_final: 0.7976 (m-10) REVERT: B 248 MET cc_start: 0.9035 (tpp) cc_final: 0.8779 (mmm) REVERT: B 303 LEU cc_start: 0.8261 (tp) cc_final: 0.7874 (tt) REVERT: B 342 ARG cc_start: 0.7486 (ppt170) cc_final: 0.7118 (ppt90) REVERT: B 431 GLU cc_start: 0.7687 (mp0) cc_final: 0.7483 (mm-30) REVERT: B 463 GLU cc_start: 0.7838 (tt0) cc_final: 0.7385 (tm-30) REVERT: B 473 MET cc_start: 0.6744 (ttt) cc_final: 0.6418 (mtp) REVERT: C 248 MET cc_start: 0.9066 (tpp) cc_final: 0.8771 (mmt) REVERT: C 280 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6790 (ttm170) REVERT: C 303 LEU cc_start: 0.8223 (tp) cc_final: 0.7833 (tt) REVERT: C 320 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7239 (mmt) REVERT: C 322 GLN cc_start: 0.7798 (tp40) cc_final: 0.7323 (mm-40) REVERT: C 342 ARG cc_start: 0.7348 (ppt170) cc_final: 0.7025 (ppt90) REVERT: C 351 ASP cc_start: 0.7144 (t0) cc_final: 0.6795 (t0) REVERT: C 393 GLN cc_start: 0.8688 (mt0) cc_final: 0.8380 (mt0) REVERT: C 463 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7560 (tm-30) outliers start: 29 outliers final: 15 residues processed: 175 average time/residue: 1.1759 time to fit residues: 220.4341 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 : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR 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 273 VAL Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 433 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 280 ARG Chi-restraints excluded: chain C residue 320 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 1 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 34 optimal weight: 0.0970 chunk 108 optimal weight: 0.1980 chunk 85 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.142086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.102529 restraints weight = 11285.808| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.77 r_work: 0.2928 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3269 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= 0.138 Angle : 0.486 6.741 12936 Z= 0.247 Chirality : 0.037 0.122 1644 Planarity : 0.003 0.027 1572 Dihedral : 3.655 17.938 1293 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.51 % Allowed : 18.16 % Favored : 79.32 % 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: 1.54 (0.25), residues: 1215 helix: 1.73 (0.17), residues: 960 sheet: -1.86 (0.77), residues: 54 loop : -1.55 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 276 HIS 0.001 0.000 HIS C 41 PHE 0.012 0.001 PHE C 316 TYR 0.013 0.001 TYR C 373 ARG 0.002 0.000 ARG A 353 *********************** 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 181 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.992 Fit side-chains REVERT: A 276 TRP cc_start: 0.7373 (m100) cc_final: 0.7112 (m-90) REVERT: A 322 GLN cc_start: 0.7773 (tp40) cc_final: 0.7267 (mm-40) REVERT: A 342 ARG cc_start: 0.7050 (ppt170) cc_final: 0.6823 (ppt90) REVERT: A 393 GLN cc_start: 0.8625 (mt0) cc_final: 0.8124 (mt0) REVERT: A 431 GLU cc_start: 0.7398 (pm20) cc_final: 0.7164 (mp0) REVERT: A 463 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7445 (tm-30) REVERT: B 75 MET cc_start: 0.9152 (mmm) cc_final: 0.8804 (tpp) REVERT: B 200 TYR cc_start: 0.8270 (m-80) cc_final: 0.7923 (m-10) REVERT: B 248 MET cc_start: 0.9027 (tpp) cc_final: 0.8770 (mmm) REVERT: B 303 LEU cc_start: 0.8275 (tp) cc_final: 0.7881 (tt) REVERT: B 322 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7442 (mm-40) REVERT: B 463 GLU cc_start: 0.7857 (tt0) cc_final: 0.7432 (tm-30) REVERT: B 473 MET cc_start: 0.6820 (ttt) cc_final: 0.6491 (mtp) REVERT: C 303 LEU cc_start: 0.8238 (tp) cc_final: 0.7851 (tt) REVERT: C 320 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7321 (mmt) REVERT: C 322 GLN cc_start: 0.7765 (tp40) cc_final: 0.7230 (mm-40) REVERT: C 342 