Starting phenix.real_space_refine on Thu Sep 18 08:29:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9emc_19817/09_2025/9emc_19817.cif Found real_map, /net/cci-nas-00/data/ceres_data/9emc_19817/09_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_19817/09_2025/9emc_19817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9emc_19817/09_2025/9emc_19817.map" model { file = "/net/cci-nas-00/data/ceres_data/9emc_19817/09_2025/9emc_19817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9emc_19817/09_2025/9emc_19817.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.03, per 1000 atoms: 0.26 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: 1.21 Conformation dependent library (CDL) restraints added in 683.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.76 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: 1.93 Time building geometry restraints manager: 1.65 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.020 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.023 0.002 ARG F 330 TYR 0.044 0.003 TYR A 314 PHE 0.018 0.004 PHE B 312 TRP 0.013 0.005 TRP D 283 HIS 0.011 0.003 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.01075 (15678) covalent geometry : angle 1.34433 (21159) hydrogen bonds : bond 0.18695 ( 762) hydrogen bonds : angle 7.51688 ( 2178) *********************** 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 : 0.690 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: 0.1348 time to fit residues: 98.4413 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 : 0.454 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 GLN B 18 HIS B 42 GLN B 115 ASN B 289 GLN B 429 HIS 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.068645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.056657 restraints weight = 42118.820| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.25 r_work: 0.2739 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15678 Z= 0.177 Angle : 0.635 8.952 21159 Z= 0.338 Chirality : 0.044 0.222 2487 Planarity : 0.005 0.040 2679 Dihedral : 9.927 87.604 2339 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.15 % Allowed : 22.86 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.17), residues: 1947 helix: -1.20 (0.14), residues: 1032 sheet: -1.37 (0.29), residues: 285 loop : 0.44 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 414 TYR 0.013 0.002 TYR E 430 PHE 0.017 0.002 PHE F 297 TRP 0.015 0.003 TRP E 283 HIS 0.011 0.002 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00379 (15678) covalent geometry : angle 0.63457 (21159) hydrogen bonds : bond 0.03538 ( 762) hydrogen bonds : angle 4.38053 ( 2178) *********************** 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 314 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 245 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.5123 (tpt170) cc_final: 0.4901 (tpt170) REVERT: D 255 GLN cc_start: 0.6295 (mm-40) cc_final: 0.5772 (pt0) REVERT: D 270 SER cc_start: 0.9122 (m) cc_final: 0.8860 (t) REVERT: D 300 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8196 (mm-30) REVERT: D 303 MET cc_start: 0.8071 (mmm) cc_final: 0.7868 (mmm) REVERT: D 313 ASN cc_start: 0.7562 (m110) cc_final: 0.7259 (m110) REVERT: C 364 MET cc_start: 0.8283 (mpp) cc_final: 0.7887 (mpp) REVERT: F 88 MET cc_start: 0.8325 (mmt) cc_final: 0.8109 (mmp) REVERT: F 300 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7935 (mm-30) REVERT: F 442 TYR cc_start: 0.8392 (m-10) cc_final: 0.8189 (m-80) REVERT: E 119 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8837 (mm) REVERT: E 248 ASP cc_start: 0.7881 (m-30) cc_final: 0.7627 (m-30) REVERT: E 382 MET cc_start: 0.8973 (mmm) cc_final: 0.8736 (mmm) REVERT: E 444 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8836 (mmmt) outliers start: 69 outliers final: 28 residues processed: 303 average time/residue: 0.1250 time to fit residues: 57.3885 Evaluate side-chains 223 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS 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 350 ILE Chi-restraints excluded: chain D residue 47 VAL 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 308 SER Chi-restraints excluded: chain D residue 318 SER 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 B residue 346 SER Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 17 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 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 426 ILE Chi-restraints excluded: chain E residue 119 LEU 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 42 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 158 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN D 277 ASN C 42 GLN C 335 ASN C 380 GLN C 408 GLN E 275 