Starting phenix.real_space_refine on Fri Oct 23 08:56:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yfv_72908/10_2026/9yfv_72908.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yfv_72908/10_2026/9yfv_72908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yfv_72908/10_2026/9yfv_72908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yfv_72908/10_2026/9yfv_72908.map" model { file = "/net/cci-nas-00/data/ceres_data/9yfv_72908/10_2026/9yfv_72908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yfv_72908/10_2026/9yfv_72908.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 5630 2.51 5 N 1606 2.21 5 O 1792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9072 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2248 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 2, 'GLN:plan1': 4, 'ARG:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2288 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 2248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2248 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 2, 'GLN:plan1': 4, 'ARG:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2288 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 2.25, per 1000 atoms: 0.25 Number of scatterers: 9072 At special positions: 0 Unit cell: (108.992, 102.336, 72.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1792 8.00 N 1606 7.00 C 5630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 321.2 milliseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 8 sheets defined 54.9% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 252 through 264 Processing helix chain 'B' and resid 278 through 288 removed outlier: 4.299A pdb=" N GLU B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.513A pdb=" N LEU B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 336 Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.636A pdb=" N LYS B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 364 through 379 Processing helix chain 'B' and resid 383 through 392 Processing helix chain 'B' and resid 433 through 445 Processing helix chain 'B' and resid 457 through 469 removed outlier: 3.944A pdb=" N LYS B 462 " --> pdb=" O GLU B 458 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 488 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 502 through 517 Processing helix chain 'B' and resid 528 through 530 No H-bonds generated for 'chain 'B' and resid 528 through 530' Processing helix chain 'B' and resid 531 through 536 Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 545 through 559 Processing helix chain 'B' and resid 564 through 573 Processing helix chain 'D' and resid 252 through 263 Processing helix chain 'D' and resid 276 through 286 removed outlier: 3.613A pdb=" N ARG D 286 " --> pdb=" O GLN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 308 removed outlier: 3.618A pdb=" N LEU D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 336 Processing helix chain 'D' and resid 348 through 352 removed outlier: 3.562A pdb=" N LEU D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN D 352 " --> pdb=" O LYS D 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 348 through 352' Processing helix chain 'D' and resid 353 through 358 Processing helix chain 'D' and resid 364 through 377 removed outlier: 3.531A pdb=" N SER D 370 " --> pdb=" O GLN D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 393 Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 457 through 469 removed outlier: 3.710A pdb=" N GLN D 463 " --> pdb=" O ASP D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 488 Processing helix chain 'D' and resid 502 through 517 removed outlier: 3.592A pdb=" N ASP D 515 " --> pdb=" O LEU D 511 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET D 516 " --> pdb=" O SER D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 559 Processing helix chain 'D' and resid 566 through 573 Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 278 through 288 removed outlier: 4.325A pdb=" N GLU A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 removed outlier: 3.505A pdb=" N LEU A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 336 Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.614A pdb=" N LYS A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 383 through 392 Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 457 through 469 removed outlier: 3.943A pdb=" N LYS A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 488 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 502 through 517 Processing helix chain 'A' and resid 528 through 530 No H-bonds generated for 'chain 'A' and resid 528 through 530' Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 545 through 559 Processing helix chain 'A' and resid 564 through 573 Processing