Starting phenix.real_space_refine on Fri Mar 6 05:47:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p6x_13233/03_2026/7p6x_13233_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p6x_13233/03_2026/7p6x_13233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p6x_13233/03_2026/7p6x_13233_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p6x_13233/03_2026/7p6x_13233_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p6x_13233/03_2026/7p6x_13233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p6x_13233/03_2026/7p6x_13233.map" } resolution = 4.1 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= 0.001 sd= 0.034 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 6 5.49 5 S 71 5.16 5 C 8826 2.51 5 N 2451 2.21 5 O 2725 1.98 5 H 14395 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28474 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 5006 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain breaks: 2 Chain: "B" Number of atoms: 4877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4877 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain breaks: 2 Chain: "C" Number of atoms: 5034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 5034 Classifications: {'peptide': 322} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 311} Chain breaks: 2 Chain: "D" Number of atoms: 4430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4430 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 8, 'TRANS': 273} Chain breaks: 2 Chain: "E" Number of atoms: 4537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 4537 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain breaks: 2 Chain: "F" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 4509 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.87, per 1000 atoms: 0.17 Number of scatterers: 28474 At special positions: 0 Unit cell: (82.005, 127.8, 136.32, 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 71 16.00 P 6 15.00 O 2725 8.00 N 2451 7.00 C 8826 6.00 H 14395 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 801.8 milliseconds 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3376 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 22 sheets defined 58.3% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 14 through 19 removed outlier: 3.926A pdb=" N SER A 17 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 58 Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.638A pdb=" N ALA A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' 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: 3.589A pdb=" N TYR A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.548A pdb=" N PHE A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 320 " --> pdb=" O HIS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 382 removed outlier: 3.735A pdb=" N GLN A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.529A pdb=" N ILE A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 426 through 436 removed outlier: 3.845A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 455 removed outlier: 4.446A pdb=" N LYS A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 Processing helix chain 'B' and resid 17 through 19 No H-bonds generated for 'chain 'B' and resid 17 through 19' Processing helix chain 'B' and resid 42 through 58 removed outlier: 3.608A pdb=" N GLU B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 107 through 119 removed outlier: 3.506A pdb=" N VAL B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 272 through 290 removed outlier: 3.574A pdb=" N GLU B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 367 through 382 removed outlier: 3.817A pdb=" N GLN B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 401 removed outlier: 3.840A pdb=" N ASN B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 removed outlier: 4.048A pdb=" N SER B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.686A pdb=" N VAL B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 452 Processing helix chain 'C' and resid 11 through 17 removed outlier: 3.857A pdb=" N SER C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 58 Processing helix chain 'C' and resid 76 through 88 removed outlier: 3.548A pdb=" N ALA C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 107 through 118 removed outlier: 3.633A pdb=" N ARG C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 246 Processing helix chain 'C' and resid 272 through 289 removed outlier: 3.503A pdb=" N ARG C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 367 through 383 removed outlier: 3.574A pdb=" N ILE C 377 " --> pdb=" O GLN C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 removed outlier: 3.540A pdb=" N LEU C 391 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.921A pdb=" N SER C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 420 Processing helix chain 'C' and resid 426 through 436 Processing helix chain 'C' and resid 439 through 451 removed outlier: 4.357A pdb=" N LYS C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 65 removed outlier: 3.675A pdb=" N ARG D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.698A pdb=" N GLY D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 109 Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.588A pdb=" N ALA D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 252 removed outlier: 3.977A pdb=" N ILE D 250 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 286 removed outlier: 3.591A pdb=" N ARG D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 4.071A pdb=" N PHE