Starting phenix.real_space_refine on Fri Jun 13 20:00:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9emc_19817/06_2025/9emc_19817.cif Found real_map, /net/cci-nas-00/data/ceres_data/9emc_19817/06_2025/9emc_19817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9emc_19817/06_2025/9emc_19817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9emc_19817/06_2025/9emc_19817.map" model { file = "/net/cci-nas-00/data/ceres_data/9emc_19817/06_2025/9emc_19817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9emc_19817/06_2025/9emc_19817.cif" } resolution = 3.26 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= 0.001 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 75 5.16 5 C 9672 2.51 5 N 2718 2.21 5 O 3000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15489 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2476 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 2 Chain: "D" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2623 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 9, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2476 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 2 Chain: "C" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2476 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 2 Chain: "F" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2623 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 9, 'TRANS': 327} Chain breaks: 1 Chain: "E" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2623 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 9, 'TRANS': 327} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.52, per 1000 atoms: 0.61 Number of scatterers: 15489 At special positions: 0 Unit cell: (129.043, 126.562, 87.6832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 75 16.00 P 18 15.00 Mg 6 11.99 O 3000 8.00 N 2718 7.00 C 9672 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: 3.52 Conformation dependent library (CDL) restraints added in 2.0 seconds 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 54.2% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.606A pdb=" N LYS A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 99 through 102 removed outlier: 4.020A pdb=" N TYR A 102 " --> pdb=" O SER A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 107 through 119 Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 272 through 289 removed outlier: 3.582A pdb=" N ARG A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.926A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.753A pdb=" N SER A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 removed outlier: 3.582A pdb=" N ALA A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.581A pdb=" N VAL A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 450 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.873A pdb=" N GLY D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 125 Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 255 through 259 removed outlier: 3.954A pdb=" N LEU D 258 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 287 Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.730A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 347 through 352 Processing helix chain 'D' and resid 363 through 378 Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 398 through 416 removed outlier: 3.742A pdb=" N ALA D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 removed outlier: 3.538A pdb=" N ILE D 426 " --> pdb=" O GLN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 446 removed outlier: 3.936A pdb=" N GLU D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR D 446 " --> pdb=" O TYR D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 449 No H-bonds generated for 'chain 'D' and resid 447 through 449' Processing helix chain 'B' and resid 42 through 59 removed outlier: 3.607A pdb=" N LYS B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 99 through 102 removed outlier: 4.020A pdb=" N TYR B 102 " --> pdb=" O SER B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 240 through 247 Processing helix chain 'B' and resid 272 through 289 removed outlier: 3.581A pdb=" N ARG B 276 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 308 through 320 removed outlier: 3.926A pdb=" N ARG B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 350 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 367 through 382 Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 402 through 408 removed outlier: 3.753A pdb=" N SER B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 removed outlier: 3.582A pdb=" N ALA B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.581A pdb=" N VAL B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 450 Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.607A pdb=" N LYS C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 88 Processing helix chain 'C' and resid 99 through 102 removed outlier: 4.021A pdb=" N TYR C 102 " --> pdb=" O SER C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 240 through 247 Processing helix chain 'C' and resid 