helix chain 'C' and resid 252 through 263 Processing helix chain 'C' and resid 276 through 286 removed outlier: 3.603A pdb=" N ARG C 286 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 308 removed outlier: 3.576A pdb=" N LEU C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 336 Processing helix chain 'C' and resid 348 through 352 removed outlier: 3.590A pdb=" N LEU C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN C 352 " --> pdb=" O LYS C 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 348 through 352' Processing helix chain 'C' and resid 353 through 358 Processing helix chain 'C' and resid 364 through 378 removed outlier: 3.556A pdb=" N SER C 370 " --> pdb=" O GLN C 366 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 433 through 446 Processing helix chain 'C' and resid 457 through 469 removed outlier: 3.792A pdb=" N GLN C 463 " --> pdb=" O ASP C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 488 Processing helix chain 'C' and resid 502 through 517 removed outlier: 3.604A pdb=" N ASP C 515 " --> pdb=" O LEU C 511 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET C 516 " --> pdb=" O SER C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 559 Processing helix chain 'C' and resid 566 through 573 Processing sheet with id=AA1, first strand: chain 'B' and resid 293 through 295 removed outlier: 6.712A pdb=" N VAL B 248 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 474 through 476 removed outlier: 8.331A pdb=" N ILE B 475 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 452 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE B 427 " --> pdb=" O THR B 451 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE B 453 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 429 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N HIS B 426 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEU B 497 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE B 428 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS B 521 " --> pdb=" O ARG B 494 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR B 522 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU B 544 " --> pdb=" O THR B 522 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 524 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 293 through 295 removed outlier: 8.271A pdb=" N ILE D 294 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL D 271 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE D 246 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE D 272 " --> pdb=" O PHE D 246 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL D 248 " --> pdb=" O ILE D 272 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE D 247 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR D 341 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU D 363 " --> pdb=" O THR D 341 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU D 343 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 473 through 476 removed outlier: 7.589A pdb=" N VAL D 450 " --> pdb=" O ASP D 473 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE D 475 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL D 452 " --> pdb=" O ILE D 475 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N HIS D 426 " --> pdb=" O ALA D 495 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N LEU D 497 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE D 428 " --> pdb=" O LEU D 497 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR D 522 " --> pdb=" O ILE D 542 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU D 544 " --> pdb=" O THR D 522 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU D 524 " --> pdb=" O LEU D 544 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 295 removed outlier: 6.703A pdb=" N VAL A 248 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 476 removed outlier: 8.360A pdb=" N ILE A 475 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 452 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE A 427 " --> pdb=" O THR A 451 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE A 453 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 429 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N HIS A 426 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LEU A 497 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 428 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS A 521 " --> pdb=" O ARG A 494 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR A 522 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU A 544 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 524 " --> pdb=" O LEU A 544 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 293 through 295 removed outlier: 8.286A pdb=" N ILE C 294 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C 