D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 352 removed outlier: 3.754A pdb=" N ASP D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 378 removed outlier: 3.565A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 398 through 414 removed outlier: 3.724A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 435 through 449 removed outlier: 5.134A pdb=" N TYR D 446 " --> pdb=" O TYR D 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 65 removed outlier: 3.563A pdb=" N ARG E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU E 61 " --> pdb=" O GLY E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 95 Processing helix chain 'E' and resid 114 through 126 Processing helix chain 'E' and resid 244 through 248 Processing helix chain 'E' and resid 269 through 287 removed outlier: 3.538A pdb=" N GLU E 285 " --> pdb=" O ALA E 281 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY E 287 " --> pdb=" O TRP E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 305 through 316 removed outlier: 3.939A pdb=" N PHE E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 352 removed outlier: 3.661A pdb=" N ASP E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 378 removed outlier: 3.555A pdb=" N GLU E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU E 378 " --> pdb=" O ARG E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 removed outlier: 3.523A pdb=" N ARG E 392 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 414 removed outlier: 3.950A pdb=" N GLN E 404 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU E 411 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 417 No H-bonds generated for 'chain 'E' and resid 415 through 417' Processing helix chain 'E' and resid 422 through 433 Processing helix chain 'E' and resid 435 through 453 removed outlier: 3.559A pdb=" N ALA E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE E 450 " --> pdb=" O TYR E 446 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU E 451 " --> pdb=" O GLN E 447 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN E 453 " --> pdb=" O ALA E 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 65 removed outlier: 3.660A pdb=" N GLU F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.706A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 126 Processing helix chain 'F' and resid 244 through 251 removed outlier: 3.574A pdb=" N VAL F 249 " --> pdb=" O HIS F 245 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE F 250 " --> pdb=" O GLU F 246 " (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 317 removed outlier: 3.958A pdb=" N PHE F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 317 " --> pdb=" O ASN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 352 removed outlier: 3.689A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 378 removed outlier: 3.605A pdb=" N GLU F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 414 removed outlier: 3.544A pdb=" N GLN F 404 " --> pdb=" O ARG F 400 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 411 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 removed outlier: 3.531A pdb=" N SER F 431 " --> pdb=" O LYS F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 452 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.532A pdb=" N LEU A 39 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.458A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU A 299 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA A 330 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 301 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 239 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 386 removed outlier: 7.403A pdb=" N ASN A 385 " --> pdb=" O ILE A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 437 through 438 removed outlier: 4.151A pdb=" N ILE F 356 " --> pdb=" O TYR A 438 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL F 73 " --> pdb=" O MET F 326 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N THR F 328 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE F 75 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.541A pdb=" N LEU B 39 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.197A pdb=" N LEU B 299 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA B 330 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 301 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 120 through 122 Processing sheet with id=AB1, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AB2, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AB3, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB4, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.275A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU C 299 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA C 330 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 301 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N SER C 331 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 68 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 236 through 239 Processing sheet with id=AB6, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AB7, first strand: chain 'C' and resid 437 through 438 removed outlier: 4.229A pdb=" N ILE E 356 " --> pdb=" O TYR C 438 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR E 328 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU E 296 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA E 327 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE E 298 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 100 through 104 Processing sheet with id=AB9, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AC1, first strand: chain 'E' and resid 127 through 130 Processing sheet with id=AC2, first strand: chain 'E' and resid 332 through 334 Processing sheet with id=AC3, first strand: chain 'F' and resid 242 through 243 Processing sheet with id=AC4, first strand: chain 'F' and resid 332 through 334 717 hydrogen bonds defined for protein. 