272 through 289 removed outlier: 3.582A pdb=" N ARG C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 320 removed outlier: 3.926A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 350 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 367 through 382 Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 402 through 408 removed outlier: 3.753A pdb=" N SER C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 421 removed outlier: 3.582A pdb=" N ALA C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 437 removed outlier: 3.581A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.872A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 244 through 251 Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.955A pdb=" N LEU F 258 " --> pdb=" O GLN F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 287 Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.730A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 378 Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.743A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 removed outlier: 3.537A pdb=" N ILE F 426 " --> pdb=" O GLN F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 446 removed outlier: 3.936A pdb=" N GLU F 445 " --> pdb=" O GLN F 441 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR F 446 " --> pdb=" O TYR F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 449 No H-bonds generated for 'chain 'F' and resid 447 through 449' Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 95 removed outlier: 3.872A pdb=" N GLY E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 244 through 251 Processing helix chain 'E' and resid 255 through 259 removed outlier: 3.954A pdb=" N LEU E 258 " --> pdb=" O GLN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 287 Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 305 through 316 removed outlier: 3.730A pdb=" N ARG E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 346 Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 363 through 378 Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.742A pdb=" N ALA E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 433 removed outlier: 3.538A pdb=" N ILE E 426 " --> pdb=" O GLN E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 446 removed outlier: 3.936A pdb=" N GLU E 445 " --> pdb=" O GLN E 441 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR E 446 " --> pdb=" O TYR E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 449 No H-bonds generated for 'chain 'E' and resid 447 through 449' Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.514A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 299 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA A 330 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A 301 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 239 Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 337 removed outlier: 3.516A pdb=" N CYS A 336 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 346 " --> pdb=" O CYS A 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AA6, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.664A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 77 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR D 359 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA D 76 " --> pdb=" O THR D 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 238 through 243 Processing sheet with id=AA8, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AB1, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.514A pdb=" N CYS B 94 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASP B 302 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N MET B 96 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B 299 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA B 330 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 301 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 236 through 239 Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 337 removed outlier: 3.515A pdb=" N CYS B 336 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 346 " --> pdb=" O CYS B 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB5, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.515A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU C 299 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA C 330 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 301 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N SER C 331 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU C 68 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 236 through 239 Processing sheet with id=AB7, first strand: chain 'C' and resid 336 through 337 removed outlier: 3.516A pdb=" N CYS C 336 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER C 346 " --> pdb=" O CYS C 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.665A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY F 77 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR F 359 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ALA F 76 " --> pdb=" O THR F 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 238 through 243 Processing sheet with id=AC2, first strand: chain 'F' and resid 333 through 334 Processing sheet with id=AC3, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.664A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY E 77 " --> pdb=" O THR E 328 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR E 359 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA E 76 " --> pdb=" O THR E 359 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 238 through 243 Processing sheet with id=AC6, first strand: chain 'E' and resid 333 through 334 762 hydrogen bonds defined for protein. 