271 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE C 246 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE C 272 " --> pdb=" O PHE C 246 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C 248 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE C 247 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 476 removed outlier: 7.611A pdb=" N VAL C 450 " --> pdb=" O ASP C 473 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ILE C 475 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL C 452 " --> pdb=" O ILE C 475 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N HIS C 426 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU C 497 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE C 428 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR C 522 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N LEU C 544 " --> pdb=" O THR C 522 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 524 " --> pdb=" O LEU C 544 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3190 1.34 - 1.46: 1523 1.46 - 1.58: 4359 1.58 - 1.70: 0 1.70 - 1.81: 72 Bond restraints: 9144 Sorted by residual: bond pdb=" CA ASP B 519 " pdb=" CB ASP B 519 " ideal model delta sigma weight residual 1.533 1.558 -0.025 2.15e-02 2.16e+03 1.32e+00 bond pdb=" CA ASP A 519 " pdb=" CB ASP A 519 " ideal model delta sigma weight residual 1.532 1.556 -0.024 2.23e-02 2.01e+03 1.17e+00 bond pdb=" CB ASP A 519 " pdb=" CG ASP A 519 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.16e+00 bond pdb=" CB ASP B 519 " pdb=" CG ASP B 519 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 bond pdb=" CA GLN A 445 " pdb=" CB GLN A 445 " ideal model delta sigma weight residual 1.524 1.537 -0.013 1.31e-02 5.83e+03 9.79e-01 ... (remaining 9139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 12119 1.44 - 2.87: 209 2.87 - 4.31: 49 4.31 - 5.74: 3 5.74 - 7.18: 6 Bond angle restraints: 12386 Sorted by residual: angle pdb=" CA GLN A 445 " pdb=" CB GLN A 445 " pdb=" CG GLN A 445 " ideal model delta sigma weight residual 114.10 121.28 -7.18 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CA GLN B 445 " pdb=" CB GLN B 445 " pdb=" CG GLN B 445 " ideal model delta sigma weight residual 114.10 120.94 -6.84 2.00e+00 2.50e-01 1.17e+01 angle pdb=" C LYS B 355 " pdb=" N MET B 356 " pdb=" CA MET B 356 " ideal model delta sigma weight residual 122.38 116.41 5.97 1.81e+00 3.05e-01 1.09e+01 angle pdb=" C LYS A 355 " pdb=" N MET A 356 " pdb=" CA MET A 356 " ideal model delta sigma weight residual 122.38 116.90 5.48 1.81e+00 3.05e-01 9.15e+00 angle pdb=" C GLU C 562 " pdb=" CA GLU C 562 " pdb=" CB GLU C 562 " ideal model delta sigma weight residual 115.89 112.17 3.72 1.32e+00 5.74e-01 7.95e+00 ... (remaining 12381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4908 17.11 - 34.22: 583 34.22 - 51.33: 184 51.33 - 68.43: 37 68.43 - 85.54: 6 Dihedral angle restraints: 5718 sinusoidal: 2190 harmonic: 3528 Sorted by residual: dihedral pdb=" CA ASP A 528 " pdb=" C ASP A 528 " pdb=" N SER A 529 " pdb=" CA SER A 529 " ideal model delta harmonic sigma weight residual -180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ASP B 528 " pdb=" C ASP B 528 " pdb=" N SER B 529 " pdb=" CA SER B 529 " ideal model delta harmonic sigma weight residual 180.00 -161.79 -18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP A 244 " pdb=" C ASP A 244 " pdb=" N HIS A 245 " pdb=" CA HIS A 245 " ideal model delta harmonic sigma weight residual -180.00 -162.28 -17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 900 0.029 - 0.058: 424 0.058 - 0.087: 108 0.087 - 0.116: 86 0.116 - 0.145: 28 Chirality restraints: 1546 Sorted by residual: chirality pdb=" CA MET B 356 " pdb=" N MET B 356 " pdb=" C MET B 356 " pdb=" CB MET B 356 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA MET A 356 " pdb=" N MET A 356 " pdb=" C MET A 356 " pdb=" CB MET A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE A 294 " pdb=" N ILE A 294 " pdb=" C ILE A 294 " pdb=" CB ILE A 294 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1543 not shown) Planarity restraints: 1624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 475 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 476 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 476 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 476 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 475 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO A 476 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 476 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 476 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 279 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C ASP A 279 " -0.025 2.00e-02 2.50e+03 pdb=" O ASP A 279 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 