2091 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.85 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 14377 1.05 - 1.27: 2144 1.27 - 1.48: 5185 1.48 - 1.70: 6810 1.70 - 1.91: 124 Bond restraints: 28640 Sorted by residual: bond pdb=" C ARG E 273 " pdb=" O ARG E 273 " ideal model delta sigma weight residual 1.236 1.145 0.092 1.16e-02 7.43e+03 6.27e+01 bond pdb=" C SER B 89 " pdb=" O SER B 89 " ideal model delta sigma weight residual 1.236 1.319 -0.084 1.21e-02 6.83e+03 4.79e+01 bond pdb=" O3B ADP A 501 " pdb=" PB ADP A 501 " ideal model delta sigma weight residual 1.510 1.373 0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C PRO D 322 " pdb=" O PRO D 322 " ideal model delta sigma weight residual 1.235 1.152 0.083 1.30e-02 5.92e+03 4.07e+01 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.364 0.126 2.00e-02 2.50e+03 3.96e+01 ... (remaining 28635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 50847 3.77 - 7.54: 1082 7.54 - 11.31: 52 11.31 - 15.08: 7 15.08 - 18.85: 1 Bond angle restraints: 51989 Sorted by residual: angle pdb=" N TYR D 442 " pdb=" CA TYR D 442 " pdb=" C TYR D 442 " ideal model delta sigma weight residual 113.02 102.88 10.14 1.20e+00 6.94e-01 7.14e+01 angle pdb=" CA ASP E 385 " pdb=" CB ASP E 385 " pdb=" CG ASP E 385 " ideal model delta sigma weight residual 112.60 105.26 7.34 1.00e+00 1.00e+00 5.39e+01 angle pdb=" C ALA F 281 " pdb=" N GLU F 282 " pdb=" CA GLU F 282 " ideal model delta sigma weight residual 120.63 130.38 -9.75 1.36e+00 5.41e-01 5.14e+01 angle pdb=" C ALA E 281 " pdb=" N GLU E 282 " pdb=" CA GLU E 282 " ideal model delta sigma weight residual 120.63 129.72 -9.09 1.36e+00 5.41e-01 4.47e+01 angle pdb=" C LYS C 285 " pdb=" N TYR C 286 " pdb=" CA TYR C 286 " ideal model delta sigma weight residual 120.44 129.50 -9.06 1.36e+00 5.41e-01 4.43e+01 ... (remaining 51984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.73: 12782 31.73 - 63.46: 410 63.46 - 95.18: 24 95.18 - 126.91: 3 126.91 - 158.64: 2 Dihedral angle restraints: 13221 sinusoidal: 7512 harmonic: 5709 Sorted by residual: dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 141.36 158.64 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 146.27 153.74 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual 300.00 177.81 122.19 1 2.00e+01 2.50e-03 3.68e+01 ... (remaining 13218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1417 0.093 - 0.186: 722 0.186 - 0.279: 131 0.279 - 0.372: 14 0.372 - 0.465: 4 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CA ARG B 14 " pdb=" N ARG B 14 " pdb=" C ARG B 14 " pdb=" CB ARG B 14 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CA GLU A 86 " pdb=" N GLU A 86 " pdb=" C GLU A 86 " pdb=" CB GLU A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB THR D 241 " pdb=" CA THR D 241 " pdb=" OG1 THR D 241 " pdb=" CG2 THR D 241 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 2285 not shown) Planarity restraints: 4185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 369 " 0.211 2.00e-02 2.50e+03 3.87e-01 2.25e+03 pdb=" CD GLN A 369 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN A 369 " -0.204 2.00e-02 2.50e+03 pdb=" NE2 GLN A 369 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 369 " 0.641 2.00e-02 2.50e+03 pdb="HE22 GLN A 369 " -0.635 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 447 " -0.138 2.00e-02 2.50e+03 1.54e-01 3.55e+02 pdb=" CD GLN E 447 " 0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN E 447 " 0.134 2.00e-02 2.50e+03 pdb=" NE2 GLN E 447 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN E 447 " 0.228 2.00e-02 2.50e+03 pdb="HE22 GLN E 447 " -0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 447 " -0.127 2.00e-02 2.50e+03 1.41e-01 2.98e+02 pdb=" CD GLN D 447 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN D 447 " 0.123 2.00e-02 2.50e+03 pdb=" NE2 GLN D 447 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN D 447 " 0.209 2.00e-02 2.50e+03 pdb="HE22 GLN D 447 " -0.210 2.00e-02 2.50e+03 ... (remaining 4182 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1537 2.17 - 2.78: 58634 2.78 - 3.39: 76393 3.39 - 3.99: 99613 3.99 - 4.60: 157104 Nonbonded interactions: 393281 Sorted by model distance: nonbonded pdb="HD21 LEU E 324 " pdb=" HE3 MET E 326 " model vdw 1.564 2.440 nonbonded pdb=" HZ3 LYS B 108 " pdb=" OD2 ASP B 308 " model vdw 1.602 2.450 nonbonded pdb=" HG1 THR D 397 " pdb=" OD2 ASP D 435 " model vdw 1.635 2.450 nonbonded pdb=" HG1 THR D 101 " pdb="HD12 LEU D 296 " model vdw 1.639 2.270 nonbonded pdb=" O THR E 116 " pdb=" HG1 THR E 120 " model vdw 1.659 2.450 ... (remaining 393276 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 123 or (resid 238 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG \ 11 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 2 \ 39 through 247 or (resid 271 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or nam \ e HG13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name \ HD13)) or resid 272 through 452 or resid 501)) selection = (chain 'B' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 7 through 247 or resid 271 \ through 501)) selection = (chain 'C' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 7 through 123 or (resid 23 \ 8 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 \ or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or nam \ e HG22 or name HG23)) or resid 239 through 247 or (resid 271 and (name N or name \ CA or name C or name O or name CB or name CG1 or name CG2 or name CD1 or name H \ A or name HB or name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or \ name HD11 or name HD12 or name HD13)) or resid 272 through 501)) } ncs_group { reference = (chain 'D' and (resid 43 through 127 or resid 243 through 283 or (resid 284 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 285 through 449)) selection = (chain 'E' and (resid 43 through 127 or resid 243 through 253 or resid 267 throu \ gh 283 or (resid 284 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 285 through 449)) selection = (chain 'F' and (resid 43 through 127 or resid 243 through 449)) } 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=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.850 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.017 0.137 14245 Z= 1.191 Angle : 1.825 14.728 19216 Z= 1.234 Chirality : 0.104 0.465 2288 Planarity : 0.010 0.055 2444 Dihedral : 12.652 158.638 5423 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.92 % Allowed : 3.92 % Favored : 95.16 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.16), residues: 1777 helix: -2.99 (0.12), residues: 987 sheet: -1.05 (0.37), residues: 180 loop : -1.72 (0.22), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.004 ARG D 353 TYR 0.065 0.013 TYR E 387 PHE 0.059 0.011 PHE F 123 TRP 0.020 0.003 TRP D 283 HIS 0.039 0.008 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.01747 (14245) covalent geometry : angle 1.82515 (19216) hydrogen bonds : bond 0.29074 ( 717) hydrogen bonds : angle 9.58603 ( 2091) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 337 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 LEU cc_start: 0.9544 (mt) cc_final: 0.9112 (mt) REVERT: C 1 MET cc_start: 0.2636 (ptp) cc_final: 0.1649 (ppp) REVERT: C 52 ILE cc_start: 0.9592 (mm) cc_final: 0.9387 (tp) REVERT: C 56 ILE cc_start: 0.9552 (mt) cc_final: 0.9297 (tp) REVERT: C 61 MET cc_start: 0.8630 (mmm) cc_final: 0.8380 (tmm) REVERT: E 109 PHE cc_start: 0.9178 (m-80) cc_final: 0.8855 (m-10) REVERT: F 108 ILE cc_start: 0.9515 (pt) cc_final: 0.9239 (mm) REVERT: F 243 SER cc_start: 0.7987 (OUTLIER) cc_final: 0.7781 (t) REVERT: F 452 PHE cc_start: 0.8917 (t80) cc_final: 0.8646 (t80) outliers start: 14 outliers final: 3 residues processed: 350 average time/residue: 0.2889 time to fit residues: 143.3735 Evaluate side-chains 226 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 149 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 HIS ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN F 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.034891 restraints weight = 222472.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.036879 restraints weight = 98678.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.038371 restraints weight = 59479.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.039405 restraints weight = 41098.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.040142 restraints weight = 31541.997| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14245 Z= 0.160 Angle : 0.667 6.821 19216 Z= 0.356 Chirality : 0.043 0.166 2288 Planarity : 0.005 0.045 2444 Dihedral : 7.884 138.806 1977 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.18), residues: 1777 helix: -1.18 (0.14), residues: 1054 sheet: -0.76 (0.36), residues: 186 loop : -1.44 (0.23), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 314 TYR 0.017 0.002 TYR B 314 PHE 0.020 0.002 PHE C 116 TRP 0.004 0.001 TRP D 283 HIS 0.006 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00326 (14245) covalent geometry : angle 0.66728 (19216) hydrogen bonds : bond 0.06499 ( 717) hydrogen bonds : angle 5.63831 ( 2091) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 CYS cc_start: 0.9702 (m) cc_final: 0.9494 (m) REVERT: A 311 CYS cc_start: 0.9583 (m) cc_final: 0.9378 (m) REVERT: A 314 TYR cc_start: 0.9062 (t80) cc_final: 0.8807 (t80) REVERT: A 319 LEU cc_start: 0.9645 (tp) cc_final: 0.9402 (tp) REVERT: B 55 LEU cc_start: 0.9835 (mt) cc_final: 0.9633 (mt) REVERT: B 61 MET cc_start: 0.9315 (mmp) cc_final: 0.9057 (mmm) REVERT: B 326 ILE cc_start: 0.9698 (mm) cc_final: 0.9302 (tp) REVERT: C 110 GLU cc_start: 0.9681 (mp0) cc_final: 0.9469 (mp0) REVERT: C 113 MET cc_start: 0.9220 (ppp) cc_final: 0.8873 (ppp) REVERT: C 336 CYS cc_start: 0.7642 (m) cc_final: 0.7332 (m) REVERT: E 67 LYS cc_start: 0.9528 (mttt) cc_final: 0.9032 (mttt) REVERT: E 88 MET cc_start: 0.9702 (mmm) cc_final: 0.9493 (mmm) REVERT: E 433 PHE cc_start: 0.9137 (m-80) cc_final: 0.8685 (m-80) REVERT: E 450 PHE cc_start: 0.8389 (p90) cc_final: 0.8051 (p90) REVERT: F 62 MET cc_start: 0.9789 (ttm) cc_final: 0.8962 (tpp) REVERT: F 300 GLU cc_start: 0.9052 (tt0) cc_final: 0.8832 (tt0) REVERT: F 452 PHE cc_start: 0.9079 (t80) cc_final: 0.8833 (t80) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2960 time to fit residues: 110.3473 Evaluate side-chains 196 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 70 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN C 236 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.045485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.033596 restraints weight = 235533.