2178 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: 5.59 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4362 1.33 - 1.45: 2348 1.45 - 1.57: 8818 1.57 - 1.69: 18 1.69 - 1.81: 132 Bond restraints: 15678 Sorted by residual: bond pdb=" N ILE B 52 " pdb=" CA ILE B 52 " ideal model delta sigma weight residual 1.460 1.501 -0.041 1.21e-02 6.83e+03 1.16e+01 bond pdb=" N ILE C 52 " pdb=" CA ILE C 52 " ideal model delta sigma weight residual 1.460 1.500 -0.040 1.21e-02 6.83e+03 1.11e+01 bond pdb=" N ILE A 52 " pdb=" CA ILE A 52 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" N VAL A 327 " pdb=" CA VAL A 327 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 1.03e+01 bond pdb=" N VAL B 327 " pdb=" CA VAL B 327 " ideal model delta sigma weight residual 1.459 1.496 -0.038 1.20e-02 6.94e+03 9.86e+00 ... (remaining 15673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 18630 1.99 - 3.99: 2134 3.99 - 5.98: 338 5.98 - 7.98: 48 7.98 - 9.97: 9 Bond angle restraints: 21159 Sorted by residual: angle pdb=" CA GLY C 297 " pdb=" C GLY C 297 " pdb=" O GLY C 297 " ideal model delta sigma weight residual 121.78 117.41 4.37 9.10e-01 1.21e+00 2.30e+01 angle pdb=" CA GLY A 297 " pdb=" C GLY A 297 " pdb=" O GLY A 297 " ideal model delta sigma weight residual 121.78 117.44 4.34 9.10e-01 1.21e+00 2.27e+01 angle pdb=" CA GLY B 297 " pdb=" C GLY B 297 " pdb=" O GLY B 297 " ideal model delta sigma weight residual 121.78 117.46 4.32 9.10e-01 1.21e+00 2.26e+01 angle pdb=" N ILE B 323 " pdb=" CA ILE B 323 " pdb=" C ILE B 323 " ideal model delta sigma weight residual 113.43 108.40 5.03 1.09e+00 8.42e-01 2.13e+01 angle pdb=" N ILE A 323 " pdb=" CA ILE A 323 " pdb=" C ILE A 323 " ideal model delta sigma weight residual 113.43 108.45 4.98 1.09e+00 8.42e-01 2.08e+01 ... (remaining 21154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8268 17.93 - 35.87: 1121 35.87 - 53.80: 286 53.80 - 71.73: 90 71.73 - 89.67: 30 Dihedral angle restraints: 9795 sinusoidal: 4125 harmonic: 5670 Sorted by residual: dihedral pdb=" CA ASP C 343 " pdb=" C ASP C 343 " pdb=" N ILE C 344 " pdb=" CA ILE C 344 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ASP B 343 " pdb=" C ASP B 343 " pdb=" N ILE B 344 " pdb=" CA ILE B 344 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP A 343 " pdb=" C ASP A 343 " pdb=" N ILE A 344 " pdb=" CA ILE A 344 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 9792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1796 0.082 - 0.163: 570 0.163 - 0.245: 102 0.245 - 0.326: 13 0.326 - 0.408: 6 Chirality restraints: 2487 Sorted by residual: chirality pdb=" CB VAL A 238 " pdb=" CA VAL A 238 " pdb=" CG1 VAL A 238 " pdb=" CG2 VAL A 238 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB VAL B 238 " pdb=" CA VAL B 238 " pdb=" CG1 VAL B 238 " pdb=" CG2 VAL B 238 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CB VAL C 238 " pdb=" CA VAL C 238 " pdb=" CG1 VAL C 238 " pdb=" CG2 VAL C 238 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 2484 not shown) Planarity restraints: 2679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 72 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C PRO B 72 " 0.073 2.00e-02 2.50e+03 pdb=" O PRO B 72 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY B 73 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 72 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C PRO A 72 " -0.072 2.00e-02 2.50e+03 pdb=" O PRO A 72 " 0.028 2.00e-02 2.50e+03 pdb=" N GLY A 73 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 72 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C PRO C 72 " 0.072 2.00e-02 2.50e+03 pdb=" O PRO C 72 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY C 73 " -0.024 2.00e-02 2.50e+03 ... (remaining 2676 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 232 2.64 - 3.20: 12668 3.20 - 3.77: 24775 3.77 - 4.33: 35551 4.33 - 4.90: 56782 Nonbonded interactions: 130008 Sorted by model distance: nonbonded pdb=" O3G ATP A 501 " pdb="MG MG A 502 " model vdw 2.075 2.170 nonbonded pdb=" O3G ATP C 501 " pdb="MG MG C 502 " model vdw 2.076 2.170 nonbonded pdb=" O3G ATP B 501 " pdb="MG MG B 502 " model vdw 2.076 2.170 nonbonded pdb=" OG1 THR F 84 " pdb="MG MG F 502 " model vdw 2.088 2.170 nonbonded pdb=" OG1 THR D 84 " pdb="MG MG D 502 " model vdw 2.089 2.170 ... (remaining 130003 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.420 