280 " 0.008 2.00e-02 2.50e+03 ... (remaining 1621 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 4437 2.99 - 3.46: 9010 3.46 - 3.94: 14307 3.94 - 4.42: 16805 4.42 - 4.90: 27819 Nonbonded interactions: 72378 Sorted by model distance: nonbonded pdb=" N ASP A 503 " pdb=" OD1 ASP A 503 " model vdw 2.506 3.120 nonbonded pdb=" N ASP B 503 " pdb=" OD1 ASP B 503 " model vdw 2.508 3.120 nonbonded pdb=" C SER C 389 " pdb=" OG SER C 389 " model vdw 2.627 2.616 nonbonded pdb=" O ASP A 515 " pdb=" OD1 ASP A 515 " model vdw 2.628 3.040 nonbonded pdb=" C ASP B 519 " pdb=" OD1 ASP B 519 " model vdw 2.634 3.270 ... (remaining 72373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 242 through 381 or (resid 382 through 384 and (name N or n \ ame CA or name C or name O or name CB )) or resid 385 or (resid 386 and (name N \ or name CA or name C or name O or name CB )) or resid 387 through 562 or (resid \ 563 through 568 and (name N or name CA or name C or name O or name CB )) or resi \ d 569 through 574)) selection = (chain 'B' and (resid 242 through 381 or (resid 382 through 384 and (name N or n \ ame CA or name C or name O or name CB )) or resid 385 or (resid 386 and (name N \ or name CA or name C or name O or name CB )) or resid 387 through 562 or (resid \ 563 through 568 and (name N or name CA or name C or name O or name CB )) or resi \ d 569 through 574)) selection = (chain 'C' and (resid 242 or (resid 243 through 244 and (name N or name CA or na \ me C or name O or name CB )) or resid 245 through 276 or (resid 277 through 278 \ and (name N or name CA or name C or name O or name CB )) or resid 279 through 28 \ 0 or (resid 281 through 282 and (name N or name CA or name C or name O or name C \ B )) or resid 283 through 284 or (resid 285 through 286 and (name N or name CA o \ r name C or name O or name CB )) or resid 287 through 288 or (resid 289 through \ 291 and (name N or name CA or name C or name O or name CB )) or resid 292 throug \ h 423 or (resid 424 through 425 and (name N or name CA or name C or name O or na \ me CB )) or resid 426 through 457 or (resid 458 through 459 and (name N or name \ CA or name C or name O or name CB )) or resid 460 through 461 or (resid 462 thro \ ugh 463 and (name N or name CA or name C or name O or name CB )) or resid 464 th \ rough 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) \ or resid 467 through 469 or (resid 470 through 472 and (name N or name CA or na \ me C or name O or name CB )) or resid 473 through 574)) selection = (chain 'D' and (resid 242 or (resid 243 through 244 and (name N or name CA or na \ me C or name O or name CB )) or resid 245 through 276 or (resid 277 through 278 \ and (name N or name CA or name C or name O or name CB )) or resid 279 through 28 \ 0 or (resid 281 through 282 and (name N or name CA or name C or name O or name C \ B )) or resid 283 through 284 or (resid 285 through 286 and (name N or name CA o \ r name C or name O or name CB )) or resid 287 through 288 or (resid 289 through \ 291 and (name N or name CA or name C or name O or name CB )) or resid 292 throug \ h 423 or (resid 424 through 425 and (name N or name CA or name C or name O or na \ me CB )) or resid 426 through 457 or (resid 458 through 459 and (name N or name \ CA or name C or name O or name CB )) or resid 460 through 461 or (resid 462 thro \ ugh 463 and (name N or name CA or name C or name O or name CB )) or resid 464 th \ rough 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) \ or resid 467 through 469 or (resid 470 through 472 and (name N or name CA or na \ me C or name O or name CB )) or resid 473 through 574)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.830 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.003 0.027 9144 Z= 0.115 Angle : 0.504 7.180 12386 Z= 0.272 Chirality : 0.043 0.145 1546 Planarity : 0.003 0.044 1624 Dihedral : 16.657 85.543 3398 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 2.15 % Allowed : 25.73 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1200 helix: 1.14 (0.21), residues: 644 sheet: 0.74 (0.41), residues: 190 loop : -0.68 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 467 PHE 0.007 0.001 PHE A 549 HIS 0.001 0.000 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 9144) covalent geometry : angle 0.50418 / 0.27 (12386) hydrogen bonds : bond 0.14401 / 10.49 ( 443) hydrogen bonds : angle 4.52986 / 3.16 ( 1302) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 335 MET cc_start: 0.7867 (mtp) cc_final: 0.7432 (mtp) REVERT: B 516 MET cc_start: 0.7449 (ttm) cc_final: 0.7183 (ttt) REVERT: D 282 GLN cc_start: 0.6711 (OUTLIER) cc_final: 0.6327 (mm-40) REVERT: D 305 LYS cc_start: 0.7718 (ptmm) cc_final: 0.7411 (ttmm) REVERT: A 335 MET cc_start: 0.7695 (mtp) cc_final: 