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.054228 restraints weight = 42488.190| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.46 r_work: 0.2681 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15678 Z= 0.139 Angle : 0.530 7.260 21159 Z= 0.280 Chirality : 0.042 0.163 2487 Planarity : 0.004 0.056 2679 Dihedral : 8.408 64.402 2336 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.95 % Allowed : 22.08 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.18), residues: 1947 helix: 0.38 (0.16), residues: 1035 sheet: -0.92 (0.29), residues: 285 loop : 0.38 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 284 TYR 0.010 0.001 TYR F 430 PHE 0.019 0.002 PHE F 297 TRP 0.005 0.001 TRP E 283 HIS 0.003 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00326 (15678) covalent geometry : angle 0.53002 (21159) hydrogen bonds : bond 0.03538 ( 762) hydrogen bonds : angle 3.94404 ( 2178) *********************** 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 223 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8809 (t80) REVERT: A 364 MET cc_start: 0.8906 (mpp) cc_final: 0.8471 (mpp) REVERT: D 270 SER cc_start: 0.9182 (m) cc_final: 0.8927 (t) REVERT: D 274 GLU cc_start: 0.9374 (tp30) cc_final: 0.8995 (tm-30) REVERT: D 447 GLN cc_start: 0.5295 (tp-100) cc_final: 0.5015 (tp40) REVERT: B 42 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7762 (mt0) REVERT: C 273 ASP cc_start: 0.8255 (m-30) cc_final: 0.7945 (t70) REVERT: C 364 MET cc_start: 0.8549 (mpp) cc_final: 0.8186 (mpp) REVERT: F 313 ASN cc_start: 0.8039 (m-40) cc_final: 0.7683 (m110) REVERT: F 405 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.8922 (mp) REVERT: E 306 ILE cc_start: 0.8725 (pt) cc_final: 0.8416 (tp) REVERT: E 440 THR cc_start: 0.9441 (m) cc_final: 0.9093 (p) REVERT: E 444 LYS cc_start: 0.9234 (mmmm) cc_final: 0.8973 (mmmt) outliers start: 49 outliers final: 16 residues processed: 217 average time/residue: 0.1204 time to fit residues: 40.6219 Evaluate side-chains 175 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE 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 B residue 42 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 344 ILE 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 236 LYS Chi-restraints excluded: chain F residue 260 LEU 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 119 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 108 optimal weight: 2.9990 chunk 135 optimal weight: 0.0570 chunk 107 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 117 optimal weight: 0.0010 chunk 43 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.5906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN D 277 ASN C 42 GLN C 335 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.067643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.054970 restraints weight = 42327.704| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.50 r_work: 0.2697 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.7074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15678 Z= 0.094 Angle : 0.468 8.996 21159 Z= 0.243 Chirality : 0.041 0.223 2487 Planarity : 0.003 0.047 2679 Dihedral : 8.097 60.004 2335 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.35 % Allowed : 21.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.19), residues: 1947 helix: 1.01 (0.16), residues: 1038 sheet: -0.68 (0.29), residues: 285 loop : 0.48 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 353 TYR 0.012 0.001 TYR E 430 PHE 0.012 0.001 PHE F 297 TRP 0.003 0.000 TRP E 283 HIS 0.003 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00210 (15678) covalent geometry : angle 0.46796 (21159) hydrogen bonds : bond 0.02566 ( 762) hydrogen bonds : angle 3.62418 ( 2178) *********************** 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 202 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8889 (t80) REVERT: A 295 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8342 (m) REVERT: A 364 MET cc_start: 0.9040 (mpp) cc_final: 0.8505 (mpp) REVERT: D 270 SER cc_start: 0.9181 (m) cc_final: 0.8829 (t) REVERT: D 274 GLU cc_start: 0.9392 (tp30) cc_final: 0.9188 (tp30) REVERT: D 300 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8658 (mm-30) REVERT: D 446 TYR cc_start: 0.8790 (m-10) cc_final: 0.8573 (m-10) REVERT: D 447 GLN cc_start: 0.5253 (tp-100) cc_final: 0.4990 (tp40) REVERT: C 273 ASP cc_start: 0.8278 (m-30) cc_final: 0.7971 (t70) REVERT: C 364 MET cc_start: 0.8713 (mpp) cc_final: 0.8355 (mpp) REVERT: F 313 ASN cc_start: 0.8037 (m-40) cc_final: 0.7728 (m110) REVERT: F 378 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: F 405 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.8929 (mp) REVERT: E 119 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.9001 (mm) REVERT: E 306 ILE cc_start: 0.8732 (pt) cc_final: 0.8502 (tp) REVERT: E 440 THR cc_start: 0.9472 (m) cc_final: 0.9078 (p) REVERT: E 444 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8997 (mmmt) outliers start: 39 outliers final: 17 residues processed: 196 average time/residue: 0.1164 time to fit residues: 35.8298 Evaluate side-chains 169 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 323 ILE 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 127 ILE Chi-restraints excluded: chain F residue 265 THR 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 400 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 119 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN C 335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.066236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.053669 restraints weight = 42727.640| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.45 r_work: 0.2678 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.7856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15678 Z= 0.103 Angle : 0.456 7.694 21159 Z= 0.239 Chirality : 0.040 0.178 2487 Planarity : 0.003 0.029 2679 Dihedral : 7.650 59.953 2335 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.95 % Allowed : 21.12 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.19), residues: 1947 helix: 1.24 (0.17), residues: 1059 sheet: -0.46 (0.30), residues: 285 loop : 0.34 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 284 TYR 0.010 0.001 TYR D 430 PHE 0.019 0.001 PHE D 297 TRP 0.003 0.000 TRP E 283 HIS 0.014 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00237 (15678) covalent geometry : angle 0.45591 (21159) hydrogen bonds : bond 0.02635 ( 762) hydrogen bonds : angle 3.48354 ( 2178) *********************** 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 200 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9388 (m-80) cc_final: 0.9068 (m-80) REVERT: A 116 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8926 (t80) REVERT: A 264 MET cc_start: 0.5805 (pmm) cc_final: 0.5085 (pmm) REVERT: A 364 MET cc_start: 0.9073 (mpp) cc_final: 0.8568 (mpp) REVERT: D 270 SER cc_start: 0.9184 (m) cc_final: 0.8852 (t) REVERT: D 274 GLU cc_start: 0.9421 (tp30) cc_final: 0.9129 (tp30) REVERT: D 300 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8706 (mm-30) REVERT: D 375 CYS cc_start: 0.8524 (m) cc_final: 0.8302 (m) REVERT: D 446 TYR cc_start: 0.8821 (m-10) cc_final: 0.8581 (m-10) REVERT: D 447 GLN cc_start: 0.5543 (tp-100) cc_final: 0.5314 (tp40) REVERT: B 102 TYR cc_start: 0.9366 (m-80) cc_final: 0.9111 (m-80) REVERT: B 316 HIS cc_start: 0.8734 (m-70) cc_final: 0.8487 (m-70) REVERT: C 273 ASP cc_start: 0.8387 (m-30) cc_final: 0.8136 (t70) REVERT: C 364 MET cc_start: 0.8875 (mpp) cc_final: 0.8521 (mpp) REVERT: F 246 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8423 (mp0) REVERT: F 313 ASN cc_start: 0.8218 (m-40) cc_final: 0.7907 (m110) REVERT: F 378 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: F 405 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9000 (mp) REVERT: E 313 ASN cc_start: 0.8838 (m-40) cc_final: 0.8415 (m110) REVERT: E 382 MET cc_start: 0.8988 (mmm) cc_final: 0.8692 (mtp) REVERT: E 440 THR cc_start: 0.9489 (m) cc_final: 0.9094 (p) outliers start: 49 outliers final: 28 residues processed: 194 average time/residue: 0.1133 time to fit residues: 34.5366 Evaluate side-chains 170 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain C residue 264 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 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 312 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 F residue 407 THR 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 400 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 96 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 240 HIS F 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.065416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.052640 restraints weight = 42740.845| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.48 r_work: 0.2637 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.8647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15678 Z= 0.117 Angle : 0.470 7.157 21159 Z= 0.245 Chirality : 0.041 0.191 2487 Planarity : 0.003 0.028 2679 Dihedral : 7.544 56.652 2335 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.29 % Allowed : 21.42 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.19), residues: 1947 helix: 1.43 (0.17), residues: 1059 sheet: -0.26 (0.30), residues: 285 loop : 0.35 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 284 TYR 0.011 0.001 TYR E 430 PHE 0.014 0.001 PHE D 297 TRP 0.002 0.000 TRP F 283 HIS 0.005 0.001 HIS B 348 Details of bonding