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 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 : 0.011 0.111 15678 Z= 0.547 Angle : 1.344 9.972 21159 Z= 0.825 Chirality : 0.082 0.408 2487 Planarity : 0.009 0.058 2679 Dihedral : 18.595 89.668 6129 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.44 % Allowed : 18.65 % 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: -3.73 (0.16), residues: 1947 helix: -3.87 (0.09), residues: 993 sheet: -1.79 (0.31), residues: 252 loop : 0.02 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.005 TRP D 283 HIS 0.011 0.003 HIS B 241 PHE 0.018 0.004 PHE B 312 TYR 0.044 0.003 TYR A 314 ARG 0.023 0.002 ARG F 330 Details of bonding type rmsd hydrogen bonds : bond 0.18695 ( 762) hydrogen bonds : angle 7.51688 ( 2178) covalent geometry : bond 0.01075 (15678) covalent geometry : angle 1.34433 (21159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 487 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 3 residues processed: 502 average time/residue: 0.3215 time to fit residues: 233.7630 Evaluate side-chains 264 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 261 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain F residue 380 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 10.0000 chunk 147 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 42 GLN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN A 420 ASN D 25 HIS D 277 ASN D 302 HIS D 341 GLN B 18 HIS B 42 GLN B 115 ASN B 289 GLN C 13 GLN C 18 HIS C 115 ASN C 332 ASN C 335 ASN C 373 GLN ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 GLN E 25 HIS ** E 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 GLN E 404 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.069519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.057479 restraints weight = 41743.715| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.24 r_work: 0.2755 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15678 Z= 0.147 Angle : 0.606 8.569 21159 Z= 0.322 Chirality : 0.043 0.236 2487 Planarity : 0.005 0.041 2679 Dihedral : 9.903 89.693 2339 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.25 % Allowed : 23.35 % Favored : 73.41 % 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: -1.42 (0.17), residues: 1947 helix: -1.28 (0.14), residues: 1029 sheet: -1.45 (0.29), residues: 288 loop : 0.46 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 283 HIS 0.005 0.001 HIS A 316 PHE 0.020 0.002 PHE C 300 TYR 0.013 0.001 TYR E 430 ARG 0.007 0.001 ARG D 414 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 762) hydrogen bonds : angle 4.39377 ( 2178) covalent geometry : bond 0.00342 (15678) covalent geometry : angle 0.60649 (21159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASN cc_start: 0.8911 (m-40) cc_final: 0.8678 (m-40) REVERT: A 116 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8856 (t80) REVERT: A 420 ASN cc_start: 0.9289 (t160) cc_final: 0.9023 (m110) REVERT: D 255 GLN cc_start: 0.6278 (mm-40) cc_final: 0.5589 (pt0) REVERT: D 300 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8004 (mm-30) REVERT: D 303 MET cc_start: 0.7727 (mmm) cc_final: 0.7413 (mmm) REVERT: D 313 ASN cc_start: 0.7224 (m110) cc_final: 0.6944 (m110) REVERT: D 380 VAL cc_start: 0.9075 (p) cc_final: 0.8793 (p) REVERT: C 91 VAL cc_start: 0.8915 (t) cc_final: 0.8633 (m) REVERT: C 364 MET cc_start: 0.8085 (mpp) cc_final: 0.7662 (mpp) REVERT: F 300 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7759 (mm-30) REVERT: F 442 TYR cc_start: 0.8380 (m-10) cc_final: 0.8152 (m-10) REVERT: E 244 LEU cc_start: 0.8753 (mt) cc_final: 0.8510 (mp) REVERT: E 248 ASP cc_start: 0.7706 (m-30) cc_final: 0.7446 (m-30) REVERT: E 440 THR cc_start: 0.9301 (m) cc_final: 0.8870 (p) REVERT: E 444 LYS cc_start: 0.9046 (mmmm) cc_final: 0.8843 (mmmt) outliers start: 54 outliers final: 22 residues processed: 318 average time/residue: 0.2703 time to fit residues: 134.0884 Evaluate side-chains 243 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 171 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 54 optimal weight: 0.2980 chunk 105 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN D 277 ASN C 42 GLN C 380 GLN F 240 HIS E 275 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.068313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.055555 restraints weight = 41980.516| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.49 r_work: 0.2707 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15678 Z= 0.139 Angle : 0.540 7.750 21159 Z= 0.284 Chirality : 0.042 0.154 2487 Planarity : 0.004 0.078 2679 Dihedral : 8.331 74.011 2336 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.67 % Allowed : 21.96 % Favored : 74.37 % 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: 0.07 (0.18), residues: 1947 helix: 0.31 (0.16), residues: 1032 sheet: -0.92 (0.29), residues: 285 loop : 0.45 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 283 HIS 0.003 0.001 HIS B 20 PHE 0.018 0.002 PHE A 329 TYR 0.014 0.001 TYR E 430 ARG 0.008 0.000 ARG D 284 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 