0.7340 (mtp) REVERT: A 516 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7259 (ttt) REVERT: C 282 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6482 (mm-40) REVERT: C 305 LYS cc_start: 0.7702 (ptmm) cc_final: 0.7413 (ttmm) REVERT: C 484 VAL cc_start: 0.8258 (p) cc_final: 0.8007 (t) outliers start: 22 outliers final: 13 residues processed: 115 average time/residue: 0.4868 time to fit residues: 60.3253 Evaluate side-chains 112 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain D residue 282 GLN Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 571 MET Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 571 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117] chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 384 ASN D 274 ASN A 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.174371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.145485 restraints weight = 9157.588| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.65 r_work: 0.3475 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9144 Z= 0.181 Angle : 0.549 6.373 12386 Z= 0.282 Chirality : 0.045 0.141 1546 Planarity : 0.003 0.038 1624 Dihedral : 5.988 50.950 1286 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.99 % Allowed : 22.99 % Favored : 72.02 % 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: 0.57 (0.25), residues: 1200 helix: 1.14 (0.21), residues: 634 sheet: 0.64 (0.46), residues: 158 loop : -0.87 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 PHE 0.013 0.002 PHE B 508 HIS 0.003 0.001 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 ( 9144) covalent geometry : angle 0.54890 / 0.28 (12386) hydrogen bonds : bond 0.04200 / 2.91 ( 443) hydrogen bonds : angle 3.77998 / 2.66 ( 1302) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 100 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 335 MET cc_start: 0.7778 (mtp) cc_final: 0.7259 (mtp) REVERT: B 516 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7342 (ttt) REVERT: D 305 LYS cc_start: 0.7865 (ptmm) cc_final: 0.7549 (ttmm) REVERT: D 478 ASP cc_start: 0.7354 (p0) cc_final: 0.7070 (p0) REVERT: A 273 SER cc_start: 0.8568 (t) cc_final: 0.8349 (t) REVERT: A 335 MET cc_start: 0.7722 (mtp) cc_final: 0.7227 (mtp) REVERT: A 516 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7350 (ttt) REVERT: C 305 LYS cc_start: 0.7838 (ptmm) cc_final: 0.7508 (ttmm) REVERT: C 484 VAL cc_start: 0.8121 (p) cc_final: 0.7914 (t) outliers start: 51 outliers final: 18 residues processed: 133 average time/residue: 0.4475 time to fit residues: 64.5758 Evaluate side-chains 111 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 571 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 531 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [119, 117, 118, 26, 50, 60, 91, 71, 2, 34, 80] chunk 119 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 71 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.176025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147306 restraints weight = 9094.113| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.65 r_work: 0.3500 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9144 Z= 0.116 Angle : 0.482 6.218 12386 Z= 0.248 Chirality : 0.043 0.131 1546 Planarity : 0.003 0.034 1624 Dihedral : 4.484 48.179 1260 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.09 % Allowed : 23.58 % Favored : 71.33 % 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: 0.79 (0.25), residues: 1200 helix: 1.34 (0.22), residues: 634 sheet: 0.70 (0.46), residues: 158 loop : -0.80 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 375 PHE 0.007 0.001 PHE B 508 HIS 0.001 0.000 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 9144) covalent geometry : angle 0.48200 / 0.25 (12386) hydrogen bonds : bond 0.03382 / 2.36 ( 443) hydrogen bonds : angle 3.59670 / 2.56 ( 1302) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 99 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 318 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8265 (mt) REVERT: B 516 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7325 (ttt) REVERT: D 282 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.6393 (mm-40) REVERT: D 305 LYS cc_start: 0.7841 (ptmm) cc_final: 0.7498 (ttmm) REVERT: A 516 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7360 (ttt) REVERT: C 282 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6379 (mm-40) REVERT: C 305 LYS cc_start: 0.7870 (ptmm) cc_final: 0.7573 (ttmm) outliers start: 52 outliers final: 27 residues processed: 134 average time/residue: 0.4737 time to fit residues: 68.6517 Evaluate side-chains 125 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 282 GLN Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 516 MET Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 