type rmsd covalent geometry : bond 0.00273 (15678) covalent geometry : angle 0.46999 (21159) hydrogen bonds : bond 0.02628 ( 762) hydrogen bonds : angle 3.48678 ( 2178) *********************** 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 179 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9353 (m-80) cc_final: 0.9104 (m-80) REVERT: A 116 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8928 (t80) REVERT: A 264 MET cc_start: 0.5838 (pmm) cc_final: 0.5281 (pmm) REVERT: A 364 MET cc_start: 0.9041 (mpp) cc_final: 0.8618 (mpp) REVERT: D 270 SER cc_start: 0.9132 (m) cc_final: 0.8765 (t) REVERT: D 274 GLU cc_start: 0.9391 (tp30) cc_final: 0.9030 (tp30) REVERT: D 447 GLN cc_start: 0.5613 (tp-100) cc_final: 0.5394 (tp40) REVERT: B 74 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8927 (p) REVERT: B 273 ASP cc_start: 0.8970 (m-30) cc_final: 0.8732 (t70) REVERT: B 311 CYS cc_start: 0.8989 (m) cc_final: 0.8668 (m) REVERT: C 364 MET cc_start: 0.8910 (mpp) cc_final: 0.8540 (mpp) REVERT: F 246 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8445 (mp0) REVERT: F 313 ASN cc_start: 0.8432 (m-40) cc_final: 0.8209 (m110) REVERT: F 378 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: F 405 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.8994 (mp) REVERT: E 248 ASP cc_start: 0.8535 (m-30) cc_final: 0.8329 (m-30) outliers start: 38 outliers final: 26 residues processed: 171 average time/residue: 0.1141 time to fit residues: 30.3128 Evaluate side-chains 160 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 47 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 257 PHE Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 264 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 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 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 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 55 optimal weight: 0.7980 chunk 140 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN C 335 ASN F 240 HIS E 25 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.050501 restraints weight = 43226.569| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.45 r_work: 0.2600 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.9126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15678 Z= 0.155 Angle : 0.505 12.977 21159 Z= 0.264 Chirality : 0.042 0.222 2487 Planarity : 0.003 0.038 2679 Dihedral : 7.577 66.394 2335 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.53 % Allowed : 21.30 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.19), residues: 1947 helix: 1.55 (0.17), residues: 1059 sheet: -0.10 (0.31), residues: 285 loop : 0.22 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 333 TYR 0.014 0.001 TYR D 446 PHE 0.022 0.002 PHE E 257 TRP 0.003 0.000 TRP F 283 HIS 0.005 0.001 HIS F 302 Details of bonding type rmsd covalent geometry : bond 0.00368 (15678) covalent geometry : angle 0.50450 (21159) hydrogen bonds : bond 0.02933 ( 762) hydrogen bonds : angle 3.63420 ( 2178) *********************** 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 174 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.669 Fit side-chains REVERT: A 264 MET cc_start: 0.5909 (pmm) cc_final: 0.5437 (pmm) REVERT: A 364 MET cc_start: 0.8983 (mpp) cc_final: 0.8614 (mpp) REVERT: D 270 SER cc_start: 0.9104 (m) cc_final: 0.8743 (t) REVERT: D 274 GLU cc_start: 0.9338 (tp30) cc_final: 0.8960 (tp30) REVERT: D 300 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8860 (mm-30) REVERT: D 447 GLN cc_start: 0.5939 (tp-100) cc_final: 0.5654 (tp40) REVERT: B 273 ASP cc_start: 0.8943 (m-30) cc_final: 0.8733 (t70) REVERT: B 311 CYS cc_start: 0.9097 (m) cc_final: 0.8869 (m) REVERT: B 364 MET cc_start: 0.8634 (mpp) cc_final: 0.8348 (mpp) REVERT: C 364 MET cc_start: 0.8941 (mpp) cc_final: 0.8582 (mpp) REVERT: F 246 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8565 (mt-10) REVERT: F 378 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7220 (mp0) outliers start: 42 outliers final: 28 residues processed: 167 average time/residue: 0.1171 time to fit residues: 31.8580 Evaluate side-chains 152 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 47 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 74 THR 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 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 378 GLU 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 Chi-restraints excluded: chain E residue 426 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 70 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 161 optimal weight: 7.9990 chunk 174 optimal weight: 0.0170 chunk 61 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 98 optimal weight: 0.0970 