762) hydrogen bonds : angle 3.88718 ( 2178) covalent geometry : bond 0.00319 (15678) covalent geometry : angle 0.53962 (21159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 182 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9306 (mmm) cc_final: 0.8990 (mmm) REVERT: A 116 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8797 (t80) REVERT: A 295 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8195 (m) REVERT: A 339 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7680 (mtm110) REVERT: A 371 MET cc_start: 0.8352 (mmm) cc_final: 0.8138 (mmt) REVERT: D 270 SER cc_start: 0.9263 (m) cc_final: 0.9024 (t) REVERT: D 274 GLU cc_start: 0.9384 (tp30) cc_final: 0.9169 (tp30) REVERT: D 300 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8601 (mm-30) REVERT: D 313 ASN cc_start: 0.7668 (m110) cc_final: 0.7361 (m-40) REVERT: D 446 TYR cc_start: 0.8743 (m-80) cc_final: 0.8360 (m-80) REVERT: D 447 GLN cc_start: 0.5306 (tp-100) cc_final: 0.5031 (tp40) REVERT: B 278 GLU cc_start: 0.9112 (pt0) cc_final: 0.8908 (pt0) REVERT: C 113 MET cc_start: 0.8739 (tpp) cc_final: 0.8536 (tpp) REVERT: C 273 ASP cc_start: 0.8137 (m-30) cc_final: 0.7795 (t70) REVERT: C 364 MET cc_start: 0.8462 (mpp) cc_final: 0.8070 (mpp) REVERT: C 427 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8788 (ttmm) REVERT: F 313 ASN cc_start: 0.7716 (m-40) cc_final: 0.7363 (m110) REVERT: F 405 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.8909 (mp) REVERT: E 440 THR cc_start: 0.9420 (m) cc_final: 0.9209 (m) REVERT: E 444 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8907 (mmmt) outliers start: 61 outliers final: 22 residues processed: 235 average time/residue: 0.2748 time to fit residues: 97.3236 Evaluate side-chains 185 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 105 optimal weight: 0.0370 chunk 135 optimal weight: 0.1980 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 ASN C 18 HIS C 42 GLN E 313 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.055259 restraints weight = 42203.607| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.49 r_work: 0.2703 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.6665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15678 Z= 0.102 Angle : 0.480 9.072 21159 Z= 0.249 Chirality : 0.041 0.203 2487 Planarity : 0.003 0.033 2679 Dihedral : 8.065 64.453 2335 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.95 % Allowed : 21.90 % Favored : 75.15 % 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: 0.76 (0.19), residues: 1947 helix: 1.02 (0.16), residues: 1032 sheet: -0.65 (0.29), residues: 285 loop : 0.48 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 283 HIS 0.020 0.001 HIS F 240 PHE 0.012 0.001 PHE F 297 TYR 0.011 0.001 TYR F 340 ARG 0.005 0.000 ARG D 414 Details of bonding type rmsd hydrogen bonds : bond 0.02636 ( 762) hydrogen bonds : angle 3.65913 ( 2178) covalent geometry : bond 0.00236 (15678) covalent geometry : angle 0.48036 (21159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9297 (mmm) cc_final: 0.9041 (mmm) REVERT: A 116 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8891 (t80) REVERT: A 295 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8221 (m) REVERT: D 270 SER cc_start: 0.9317 (m) cc_final: 0.9055 (t) REVERT: D 274 GLU cc_start: 0.9415 (tp30) cc_final: 0.9153 (tp30) REVERT: D 446 TYR cc_start: 0.8773 (m-80) cc_final: 0.8310 (m-80) REVERT: D 447 GLN cc_start: 0.5436 (tp-100) cc_final: 0.5155 (tp40) REVERT: C 273 ASP cc_start: 0.8212 (m-30) cc_final: 0.7898 (t70) REVERT: C 364 MET cc_start: 0.8659 (mpp) cc_final: 0.8302 (mpp) REVERT: C 427 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8766 (ttmm) REVERT: F 313 ASN cc_start: 0.7843 (m-40) cc_final: 0.7586 (m110) REVERT: F 378 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: F 405 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.8901 (mp) REVERT: E 261 PHE cc_start: 0.9125 (m-10) cc_final: 0.8820 (m-10) REVERT: E 326 MET cc_start: 0.9244 (mtm) cc_final: 0.9022 (mtp) REVERT: E 440 THR cc_start: 0.9449 (m) cc_final: 0.8974 (p) REVERT: E 444 LYS cc_start: 0.9221 (mmmm) cc_final: 0.8974 (mmmt) outliers start: 49 outliers final: 25 residues processed: 213 average time/residue: 0.2715 time to fit residues: 91.2467 Evaluate side-chains 187 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 378 GLU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 91 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 130 optimal weight: 0.0270 chunk 54 optimal weight: 0.3980 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 ASN F 341 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054085 restraints weight = 42860.699| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.52 r_work: 0.2671 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.7569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15678 Z= 0.111 Angle : 0.474 8.003 21159 Z= 0.247 Chirality : 0.041 0.185 2487 Planarity : 0.003 0.044 2679 Dihedral : 7.695 59.527 2335 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.01 % Allowed : 21.60 % Favored : 75.39 % 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: 1.11 (0.19), residues: 1947 helix: 1.34 (0.17), residues: 1038 sheet: -0.37 (0.30), residues: 285 loop : 0.50 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 283 HIS 0.004 0.001 HIS B 393 PHE 0.017 0.001 PHE A 300 TYR 0.009 0.001 TYR C 314 ARG 0.006 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.02688 ( 762) hydrogen bonds : angle 3.55670 ( 2178) covalent geometry : bond 0.00255 (15678) covalent geometry : angle 0.47367 (21159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 149 time to evaluate : 1.767 Fit side-chains revert: symmetry clash REVERT: A 116 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8917 (t80) REVERT: A 264 MET cc_start: 0.5716 (pmm) cc_final: 0.4991 (pmm) REVERT: A 364 MET cc_start: 0.8996 (mpp) cc_final: 0.8499 (mpp) REVERT: D 270 SER cc_start: 0.9349 (m) cc_final: 0.9074 (t) REVERT: D 274 GLU cc_start: 0.9422 (tp30) cc_final: 0.9101 (tp30) REVERT: D 375 CYS cc_start: 0.8465 (m) cc_final: 0.8187 (m) REVERT: D 447 GLN cc_start: 0.5529 (tp-100) cc_final: 0.5288 (tp40) REVERT: B 333 ARG cc_start: 0.7735 (tpp-160) cc_final: 0.6704 (mmt180) REVERT: B 364 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8209 (mpp) REVERT: C 273 ASP cc_start: 0.8360 (m-30) cc_final: 0.8081 (t70) REVERT: C 364 MET cc_start: 0.8826 (mpp) cc_final: 0.8449 (mpp) REVERT: C 427 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8777 (ttmm) REVERT: F 313 ASN cc_start: 0.8107 (m-40) cc_final: 0.7854 (m110) REVERT: F 405 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.8998 (mp) REVERT: E 261 PHE cc_start: 0.9070 (m-10) cc_final: 0.8843 (m-80) REVERT: E 270 SER cc_start: 0.8514 (m) cc_final: 0.8291 (p) REVERT: E 313 ASN cc_start: 0.8798 (m-40) cc_final: 0.8346 (m110) REVERT: E 382 MET cc_start: 0.9005 (mmm) cc_final: 0.8458 (mtp) REVERT: E 444 LYS cc_start: 0.9276 (mmmm) cc_final: 0.9019 (mmmt) outliers start: 50 outliers final: 28 residues processed: 191 average time/residue: 0.2463 time to fit residues: 72.6852 Evaluate side-chains 169 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain E residue 426 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 43 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 78 optimal weight: 0.0050 chunk 67 optimal weight: 0.0970 chunk 21 optimal weight: 0.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN A 420 ASN A 429 HIS ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.054191 restraints weight = 42686.611| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.51 r_work: 0.2680 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.7943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15678 Z= 0.097 Angle : 0.453 6.239 21159 Z= 0.238 Chirality : 0.040 0.194 2487 Planarity : 0.003 0.028 2679 Dihedral : 7.558 57.256 2335 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.29 % Allowed : 21.90 % Favored : 75.81 % 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: 1.17 (0.19), residues: 1947 helix: 1.45 (0.17), residues: 1050 sheet: -0.21 (0.30), residues: 285 loop : 0.30 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 283 HIS 0.004 0.001 HIS A 429 PHE 0.011 0.001 PHE B 300 TYR 0.016 0.001 TYR D 446 ARG 0.007 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.02473 ( 762) hydrogen bonds : angle 3.48269 ( 2178) covalent geometry : bond 0.00223 (15678) covalent geometry : angle 0.45319 (21159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9297 (m-80) cc_final: 0.9088 (m-80) REVERT: A 116 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8845 (t80) REVERT: A 264 MET cc_start: 0.5827 (pmm) cc_final: 0.5196 (pmm) REVERT: A 333 ARG cc_start: 0.4585 (tpt170) cc_final: 0.4218 (tpm170) REVERT: A 364 MET cc_start: 0.8967 (mpp) cc_final: 0.8434 (mpp) REVERT: D 270 SER cc_start: 0.9315 (m) cc_final: 0.9031 (t) REVERT: D 274 GLU cc_start: 0.9424 (tp30) cc_final: 0.9092 (tp30) REVERT: B 333 ARG cc_start: 0.7881 (tpp-160) cc_final: 0.6602 (mmt180) REVERT: B 364 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8246 (mpp) REVERT: C 273 ASP cc_start: 0.8430 (m-30) cc_final: 0.8147 (t70) REVERT: C 364 MET cc_start: 0.8841 (mpp) cc_final: 0.8470 (mpp) REVERT: C 427 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8805 (ttmm) REVERT: F 313 ASN cc_start: 0.8111 (m-40) cc_final: 0.7752 (m110) REVERT: F 405 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.8949 (mp) REVERT: E 270 SER cc_start: 0.8642 (m) cc_final: 0.8393 (p) REVERT: E 277 ASN cc_start: 0.9085 (m110) cc_final: 0.8784 (m110) REVERT: E 313 ASN cc_start: 0.8777 (m-40) cc_final: 0.8507 (m110) outliers start: 38 outliers final: 24 residues processed: 178 average time/residue: 0.2420 time to fit residues: 67.8186 Evaluate side-chains 166 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 24 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 185 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.065786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.053058 restraints weight = 