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.035488 restraints weight = 105377.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.036790 restraints weight = 63307.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.037787 restraints weight = 44995.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.038479 restraints weight = 34534.939| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 14245 Z= 0.257 Angle : 0.650 6.461 19216 Z= 0.352 Chirality : 0.040 0.168 2288 Planarity : 0.004 0.032 2444 Dihedral : 7.571 142.858 1977 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.19), residues: 1777 helix: -0.27 (0.15), residues: 1052 sheet: -0.44 (0.34), residues: 199 loop : -1.25 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 374 TYR 0.025 0.001 TYR F 446 PHE 0.030 0.002 PHE F 450 TRP 0.005 0.001 TRP D 283 HIS 0.006 0.002 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00486 (14245) covalent geometry : angle 0.64982 (19216) hydrogen bonds : bond 0.04751 ( 717) hydrogen bonds : angle 5.36364 ( 2091) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 CYS cc_start: 0.9525 (m) cc_final: 0.9141 (m) REVERT: A 312 PHE cc_start: 0.9243 (m-80) cc_final: 0.8683 (m-80) REVERT: B 61 MET cc_start: 0.9343 (mmp) cc_final: 0.9113 (mmm) REVERT: B 116 PHE cc_start: 0.9717 (t80) cc_final: 0.9515 (t80) REVERT: B 326 ILE cc_start: 0.9739 (mm) cc_final: 0.9084 (tp) REVERT: C 1 MET cc_start: 0.0883 (ppp) cc_final: 0.0447 (ppp) REVERT: C 110 GLU cc_start: 0.9711 (mp0) cc_final: 0.9501 (mp0) REVERT: C 113 MET cc_start: 0.9284 (ppp) cc_final: 0.8905 (ppp) REVERT: C 336 CYS cc_start: 0.7992 (m) cc_final: 0.7626 (m) REVERT: D 299 ASP cc_start: 0.9338 (t0) cc_final: 0.9105 (t0) REVERT: D 303 MET cc_start: 0.9697 (mmp) cc_final: 0.9456 (mmm) REVERT: E 62 MET cc_start: 0.9695 (tpp) cc_final: 0.9475 (tpp) REVERT: E 303 MET cc_start: 0.9616 (mmp) cc_final: 0.9176 (mmp) REVERT: E 326 MET cc_start: 0.9693 (mpp) cc_final: 0.9375 (mpp) REVERT: E 443 MET cc_start: 0.9178 (tpp) cc_final: 0.8772 (tpp) REVERT: F 62 MET cc_start: 0.9821 (ttm) cc_final: 0.9088 (tpp) REVERT: F 443 MET cc_start: 0.9295 (tpp) cc_final: 0.8886 (tpp) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2889 time to fit residues: 86.7688 Evaluate side-chains 172 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 134 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.045372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.033429 restraints weight = 229904.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.035350 restraints weight = 104091.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.036718 restraints weight = 62578.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.037671 restraints weight = 43640.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.038372 restraints weight = 33679.735| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14245 Z= 0.174 Angle : 0.563 6.186 19216 Z= 0.296 Chirality : 0.039 0.130 2288 Planarity : 0.003 0.035 2444 Dihedral : 7.312 141.638 1977 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1777 helix: 0.22 (0.16), residues: 1058 sheet: -0.23 (0.34), residues: 200 loop : -1.11 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 276 TYR 0.013 0.001 TYR F 446 PHE 0.014 0.002 PHE F 450 TRP 0.004 0.001 TRP F 283 HIS 0.006 0.001 HIS E 344 Details of bonding type rmsd covalent geometry : bond 0.00338 (14245) covalent geometry : angle 0.56252 (19216) hydrogen bonds : bond 0.03950 ( 717) hydrogen bonds : angle 4.87791 ( 2091) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 CYS cc_start: 0.9460 (m) cc_final: 0.9168 (m) REVERT: A 312 PHE cc_start: 0.9150 (m-80) cc_final: 0.8614 (m-80) REVERT: B 54 GLU cc_start: 0.9706 (mm-30) cc_final: 0.9294 (mp0) REVERT: B 326 ILE cc_start: 0.9683 (mm) cc_final: 0.9346 (tp) REVERT: C 113 MET cc_start: 0.9258 (ppp) cc_final: 0.8814 (ppp) REVERT: C 303 GLU cc_start: 0.8942 (mp0) cc_final: 0.8659 (mp0) REVERT: C 336 CYS cc_start: 0.8096 (m) cc_final: 0.7781 (m) REVERT: D 117 GLU cc_start: 0.9685 (mp0) cc_final: 0.9385 (mp0) REVERT: D 299 ASP cc_start: 0.9335 (t0) cc_final: 0.9097 (t0) REVERT: E 326 MET cc_start: 0.9561 (mpp) cc_final: 0.9116 (mpp) REVERT: E 443 MET cc_start: 0.9168 (tpp) cc_final: 0.8732 (tpp) REVERT: F 62 MET cc_start: 0.9838 (ttm) cc_final: 0.9169 (tpp) REVERT: F 88 MET cc_start: 0.9783 (mmp) cc_final: 0.9561 (mmm) REVERT: F 326 MET cc_start: 0.9699 (mtm) cc_final: 0.9002 (mpp) REVERT: F 443 MET cc_start: 0.9339 (tpp) cc_final: 0.9004 (tpp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2880 time to fit residues: 84.2449 Evaluate side-chains 167 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.044725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.033059 restraints weight = 244355.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.034912 restraints weight = 112001.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.036246 restraints weight = 67578.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.037145 restraints weight = 47303.