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN C 305 HIS E 255 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.065222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.052560 restraints weight = 43370.092| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.49 r_work: 0.2640 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.9285 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= 0.091 Angle : 0.461 7.865 21159 Z= 0.240 Chirality : 0.040 0.273 2487 Planarity : 0.003 0.044 2679 Dihedral : 7.488 63.302 2335 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.11 % Allowed : 21.60 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.19), residues: 1947 helix: 1.64 (0.17), residues: 1056 sheet: -0.05 (0.31), residues: 285 loop : 0.30 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 333 TYR 0.017 0.001 TYR D 446 PHE 0.013 0.001 PHE D 297 TRP 0.001 0.000 TRP E 283 HIS 0.004 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00205 (15678) covalent geometry : angle 0.46128 (21159) hydrogen bonds : bond 0.02402 ( 762) hydrogen bonds : angle 3.41149 ( 2178) *********************** 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 169 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.653 Fit side-chains REVERT: A 102 TYR cc_start: 0.9454 (m-80) cc_final: 0.9241 (m-80) REVERT: A 264 MET cc_start: 0.5748 (pmm) cc_final: 0.5335 (pmm) REVERT: A 364 MET cc_start: 0.8993 (mpp) cc_final: 0.8574 (mpp) REVERT: D 270 SER cc_start: 0.9108 (m) cc_final: 0.8597 (t) REVERT: D 447 GLN cc_start: 0.5886 (tp-100) cc_final: 0.5679 (tp40) REVERT: B 273 ASP cc_start: 0.8874 (m-30) cc_final: 0.8648 (t70) REVERT: B 311 CYS cc_start: 0.9112 (m) cc_final: 0.8852 (m) REVERT: C 364 MET cc_start: 0.8973 (mpp) cc_final: 0.8631 (mpp) REVERT: F 135 THR cc_start: 0.6306 (p) cc_final: 0.5922 (p) REVERT: F 246 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8536 (mt-10) REVERT: F 255 GLN cc_start: 0.8563 (mp10) cc_final: 0.8329 (pp30) REVERT: F 261 PHE cc_start: 0.8648 (m-80) cc_final: 0.8222 (m-10) REVERT: E 271 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8397 (mp0) outliers start: 35 outliers final: 27 residues processed: 163 average time/residue: 0.1098 time to fit residues: 29.0284 Evaluate side-chains 156 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 375 CYS 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 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 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 271 GLU 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 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 184 optimal weight: 0.0020 chunk 167 optimal weight: 0.3980 chunk 87 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 170 optimal weight: 0.0010 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 313 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 = 0.3130 r_free = 0.3130 target = 0.066153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.053340 restraints weight = 42873.484| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.64 r_work: 0.2666 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.9414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15678 Z= 0.087 Angle : 0.457 9.337 21159 Z= 0.236 Chirality : 0.040 0.271 2487 Planarity : 0.003 0.057 2679 Dihedral : 7.231 62.861 2335 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.74 % Allowed : 22.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.19), residues: 1947 helix: 1.74 (0.17), residues: 1056 sheet: 0.04 (0.31), residues: 285 loop : 0.31 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 333 TYR 0.019 0.001 TYR D 446 PHE 0.012 0.001 PHE D 297 TRP 0.002 0.000 TRP E 283 HIS 0.005 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00193 (15678) covalent geometry : angle 0.45660 (21159) hydrogen bonds : bond 0.02312 ( 762) hydrogen bonds : angle 3.30849 ( 2178) *********************** 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 170 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.686 Fit side-chains REVERT: A 96 MET cc_start: 0.9244 (ttm) cc_final: 0.9001 (ttm) REVERT: A 102 TYR cc_start: 0.9440 (m-80) cc_final: 0.9207 (m-80) REVERT: A 264 MET cc_start: 0.5724 (pmm) cc_final: 0.5359 (pmm) REVERT: A 364 MET cc_start: 0.8979 (mpp) cc_final: 0.8738 (mpp) REVERT: D 88 MET cc_start: 0.8549 (mmt) cc_final: 0.8296 (mmp) REVERT: D 270 SER cc_start: 0.9004 (m) cc_final: 0.8681 (p) REVERT: D 382 MET cc_start: 0.9130 (mtp) cc_final: 0.8438 (mtp) REVERT: D 387 TYR cc_start: 0.8545 (m-80) cc_final: 0.8072 (m-80) REVERT: B 264 MET cc_start: 0.5058 (pmm) cc_final: 0.4653 (pmm) REVERT: B 273 ASP cc_start: 0.8886 (m-30) cc_final: 0.8662 (t70) REVERT: B 311 CYS cc_start: 0.9092 (m) cc_final: 0.8755 (m) REVERT: C 364 MET