42908.092| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.53 r_work: 0.2660 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.8585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15678 Z= 0.111 Angle : 0.478 9.508 21159 Z= 0.249 Chirality : 0.041 0.172 2487 Planarity : 0.003 0.031 2679 Dihedral : 7.396 56.162 2335 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.05 % Allowed : 21.84 % Favored : 76.11 % 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 (0.19), residues: 1947 helix: 1.54 (0.17), residues: 1056 sheet: -0.10 (0.31), residues: 285 loop : 0.36 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 283 HIS 0.002 0.001 HIS D 27 PHE 0.022 0.001 PHE D 297 TYR 0.016 0.001 TYR D 446 ARG 0.007 0.000 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.02604 ( 762) hydrogen bonds : angle 3.48098 ( 2178) covalent geometry : bond 0.00258 (15678) covalent geometry : angle 0.47812 (21159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 1.945 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.9197 (mmm) cc_final: 0.8993 (mmm) REVERT: A 102 TYR cc_start: 0.9348 (m-80) cc_final: 0.9052 (m-80) REVERT: A 264 MET cc_start: 0.5904 (pmm) cc_final: 0.5407 (pmm) REVERT: A 364 MET cc_start: 0.8979 (mpp) cc_final: 0.8549 (mpp) REVERT: D 88 MET cc_start: 0.8609 (mmt) cc_final: 0.8323 (mmp) REVERT: D 270 SER cc_start: 0.9276 (m) cc_final: 0.8946 (t) REVERT: D 274 GLU cc_start: 0.9369 (tp30) cc_final: 0.9013 (tp30) REVERT: D 371 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8738 (mm) REVERT: B 273 ASP cc_start: 0.9006 (m-30) cc_final: 0.8765 (t70) REVERT: B 316 HIS cc_start: 0.8621 (m-70) cc_final: 0.8414 (m-70) REVERT: B 333 ARG cc_start: 0.7800 (tpp-160) cc_final: 0.6827 (mmt180) REVERT: C 364 MET cc_start: 0.8861 (mpp) cc_final: 0.8504 (mpp) REVERT: C 427 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8862 (ttmm) REVERT: F 258 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8977 (tp) REVERT: F 405 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.8978 (mp) REVERT: E 270 SER cc_start: 0.8726 (m) cc_final: 0.8423 (p) REVERT: E 313 ASN cc_start: 0.8764 (m-40) cc_final: 0.8515 (m110) outliers start: 34 outliers final: 22 residues processed: 171 average time/residue: 0.2612 time to fit residues: 69.7355 Evaluate side-chains 160 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 GLN F 240 HIS F 313 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.061644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.048790 restraints weight = 43820.133| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 3.47 r_work: 0.2542 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.9358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15678 Z= 0.214 Angle : 0.556 9.613 21159 Z= 0.290 Chirality : 0.043 0.225 2487 Planarity : 0.004 0.042 2679 Dihedral : 7.778 69.876 2335 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.99 % Allowed : 21.96 % Favored : 76.05 % 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: 1.23 (0.19), residues: 1947 helix: 1.49 (0.17), residues: 1059 sheet: -0.07 (0.31), residues: 285 loop : 0.25 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 283 HIS 0.005 0.001 HIS B 305 PHE 0.047 0.002 PHE D 297 TYR 0.017 0.001 TYR D 446 ARG 0.006 0.001 ARG B 333 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 762) hydrogen bonds : angle 3.92370 ( 2178) covalent geometry : bond 0.00502 (15678) covalent geometry : angle 0.55572 (21159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9390 (m-80) cc_final: 0.9123 (m-80) REVERT: A 364 MET cc_start: 0.8865 (mpp) cc_final: 0.8580 (mpp) REVERT: D 270 SER cc_start: 0.9241 (m) cc_final: 0.8790 (t) REVERT: D 405 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9192 (mp) REVERT: F 258 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8933 (tp) REVERT: F 382 MET cc_start: 0.9368 (mtp) cc_final: 0.9050 (mtp) REVERT: F 387 TYR cc_start: 0.8620 (m-80) cc_final: 0.8399 (m-80) REVERT: F 405 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9058 (mp) REVERT: E 88 MET cc_start: 0.8807 (mmt) cc_final: 0.8516 (mmm) REVERT: E 270 SER cc_start: 0.8847 (m) cc_final: 0.8572 (p) REVERT: E 313 ASN cc_start: 0.8815 (m-40) cc_final: 0.8573 (m110) outliers start: 33 outliers final: 23 residues processed: 162 average time/residue: 0.2650 time to fit residues: 66.4217 Evaluate side-chains 146 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 GLN C 393 HIS F 240 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.051304 restraints weight = 43177.844| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.63 r_work: 0.2613 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.9477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 15678 Z= 0.105 Angle : 0.502 13.034 21159 Z= 0.257 Chirality : 0.041 0.270 2487 Planarity : 0.003 0.043 2679 Dihedral : 7.602 64.307 2335 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.50 % Allowed : 22.92 % Favored : 75.57 % 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: 1.35 (0.19), residues: 1947 helix: 1.61 (0.17), residues: 1053 sheet: -0.04 (0.31), residues: 