ARG cc_start: 0.7348 (ppt170) cc_final: 0.7026 (ppt90) REVERT: C 351 ASP cc_start: 0.7237 (t0) cc_final: 0.6901 (t0) REVERT: C 393 GLN cc_start: 0.8659 (mt0) cc_final: 0.8320 (mt0) REVERT: C 463 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7552 (tm-30) outliers start: 26 outliers final: 15 residues processed: 166 average time/residue: 1.1721 time to fit residues: 208.9233 Evaluate side-chains 163 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR 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 273 VAL Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 433 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 320 MET Chi-restraints excluded: chain C residue 411 VAL 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 80 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 0.0370 chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.100557 restraints weight = 11192.803| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.87 r_work: 0.2891 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3213 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= 0.192 Angle : 0.518 6.539 12936 Z= 0.263 Chirality : 0.039 0.140 1644 Planarity : 0.003 0.027 1572 Dihedral : 3.741 17.910 1293 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.51 % Allowed : 18.55 % Favored : 78.94 % 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: 1.31 (0.26), residues: 1215 helix: 1.54 (0.17), residues: 981 sheet: -1.82 (0.75), residues: 54 loop : -1.89 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS C 41 PHE 0.015 0.002 PHE C 316 TYR 0.015 0.001 TYR C 373 ARG 0.002 0.000 ARG A 353 *********************** 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 177 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.081 Fit side-chains REVERT: A 276 TRP cc_start: 0.7328 (m100) cc_final: 0.7058 (m-90) REVERT: A 322 GLN cc_start: 0.7650 (tp40) cc_final: 0.7137 (mm-40) REVERT: A 342 ARG cc_start: 0.6999 (ppt170) cc_final: 0.6760 (ppt90) REVERT: A 393 GLN cc_start: 0.8551 (mt0) cc_final: 0.7995 (mt0) REVERT: A 431 GLU cc_start: 0.7308 (pm20) cc_final: 0.7075 (mp0) REVERT: A 463 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7365 (tm-30) REVERT: B 75 MET cc_start: 0.9071 (mmm) cc_final: 0.8719 (tpp) REVERT: B 200 TYR cc_start: 0.8252 (m-80) cc_final: 0.7925 (m-10) REVERT: B 248 MET cc_start: 0.8967 (tpp) cc_final: 0.8701 (mmm) REVERT: B 322 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7413 (mm-40) REVERT: B 342 ARG cc_start: 0.7281 (ppt170) cc_final: 0.6933 (ppt90) REVERT: B 366 ASN cc_start: 0.8075 (t0) cc_final: 0.7832 (t0) REVERT: B 463 GLU cc_start: 0.7821 (tt0) cc_final: 0.7356 (tm-30) REVERT: B 473 MET cc_start: 0.6658 (ttt) cc_final: 0.6332 (mtp) REVERT: C 248 MET cc_start: 0.9065 (tpt) cc_final: 0.8834 (mmt) REVERT: C 303 LEU cc_start: 0.8035 (tp) cc_final: 0.7632 (tt) REVERT: C 320 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7239 (mmt) REVERT: C 322 GLN cc_start: 0.7734 (tp40) cc_final: 0.7243 (mm-40) REVERT: C 342 ARG cc_start: 0.7262 (ppt170) cc_final: 0.6932 (ppt90) REVERT: C 351 ASP cc_start: 0.7120 (t0) cc_final: 0.6725 (t0) REVERT: C 393 GLN cc_start: 0.8542 (mt0) cc_final: 0.8170 (mt0) REVERT: C 463 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7469 (tm-30) outliers start: 26 outliers final: 17 residues processed: 161 average time/residue: 1.1949 time to fit residues: 206.9196 Evaluate side-chains 168 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR 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 273 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 433 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 320 MET Chi-restraints excluded: chain C residue 411 VAL 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 88 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 103 