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.037833 restraints weight = 36675.058| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14245 Z= 0.273 Angle : 0.632 6.693 19216 Z= 0.339 Chirality : 0.039 0.141 2288 Planarity : 0.004 0.033 2444 Dihedral : 7.232 143.193 1977 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.19), residues: 1777 helix: 0.05 (0.15), residues: 1062 sheet: -0.32 (0.34), residues: 203 loop : -1.36 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 400 TYR 0.015 0.001 TYR B 314 PHE 0.021 0.002 PHE F 109 TRP 0.005 0.001 TRP E 283 HIS 0.008 0.002 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00509 (14245) covalent geometry : angle 0.63249 (19216) hydrogen bonds : bond 0.03910 ( 717) hydrogen bonds : angle 5.04306 ( 2091) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9228 (mmp) cc_final: 0.8499 (mmm) REVERT: A 311 CYS cc_start: 0.9468 (m) cc_final: 0.9263 (m) REVERT: B 54 GLU cc_start: 0.9689 (mm-30) cc_final: 0.9316 (mp0) REVERT: B 303 GLU cc_start: 0.8999 (pt0) cc_final: 0.8688 (pt0) REVERT: B 326 ILE cc_start: 0.9716 (mm) cc_final: 0.9371 (tp) REVERT: C 113 MET cc_start: 0.9259 (ppp) cc_final: 0.8961 (ppp) REVERT: C 303 GLU cc_start: 0.8922 (mp0) cc_final: 0.8647 (mp0) REVERT: C 312 PHE cc_start: 0.9395 (m-80) cc_final: 0.9155 (m-80) REVERT: D 326 MET cc_start: 0.9682 (mtm) cc_final: 0.9280 (mpp) REVERT: E 303 MET cc_start: 0.9725 (mmp) cc_final: 0.9354 (mmm) REVERT: E 326 MET cc_start: 0.9451 (mpp) cc_final: 0.9042 (mpp) REVERT: E 443 MET cc_start: 0.9160 (tpp) cc_final: 0.8519 (tpp) REVERT: F 62 MET cc_start: 0.9802 (ttm) cc_final: 0.9139 (tpp) REVERT: F 326 MET cc_start: 0.9661 (mtm) cc_final: 0.8974 (mpp) REVERT: F 443 MET cc_start: 0.9161 (tpp) cc_final: 0.8959 (tpp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2900 time to fit residues: 74.7542 Evaluate side-chains 152 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.044861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.033083 restraints weight = 242749.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.034974 restraints weight = 110324.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.036282 restraints weight = 66259.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.037262 restraints weight = 46974.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.037958 restraints weight = 36101.815| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14245 Z= 0.202 Angle : 0.566 6.063 19216 Z= 0.301 Chirality : 0.039 0.122 2288 Planarity : 0.003 0.036 2444 Dihedral : 7.070 139.477 1977 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1777 helix: 0.25 (0.15), residues: 1065 sheet: -0.21 (0.34), residues: 203 loop : -1.26 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 400 TYR 0.012 0.001 TYR B 314 PHE 0.020 0.002 PHE E 100 TRP 0.004 0.001 TRP F 283 HIS 0.006 0.001 HIS E 344 Details of bonding type rmsd covalent geometry : bond 0.00377 (14245) covalent geometry : angle 0.56570 (19216) hydrogen bonds : bond 0.03602 ( 717) hydrogen bonds : angle 4.82321 ( 2091) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9185 (mmp) cc_final: 0.8738 (mmm) REVERT: A 311 CYS cc_start: 0.9448 (m) cc_final: 0.9124 (m) REVERT: B 54 GLU cc_start: 0.9683 (mm-30) cc_final: 0.9348 (mp0) REVERT: B 103 SER cc_start: 0.9230 (m) cc_final: 0.8935 (t) REVERT: B 326 ILE cc_start: 0.9734 (mm) cc_final: 0.9394 (tp) REVERT: B 359 MET cc_start: 0.8698 (mpp) cc_final: 0.8473 (mpp) REVERT: C 1 MET cc_start: 0.1175 (ppp) cc_final: 0.0862 (ppp) REVERT: C 113 MET cc_start: 0.9268 (ppp) cc_final: 0.8986 (ppp) REVERT: C 303 GLU cc_start: 0.8937 (mp0) cc_final: 0.8612 (mp0) REVERT: E 303 MET cc_start: 0.9696 (mmp) cc_final: 0.9283 (mmm) REVERT: E 326 MET cc_start: 0.9436 (mpp) cc_final: 0.9029 (mpp) REVERT: E 443 MET cc_start: 0.9208 (tpp) cc_final: 0.8397 (tpp) REVERT: F 62 MET cc_start: 0.9804 (ttm) cc_final: 0.9154 (tpp) REVERT: F 88 MET cc_start: 0.9749 (mmp) cc_final: 0.9511 (mmm) REVERT: F 311 PHE cc_start: 0.9314 (t80) cc_final: 0.8836 (t80) REVERT: F 326 MET cc_start: 0.9652 (mtm) cc_final: 0.8971 (mpp) REVERT: F 443 MET cc_start: 0.9175 (tpp) cc_final: 0.8931 (tpp) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2954 time to fit residues: 78.4838 Evaluate side-chains 150 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 16 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 128 optimal weight: 0.0980 chunk 122 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.045301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.033377 restraints weight = 235869.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.035349 restraints weight = 106024.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.036755 restraints weight = 63072.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.037719 restraints weight = 43778.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.038440 restraints weight = 33614.352| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14245 Z= 0.111 Angle : 0.517 5.833 19216 Z= 0.264 Chirality : 0.039 0.135 2288 Planarity : 0.003 0.033 2444 Dihedral : 6.860 133.649 1977 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1777 helix: 0.78 (0.16), residues: 1065 sheet: -0.07 (0.35), residues: 203 loop : -0.99 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 400 TYR 0.012 0.001 TYR B 314 PHE 0.029 0.002 PHE C 312 TRP 0.003 0.001 TRP F 283 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00224 (14245) covalent geometry : angle 0.51687 (19216) hydrogen bonds : bond 0.03273 ( 717) hydrogen bonds : angle 4.34992 ( 2091) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9212 (mmp) cc_final: 0.8680 (mmm) REVERT: A 302 ASP cc_start: 0.9759 (t0) cc_final: 0.8994 (p0) REVERT: A 311 CYS cc_start: 0.9408 (m) cc_final: 0.9200 (m) REVERT: B 54 GLU cc_start: 0.9666 (mm-30) cc_final: 0.9321 (mp0) REVERT: B 103 SER cc_start: 0.9165 (m) cc_final: 0.8911 (t) REVERT: B 326 ILE cc_start: 0.9737 (mm) cc_final: 0.9391 (tp) REVERT: B 359 MET cc_start: 0.8695 (mpp) cc_final: 0.8450 (mpp) REVERT: C 