285 loop : 0.28 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 283 HIS 0.003 0.001 HIS F 302 PHE 0.019 0.001 PHE F 257 TYR 0.018 0.001 TYR D 387 ARG 0.005 0.000 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.02606 ( 762) hydrogen bonds : angle 3.57806 ( 2178) covalent geometry : bond 0.00242 (15678) covalent geometry : angle 0.50202 (21159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.920 Fit side-chains REVERT: A 96 MET cc_start: 0.9176 (ttm) cc_final: 0.8948 (ttm) REVERT: A 102 TYR cc_start: 0.9392 (m-80) cc_final: 0.9176 (m-80) REVERT: A 264 MET cc_start: 0.5616 (pmm) cc_final: 0.5042 (pmm) REVERT: A 364 MET cc_start: 0.8941 (mpp) cc_final: 0.8570 (mpp) REVERT: D 270 SER cc_start: 0.9111 (m) cc_final: 0.8790 (p) REVERT: D 405 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9057 (mp) REVERT: B 264 MET cc_start: 0.5211 (pmm) cc_final: 0.4776 (pmm) REVERT: B 278 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8728 (mt-10) REVERT: B 333 ARG cc_start: 0.7795 (tpp-160) cc_final: 0.7271 (mmt180) REVERT: F 135 THR cc_start: 0.6372 (p) cc_final: 0.5983 (p) REVERT: F 382 MET cc_start: 0.9330 (mtp) cc_final: 0.9002 (mtp) REVERT: F 387 TYR cc_start: 0.8492 (m-80) cc_final: 0.8255 (m-80) REVERT: E 270 SER cc_start: 0.8762 (m) cc_final: 0.8485 (p) outliers start: 25 outliers final: 19 residues processed: 152 average time/residue: 0.2629 time to fit residues: 61.3435 Evaluate side-chains 144 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 39 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 25 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.051420 restraints weight = 43417.143| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.64 r_work: 0.2609 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.9616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15678 Z= 0.121 Angle : 0.509 11.866 21159 Z= 0.263 Chirality : 0.041 0.260 2487 Planarity : 0.004 0.085 2679 Dihedral : 7.396 67.430 2335 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.38 % Allowed : 22.92 % Favored : 75.69 % 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: 1.35 (0.19), residues: 1947 helix: 1.62 (0.17), residues: 1056 sheet: 0.03 (0.31), residues: 285 loop : 0.22 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 283 HIS 0.005 0.001 HIS B 316 PHE 0.015 0.001 PHE B 300 TYR 0.021 0.001 TYR C 314 ARG 0.008 0.000 ARG F 353 Details of bonding type rmsd hydrogen bonds : bond 0.02723 ( 762) hydrogen bonds : angle 3.55566 ( 2178) covalent geometry : bond 0.00283 (15678) covalent geometry : angle 0.50873 (21159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.743 Fit side-chains REVERT: A 96 MET cc_start: 0.9210 (ttm) cc_final: 0.8984 (ttm) REVERT: A 102 TYR cc_start: 0.9395 (m-80) cc_final: 0.9132 (m-80) REVERT: A 364 MET cc_start: 0.8907 (mpp) cc_final: 0.8537 (mpp) REVERT: D 270 SER cc_start: 0.9104 (m) cc_final: 0.8789 (p) REVERT: D 382 MET cc_start: 0.9180 (mtp) cc_final: 0.8461 (mtp) REVERT: D 387 TYR cc_start: 0.8486 (m-80) cc_final: 0.7763 (m-80) REVERT: D 405 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9095 (mp) REVERT: B 264 MET cc_start: 0.5219 (pmm) cc_final: 0.4765 (pmm) REVERT: B 278 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8737 (mt-10) REVERT: B 333 ARG cc_start: 0.7697 (tpp-160) cc_final: 0.7218 (tpt90) REVERT: B 364 MET cc_start: 0.8823 (mpp) cc_final: 0.8606 (mpp) REVERT: F 135 THR cc_start: 0.6414 (p) cc_final: 0.6034 (p) REVERT: F 382 MET cc_start: 0.9307 (mtp) cc_final: 0.9032 (mtp) REVERT: E 270 SER cc_start: 0.8800 (m) cc_final: 0.8522 (p) REVERT: E 313 ASN cc_start: 0.8746 (m-40) cc_final: 0.8194 (m110) outliers start: 23 outliers final: 20 residues processed: 147 average time/residue: 0.3113 time to fit residues: 71.5512 Evaluate side-chains 145 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 79 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.064606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.051774 restraints weight = 43036.165| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.63 r_work: 0.2617 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.9717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15678 Z= 0.113 Angle : 0.496 11.389 21159 Z= 0.256 Chirality : 0.041 0.263 2487 Planarity : 0.004 0.081 2679 Dihedral : 7.356 67.041 2335 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.62 % Allowed : 22.56 % Favored : 75.81 % 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: 1.45 (0.19), residues: 1947 helix: 1.68 (0.17), residues: 1053 sheet: 0.07 (0.31), residues: 285 loop : 0.31 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 283 HIS 0.003 0.000 HIS D 302 PHE 0.014 0.001 PHE B 300 TYR 0.019 0.001 TYR D 446 ARG 0.008 0.000 ARG F 353 Details of bonding type rmsd hydrogen bonds : bond 0.02601 ( 762) hydrogen bonds : angle 3.51601 ( 2178) covalent geometry : bond 0.00265 (15678) covalent geometry : angle 0.49563 (21159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6209.69 seconds wall clock time: 112 minutes 15.38 seconds (6735.38 seconds total)