cc_start: 0.9021 (mpp) cc_final: 0.8645 (mpp) REVERT: C 455 MET cc_start: 0.8088 (mmm) cc_final: 0.7678 (mtm) REVERT: F 135 THR cc_start: 0.6371 (p) cc_final: 0.5986 (p) REVERT: F 246 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8418 (mp0) REVERT: F 261 PHE cc_start: 0.8551 (m-80) cc_final: 0.8133 (m-10) REVERT: F 300 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8496 (mm-30) REVERT: E 255 GLN cc_start: 0.8519 (tp40) cc_final: 0.8216 (tp40) REVERT: E 271 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8589 (mp0) outliers start: 29 outliers final: 24 residues processed: 165 average time/residue: 0.1159 time to fit residues: 30.4315 Evaluate side-chains 155 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 346 SER 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 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 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 271 GLU 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 48 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN B 289 GLN F 27 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.061563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.048510 restraints weight = 44248.454| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 3.62 r_work: 0.2539 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.9688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15678 Z= 0.231 Angle : 0.557 10.693 21159 Z= 0.293 Chirality : 0.043 0.272 2487 Planarity : 0.004 0.060 2679 Dihedral : 7.569 75.686 2335 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.81 % Allowed : 22.32 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.20), residues: 1947 helix: 1.67 (0.17), residues: 1056 sheet: 0.09 (0.32), residues: 285 loop : 0.19 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 333 TYR 0.020 0.001 TYR D 446 PHE 0.016 0.002 PHE D 311 TRP 0.005 0.001 TRP F 283 HIS 0.005 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00543 (15678) covalent geometry : angle 0.55715 (21159) hydrogen bonds : bond 0.03292 ( 762) hydrogen bonds : angle 3.78906 ( 2178) ********************** 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 156 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.686 Fit side-chains REVERT: D 270 SER cc_start: 0.9004 (m) cc_final: 0.8732 (p) REVERT: D 382 MET cc_start: 0.9208 (mtp) cc_final: 0.8703 (mtp) REVERT: B 264 MET cc_start: 0.5134 (pmm) cc_final: 0.4620 (pmm) REVERT: B 311 CYS cc_start: 0.9175 (m) cc_final: 0.8975 (m) REVERT: C 364 MET cc_start: 0.9026 (mpp) cc_final: 0.8718 (mpp) REVERT: C 455 MET cc_start: 0.8470 (mmm) cc_final: 0.7881 (mmm) REVERT: F 135 THR cc_start: 0.6531 (p) cc_final: 0.6191 (p) REVERT: F 246 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8561 (mt-10) REVERT: F 387 TYR cc_start: 0.8597 (m-80) cc_final: 0.8313 (m-80) REVERT: E 261 PHE cc_start: 0.9129 (m-10) cc_final: 0.8867 (m-80) REVERT: E 271 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8738 (mp0) outliers start: 30 outliers final: 25 residues processed: 151 average time/residue: 0.1093 time to fit residues: 26.5307 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 : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 375 CYS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 346 SER 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 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 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 271 GLU 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 49 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN B 289 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.064410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.051589 restraints weight = 43079.516| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.60 r_work: 0.2613 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.9756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15678 Z= 0.102 Angle : 0.479 8.725 21159 Z= 0.249 Chirality : 0.041 0.281 2487 Planarity : 0.004 0.084 2679 Dihedral : 7.417 73.369 2335 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.44 % Allowed : 22.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.20), residues: 1947 helix: 1.77 (0.17), residues: 1053 sheet: 0.11 (0.32), residues: 285 loop : 0.30 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 353 TYR 0.018 0.001 TYR D 446 PHE 0.014 0.001 PHE D 297 TRP 0.002 0.000 TRP F 283 HIS 0.004 0.001 HIS D 302 Details of bonding type rmsd covalent geometry : bond 0.00235 (15678) covalent geometry : angle 0.47895 (21159) hydrogen bonds : bond 0.02512 ( 762) hydrogen bonds : angle 3.45145 ( 2178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2932.38 seconds wall clock time: 51 minutes 35.94 seconds (3095.94 seconds total)