1 MET cc_start: 0.1243 (ppp) cc_final: 0.0910 (ppp) REVERT: C 110 GLU cc_start: 0.9704 (mp0) cc_final: 0.9444 (mp0) REVERT: C 113 MET cc_start: 0.9231 (ppp) cc_final: 0.8773 (ppp) REVERT: C 303 GLU cc_start: 0.8969 (mp0) cc_final: 0.8631 (mp0) REVERT: C 312 PHE cc_start: 0.9388 (m-80) cc_final: 0.8843 (m-80) REVERT: C 371 MET cc_start: 0.9573 (mtp) cc_final: 0.9146 (mtp) REVERT: D 62 MET cc_start: 0.9652 (tpp) cc_final: 0.9448 (tpp) REVERT: D 326 MET cc_start: 0.9773 (mtm) cc_final: 0.9306 (mpp) REVERT: E 326 MET cc_start: 0.9466 (mpp) cc_final: 0.9110 (mpp) REVERT: E 443 MET cc_start: 0.9212 (tpp) cc_final: 0.8389 (tpp) REVERT: F 62 MET cc_start: 0.9821 (ttm) cc_final: 0.9150 (tpp) REVERT: F 300 GLU cc_start: 0.8653 (tt0) cc_final: 0.8426 (tt0) REVERT: F 311 PHE cc_start: 0.9300 (t80) cc_final: 0.9009 (t80) REVERT: F 326 MET cc_start: 0.9608 (mtm) cc_final: 0.8912 (mpp) REVERT: F 443 MET cc_start: 0.9200 (tpp) cc_final: 0.8954 (tpp) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2894 time to fit residues: 80.6795 Evaluate side-chains 161 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 174 optimal weight: 0.0670 chunk 155 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.045438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.033490 restraints weight = 235493.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.035447 restraints weight = 105572.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.036788 restraints weight = 63206.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.037798 restraints weight = 44688.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.038505 restraints weight = 34275.467| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14245 Z= 0.101 Angle : 0.508 5.806 19216 Z= 0.258 Chirality : 0.039 0.128 2288 Planarity : 0.003 0.056 2444 Dihedral : 6.662 128.172 1977 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.20), residues: 1777 helix: 1.05 (0.16), residues: 1058 sheet: 0.04 (0.36), residues: 203 loop : -0.77 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 317 TYR 0.012 0.001 TYR B 314 PHE 0.016 0.001 PHE C 116 TRP 0.002 0.000 TRP E 283 HIS 0.005 0.001 HIS E 302 Details of bonding type rmsd covalent geometry : bond 0.00211 (14245) covalent geometry : angle 0.50829 (19216) hydrogen bonds : bond 0.03102 ( 717) hydrogen bonds : angle 4.14041 ( 2091) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9206 (mmp) cc_final: 0.8685 (mmm) REVERT: A 96 MET cc_start: 0.8873 (ppp) cc_final: 0.8668 (ppp) REVERT: A 302 ASP cc_start: 0.9745 (t0) cc_final: 0.9084 (p0) REVERT: B 54 GLU cc_start: 0.9660 (mm-30) cc_final: 0.9316 (mp0) REVERT: B 103 SER cc_start: 0.9153 (m) cc_final: 0.8950 (t) REVERT: B 326 ILE cc_start: 0.9741 (mm) cc_final: 0.9415 (tp) REVERT: B 359 MET cc_start: 0.8710 (mpp) cc_final: 0.8431 (mpp) REVERT: B 371 MET cc_start: 0.9327 (mtp) cc_final: 0.8890 (mtp) REVERT: C 1 MET cc_start: 0.1261 (ppp) cc_final: 0.0914 (ppp) REVERT: C 113 MET cc_start: 0.9169 (ppp) cc_final: 0.8860 (ppp) REVERT: C 303 GLU cc_start: 0.8973 (mp0) cc_final: 0.8610 (mp0) REVERT: C 312 PHE cc_start: 0.9416 (m-80) cc_final: 0.8987 (m-80) REVERT: C 371 MET cc_start: 0.9523 (mtp) cc_final: 0.9111 (mtp) REVERT: D 62 MET cc_start: 0.9653 (tpp) cc_final: 0.9443 (tpp) REVERT: E 326 MET cc_start: 0.9473 (mpp) cc_final: 0.8943 (mpp) REVERT: E 400 ARG cc_start: 0.8437 (mpt180) cc_final: 0.8167 (mpt180) REVERT: E 443 MET cc_start: 0.9218 (tpp) cc_final: 0.8400 (tpp) REVERT: F 62 MET cc_start: 0.9821 (ttm) cc_final: 0.9162 (tpp) REVERT: F 300 GLU cc_start: 0.8650 (tt0) cc_final: 0.8424 (tt0) REVERT: F 311 PHE cc_start: 0.9302 (t80) cc_final: 0.9002 (t80) REVERT: F 326 MET cc_start: 0.9586 (mtm) cc_final: 0.8891 (mpp) REVERT: F 443 MET cc_start: 0.9226 (tpp) cc_final: 0.8965 (tpp) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2734 time to fit residues: 76.6137 Evaluate side-chains 162 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 122 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 92 optimal weight: 0.0980 chunk 78 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.044697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.033023 restraints weight = 242850.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.034879 restraints weight = 110447.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.036237 restraints weight = 66891.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.037134 restraints weight = 46890.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.037832 restraints weight = 36518.303| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14245 Z= 0.167 Angle : 0.537 6.268 19216 Z= 0.279 Chirality : 0.038 0.123 2288 Planarity : 0.003 0.046 2444 Dihedral : 6.536 122.121 1977 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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 are not related in a simple way. whole: 0.46 (0.20), residues: 1777 helix: 0.95 (0.16), residues: 1056 sheet: 0.05 (0.36), residues: 203 loop : -0.75 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 276 TYR 0.013 0.001 TYR B 314 PHE 0.013 0.002 PHE E 100 TRP 0.003 0.001 TRP F 283 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00319 (14245) covalent geometry : angle 0.53710 (19216) hydrogen bonds : bond 0.03094 ( 717) hydrogen bonds : angle 4.29020 ( 2091) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9205 (mmp) cc_final: 0.8684 (mmm) REVERT: A 302 ASP cc_start: 0.9737 (t0) cc_final: 0.9170 (p0) REVERT: B 54 GLU cc_start: 0.9663 (mm-30) cc_final: 0.9320 (mp0) REVERT: B 326 ILE cc_start: 0.9748 (mm) cc_final: 0.9436 (tp) REVERT: B 359 MET cc_start: 0.8705 (mpp) cc_final: 0.8440 (mpp) REVERT: B 371 MET cc_start: 0.9330 (mtp) cc_final: 0.8910 (mtp) REVERT: B 438 TYR cc_start: 0.9389 (m-80) cc_final: 0.9148 (m-80) REVERT: C 1 MET cc_start: 0.1793 (ppp) cc_final: 0.1515 (ppp) REVERT: C 113 MET cc_start: 0.9191 (ppp) cc_final: 0.8883 (ppp) REVERT: C 303 GLU cc_start: 0.8972 (mp0) cc_final: 0.8619 (mp0) REVERT: C 312 PHE cc_start: 0.9473 (m-80) cc_final: 0.9136 (m-80) REVERT: C 371 MET cc_start: 0.9497 (mtp) cc_final: 0.9022 (mtp) REVERT: E 326 MET cc_start: 0.9452 (mpp) cc_final: 0.9065 (mpp) REVERT: F 62 MET cc_start: 0.9806 (ttm) cc_final: 0.9173 (tpp) REVERT: F 300 GLU cc_start: 0.8627 (tt0) cc_final: 0.8354 (tt0) REVERT: F 311 PHE cc_start: 0.9350 (t80) cc_final: 0.8830 (t80) REVERT: F 326 MET cc_start: 0.9574 (mtm) cc_final: 0.8909 (mpp) REVERT: F 443 MET cc_start: 0.9220 (tpp) cc_final: 0.8964 (tpp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2554 time to fit residues: 69.6291 Evaluate side-chains 148 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 169 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.045390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.033469 restraints weight = 235428.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.035368 restraints weight = 106198.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.036789 restraints weight = 64333.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.037760 restraints weight = 44645.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.038477 restraints weight = 34348.724| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.6092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14245 Z= 0.095 Angle : 0.509 6.700 19216 Z= 0.254 Chirality : 0.039 0.128 2288 Planarity : 0.003 0.045 2444 Dihedral : 6.434 116.792 1977 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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 are not related in a simple way. whole: 0.80 (0.20), residues: 1777 helix: 1.21 (0.16), residues: 1056 sheet: 0.13 (0.36), residues: 203 loop : -0.57 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 317 TYR 0.011 0.001 TYR B 314 PHE 0.016 0.002 PHE D 123 TRP 0.003 0.001 TRP F 283 HIS 0.003 0.001 HIS E 302 Details of bonding type rmsd covalent geometry : bond 0.00201 (14245) covalent geometry : angle 0.50930 (19216) hydrogen bonds : bond 0.02954 ( 717) hydrogen bonds : angle 3.99070 ( 2091) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9216 (mmp) cc_final: 0.8692 (mmm) REVERT: A 302 ASP cc_start: 0.9748 (t0) cc_final: 0.9216 (p0) REVERT: A 311 CYS cc_start: 0.9418 (m) cc_final: 0.9135 (m) REVERT: A 312 PHE cc_start: 0.9089 (m-80) cc_final: 0.8684 (m-80) REVERT: B 54 GLU cc_start: 0.9657 (mm-30) cc_final: 0.9323 (mp0) REVERT: B 326 ILE cc_start: 0.9746 (mm) cc_final: 0.9434 (tp) REVERT: B 359 MET cc_start: 0.8654 (mpp) cc_final: 0.8377 (mpp) REVERT: B 371 MET cc_start: 0.9317 (mtp) cc_final: 0.8866 (mtp) REVERT: B 438 TYR cc_start: 0.9377 (m-80) cc_final: 0.9156 (m-80) REVERT: C 1 MET cc_start: 0.1681 (ppp) cc_final: 0.1230 (ppp) REVERT: C 113 MET cc_start: 0.9152 (ppp) cc_final: 0.8827 (ppp) REVERT: C 303 GLU cc_start: 0.8997 (mp0) cc_final: 0.8587 (mp0) REVERT: C 312 PHE cc_start: 0.9460 (m-80) cc_final: 0.9079 (m-80) REVERT: C 371 MET cc_start: 0.9480 (mtp) cc_final: 0.9051 (mtp) REVERT: D 284 ARG cc_start: 0.9814 (tmt170) cc_final: 0.9462 (tpm170) REVERT: E 326 MET cc_start: 0.9496 (mpp) cc_final: 0.8965 (mpp) REVERT: E 443 MET cc_start: 0.9136 (tpp) cc_final: 0.8533 (tpp) REVERT: F 62 MET cc_start: 0.9816 (ttm) cc_final: 0.9169 (tpp) REVERT: F 300 GLU cc_start: 0.8616 (tt0) cc_final: 0.8386 (tt0) REVERT: F 311 PHE cc_start: 0.9312 (t80) cc_final: 0.8991 (t80) REVERT: F 326 MET cc_start: 0.9557 (mtm) cc_final: 0.8875 (mpp) REVERT: F 443 MET cc_start: 0.9248 (tpp) cc_final: 0.8957 (tpp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2475 time to fit residues: 69.8636 Evaluate side-chains 157 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 37 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.045243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.033351 restraints weight = 238417.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.035299 restraints weight = 108083.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.036681 restraints weight = 64858.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.037656 restraints weight = 45399.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.038358 restraints weight = 34930.695| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14245 Z= 0.126 Angle : 0.519 6.539 19216 Z= 0.265 Chirality : 0.039 0.124 2288 Planarity : 0.003 0.043 2444 Dihedral : 6.301 111.195 1977 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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 are not related in a simple way. whole: 0.78 (0.20), residues: 1777 helix: 1.18 (0.16), residues: 1056 sheet: 0.14 (0.36), residues: 203 loop : -0.56 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 317 TYR 0.015 0.001 TYR F 387 PHE 0.029 0.002 PHE F 450 TRP 0.003 0.001 TRP E 283 HIS 0.003 0.001 HIS B 241 Details of bonding type rmsd covalent geometry : bond 0.00250 (14245) covalent geometry : angle 0.51890 (19216) hydrogen bonds : bond 0.02924 ( 717) hydrogen bonds : angle 4.08640 ( 2091) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3900.07 seconds wall clock time: 67 minutes 21.28 seconds (4041.28 seconds total)