516 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [93, 77, 82, 95, 7, 96, 45, 53, 44, 17, 91] chunk 93 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.175977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.147931 restraints weight = 9164.319| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.61 r_work: 0.3503 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9144 Z= 0.124 Angle : 0.495 6.622 12386 Z= 0.254 Chirality : 0.043 0.158 1546 Planarity : 0.003 0.032 1624 Dihedral : 4.246 40.847 1257 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.77 % Allowed : 23.39 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.25), residues: 1200 helix: 1.40 (0.22), residues: 632 sheet: 0.89 (0.42), residues: 178 loop : -0.83 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 375 PHE 0.009 0.001 PHE B 508 HIS 0.001 0.000 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.12 ( 9144) covalent geometry : angle 0.49460 / 0.25 (12386) hydrogen bonds : bond 0.03369 / 2.36 ( 443) hydrogen bonds : angle 3.56670 / 2.54 ( 1302) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 100 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 318 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8291 (mt) REVERT: B 335 MET cc_start: 0.7733 (mtp) cc_final: 0.7230 (mtp) REVERT: B 516 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7377 (ttt) REVERT: D 282 GLN cc_start: 0.6744 (OUTLIER) cc_final: 0.6389 (mm-40) REVERT: D 305 LYS cc_start: 0.7880 (ptmm) cc_final: 0.7571 (ttmm) REVERT: D 465 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6319 (mt-10) REVERT: A 318 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8290 (mt) REVERT: A 335 MET cc_start: 0.7678 (mtp) cc_final: 0.7191 (mtp) REVERT: A 516 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7441 (ttt) REVERT: C 282 GLN cc_start: 0.6777 (OUTLIER) cc_final: 0.6382 (mm-40) REVERT: C 305 LYS cc_start: 0.7867 (ptmm) cc_final: 0.7579 (ttmm) outliers start: 59 outliers final: 27 residues processed: 139 average time/residue: 0.4385 time to fit residues: 66.2346 Evaluate side-chains 127 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 282 GLN Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 516 MET Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 516 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [109, 80, 79, 26, 51, 99, 38, 97, 34, 67, 104] chunk 109 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 393 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.172537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144599 restraints weight = 9155.930| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.58 r_work: 0.3493 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9144 Z= 0.203 Angle : 0.589 6.944 12386 Z= 0.298 Chirality : 0.046 0.159 1546 Planarity : 0.004 0.037 1624 Dihedral : 4.595 40.992 1257 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.85 % Allowed : 22.99 % Favored : 70.16 % 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: 0.43 (0.25), residues: 1200 helix: 1.07 (0.21), residues: 634 sheet: 0.31 (0.45), residues: 158 loop : -0.89 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 PHE 0.014 0.002 PHE B 508 HIS 0.003 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.20 ( 9144) covalent geometry : angle 0.58868 / 0.30 (12386) hydrogen bonds : bond 0.04162 / 2.88 ( 443) hydrogen bonds : angle 3.74088 / 2.66 ( 1302) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 97 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 318 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8372 (mt) REVERT: B 335 MET cc_start: 0.7757 (mtp) cc_final: 0.7303 (mtp) REVERT: B 494 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7134 (mtm-85) REVERT: B 516 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7381 (ttt) REVERT: D 243 LYS cc_start: 0.8257 (ptmt) cc_final: 0.7570 (ptpp) REVERT: D 282 GLN cc_start: 0.6765 (OUTLIER) cc_final: 0.6415 (mm-40) REVERT: D 305 LYS cc_start: 0.7858 (ptmm) cc_final: 0.7586 (ttmm) REVERT: D 465 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6332 (mt-10) REVERT: A 318 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8358 (mt) REVERT: A 335 MET cc_start: 0.7730 (mtp) cc_final: 0.7231 (mtp) REVERT: A 516 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7435 (ttt) REVERT: C 282 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.6401 (mm-40) REVERT: C 305 LYS cc_start: 0.7840 (ptmm) cc_final: 0.7567 (ttmm) REVERT: C 465 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6312 (mt-10) outliers start: 70 outliers final: 31 residues processed: 150 average time/residue: 0.4293 time to fit residues: 70.0875 Evaluate side-chains 127 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 282 