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.139751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098394 restraints weight = 11342.583| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.88 r_work: 0.2897 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9534 Z= 0.158 Angle : 0.503 6.160 12936 Z= 0.255 Chirality : 0.038 0.128 1644 Planarity : 0.003 0.027 1572 Dihedral : 3.697 17.327 1293 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.32 % Allowed : 19.13 % Favored : 78.55 % 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: 1.50 (0.26), residues: 1215 helix: 1.69 (0.18), residues: 978 sheet: -1.77 (0.76), residues: 54 loop : -1.84 (0.42), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 441 HIS 0.001 0.000 HIS C 41 PHE 0.014 0.001 PHE C 316 TYR 0.014 0.001 TYR C 373 ARG 0.002 0.000 ARG A 353 ********************** 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 171 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.067 Fit side-chains REVERT: A 75 MET cc_start: 0.9299 (mmp) cc_final: 0.9042 (mmp) REVERT: A 276 TRP cc_start: 0.7337 (m100) cc_final: 0.7094 (m-90) REVERT: A 342 ARG cc_start: 0.7031 (ppt170) cc_final: 0.6778 (ppt90) REVERT: A 393 GLN cc_start: 0.8656 (mt0) cc_final: 0.8166 (mt0) REVERT: A 431 GLU cc_start: 0.7381 (pm20) cc_final: 0.7160 (mp0) REVERT: B 75 MET cc_start: 0.9179 (mmm) cc_final: 0.8830 (tpp) REVERT: B 200 TYR cc_start: 0.8294 (m-80) cc_final: 0.7955 (m-10) REVERT: B 248 MET cc_start: 0.9047 (tpp) cc_final: 0.8797 (mmm) REVERT: B 322 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7390 (mm-40) REVERT: B 342 ARG cc_start: 0.7337 (ppt170) cc_final: 0.6993 (ppt90) REVERT: B 431 GLU cc_start: 0.7716 (mp0) cc_final: 0.7460 (mm-30) REVERT: B 463 GLU cc_start: 0.7928 (tt0) cc_final: 0.7466 (tm-30) REVERT: B 473 MET cc_start: 0.6637 (ttt) cc_final: 0.6321 (mtp) REVERT: C 248 MET cc_start: 0.9099 (tpt) cc_final: 0.8894 (mmt) REVERT: C 303 LEU cc_start: 0.8203 (tp) cc_final: 0.7822 (tt) REVERT: C 322 GLN cc_start: 0.7740 (tp40) cc_final: 0.7267 (mm-40) REVERT: C 342 ARG cc_start: 0.7312 (ppt170) cc_final: 0.6987 (ppt90) REVERT: C 351 ASP cc_start: 0.7190 (t0) cc_final: 0.6807 (t0) REVERT: C 393 GLN cc_start: 0.8642 (mt0) cc_final: 0.8302 (mt0) REVERT: C 463 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7537 (tm-30) outliers start: 24 outliers final: 17 residues processed: 157 average time/residue: 1.1892 time to fit residues: 200.1508 Evaluate side-chains 164 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR 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 273 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 433 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 411 VAL 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 110 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 116 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3642 r_free = 0.3642 target = 0.141867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.102157 restraints weight = 11217.178| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.77 r_work: 0.2902 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9534 Z= 0.172 Angle : 0.525 9.669 12936 Z= 0.264 Chirality : 0.038 0.137 1644 Planarity : 0.003 0.027 1572 Dihedral : 3.708 17.130 1293 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.03 % Allowed : 19.90 % Favored : 78.07 % 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: 1.51 (0.26), residues: 1215 helix: 1.68 (0.18), residues: 978 sheet: -1.70 (0.76), residues: 54 loop : -1.83 (0.42), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 19 HIS 0.001 0.000 HIS C 41 PHE 0.021 0.001 PHE C 316 TYR 0.014 0.001 TYR A 373 ARG 0.002 0.000 ARG A 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7541.72 seconds wall clock time: 131 minutes 29.19 seconds (7889.19 seconds total)