GLN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 531 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [116, 64, 92, 72, 11, 47, 115, 6, 39, 23, 0] chunk 116 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.174898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.147843 restraints weight = 9070.365| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.53 r_work: 0.3532 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9144 Z= 0.129 Angle : 0.512 7.204 12386 Z= 0.262 Chirality : 0.043 0.135 1546 Planarity : 0.003 0.035 1624 Dihedral : 4.403 39.795 1257 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 6.46 % Allowed : 22.90 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.25), residues: 1200 helix: 1.16 (0.21), residues: 646 sheet: 0.42 (0.44), residues: 158 loop : -0.81 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 PHE 0.008 0.001 PHE A 508 HIS 0.001 0.000 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 9144) covalent geometry : angle 0.51205 / 0.26 (12386) hydrogen bonds : bond 0.03368 / 2.35 ( 443) hydrogen bonds : angle 3.63801 / 2.60 ( 1302) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 97 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 318 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8270 (mt) REVERT: B 335 MET cc_start: 0.7685 (mtp) cc_final: 0.7414 (mtp) REVERT: B 494 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7112 (mtm-85) REVERT: B 516 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7399 (ttt) REVERT: D 243 LYS cc_start: 0.8257 (ptmt) cc_final: 0.7571 (ptpp) REVERT: D 282 GLN cc_start: 0.6684 (OUTLIER) cc_final: 0.6327 (mm-40) REVERT: D 305 LYS cc_start: 0.7837 (ptmm) cc_final: 0.7569 (ttmm) REVERT: D 465 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6356 (mt-10) REVERT: A 318 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8210 (mt) REVERT: A 335 MET cc_start: 0.7662 (mtp) cc_final: 0.7408 (mtp) REVERT: A 446 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8430 (mtt90) REVERT: A 516 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7398 (ttt) REVERT: A 571 MET cc_start: 0.9005 (mtm) cc_final: 0.8795 (mtm) REVERT: C 282 GLN cc_start: 0.6780 (OUTLIER) cc_final: 0.6395 (mm-40) REVERT: C 305 LYS cc_start: 0.7856 (ptmm) cc_final: 0.7566 (ttmm) REVERT: C 465 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6293 (mt-10) REVERT: C 478 ASP cc_start: 0.7332 (p0) cc_final: 0.7008 (p0) outliers start: 66 outliers final: 38 residues processed: 144 average time/residue: 0.4407 time to fit residues: 68.7502 Evaluate side-chains 139 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 91 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 282 GLN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 516 MET Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 531 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [18, 104, 26, 42, 20, 50, 3, 106, 103, 48, 88] chunk 18 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.176078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.147139 restraints weight = 9117.656| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.65 r_work: 0.3524 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9144 Z= 0.119 Angle : 0.497 7.619 12386 Z= 0.255 Chirality : 0.043 0.131 1546 Planarity : 0.003 0.036 1624 Dihedral : 4.267 37.428 1257 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.97 % Allowed : 22.99 % Favored : 71.04 % 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: 0.81 (0.25), residues: 1200 helix: 1.28 (0.21), residues: 644 sheet: 0.77 (0.42), residues: 178 loop : -0.81 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 PHE 0.007 0.001 PHE A 508 HIS 0.001 0.000 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 9144) covalent geometry : angle 0.49732 / 0.25 (12386) hydrogen bonds : bond 0.03175 / 2.22 ( 443) hydrogen bonds : angle 3.57446 / 2.56 ( 1302) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 96 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 318 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8233 (mt) REVERT: B 335 MET cc_start: 0.7619 (mtp) cc_final: 0.7395 (mtp) REVERT: B 516 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7358 (ttt) REVERT: D 243 LYS cc_start: 0.8251 (ptmt) cc_final: 0.7549 (ptpp) REVERT: D 282 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.6370 (mm-40) REVERT: D 305 LYS cc_start: 0.7809 (ptmm) cc_final: 0.7545 (ttmm) REVERT: A 318 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8219 (mt) REVERT: A 335 MET cc_start: 0.7606 (mtp) cc_final: 0.7394 (mtp) REVERT: A 446 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8426 (mtt90) REVERT: A 516 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7374 (ttt) REVERT: C 282 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6383 (mm-40) REVERT: C 305 LYS cc_start: 0.7741 (ptmm) cc_final: 0.7483 (ttmm) REVERT: C 465 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6343 (mt-10) outliers start: 61 outliers final: 41 residues processed: 141 average time/residue: 0.4299 time to fit residues: 65.8276 Evaluate side-chains 141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 92 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 282 GLN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 516 MET Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 531 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [119, 89, 31, 85, 22, 7, 83, 25, 95, 17, 70] chunk 119 optimal weight: 0.1980 chunk 89 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 22 optimal weight: 0.0040 chunk 7 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.178138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.149436 restraints weight = 9027.565| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.63 r_work: 0.3547 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9144 Z= 0.092 Angle : 0.469 8.178 12386 Z= 0.241 Chirality : 0.042 0.149 1546 Planarity : 0.003 0.033 1624 Dihedral : 4.094 35.854 1257 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.28 % Allowed : 23.97 % Favored : 70.74 % 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: 1.10 (0.25), residues: 1200 helix: 1.60 (0.22), residues: 632 sheet: 0.97 (0.42), residues: 178 loop : -0.80 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 375 PHE 0.005 0.001 PHE B 368 HIS 0.002 0.000 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.09 ( 9144) covalent geometry : angle 0.46948 / 0.24 (12386) hydrogen bonds : bond 0.02798 / 1.97 ( 443) hydrogen bonds : angle 3.50693 / 2.52 ( 1302) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 318 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8184 (mt) REVERT: B 516 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7300 (ttt) REVERT: D 243 LYS cc_start: 0.8200 (ptmt) cc_final: 0.7459 (ptpp) REVERT: D 282 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6303 (mm-40) REVERT: D 305 LYS cc_start: 0.7778 (ptmm) cc_final: 0.7495 (ttmm) REVERT: D 333 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8302 (mtpt) REVERT: A 318 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8161 (mt) REVERT: C 282 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6396 (mm-40) REVERT: C 305 LYS cc_start: 0.7722 (ptmm) cc_final: 0.7475 (ttmm) outliers start: 54 outliers final: 33 residues processed: 144 average time/residue: 0.3998 time to fit residues: 62.6472 Evaluate side-chains 136 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 282 GLN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 516 MET Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 516 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [31, 43, 14, 105, 62, 27, 44, 50, 119, 10, 116] chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 0.0030 chunk 14 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 44 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 119 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 116 optimal weight: 0.0670 overall best weight: 0.2728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 438 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.179583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.152721 restraints weight = 8896.716| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.54 r_work: 0.3581 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9144 Z= 0.089 Angle : 0.469 8.627 12386 Z= 0.240 Chirality : 0.042 0.154 1546 Planarity : 0.003 0.033 1624 Dihedral : 3.695 18.963 1254 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.01 % Allowed : 25.24 % Favored : 70.74 % 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: 1.38 (0.26), residues: 1200 helix: 1.73 (0.22), residues: 632 sheet: 1.33 (0.41), residues: 198 loop : -0.76 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 375 PHE 0.005 0.001 PHE B 368 HIS 0.002 0.000 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 ( 9144) covalent geometry : angle 0.46898 / 0.24 (12386) hydrogen bonds : bond 0.02608 / 1.84 ( 443) hydrogen bonds : angle 3.48160 / 2.50 ( 1302) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 318 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8166 (mt) REVERT: B 335 MET cc_start: 0.7681 (mtp) cc_final: 0.7317 (mtp) REVERT: B 516 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7277 (ttt) REVERT: D 243 LYS cc_start: 0.8224 (ptmt) cc_final: 0.7521 (ptpp) REVERT: D 282 GLN cc_start: 0.6732 (OUTLIER) cc_final: 0.6371 (mm-40) REVERT: D 305 LYS cc_start: 0.7801 (ptmm) cc_final: 0.7506 (ttmm) REVERT: A 318 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8147 (mt) REVERT: A 335 MET cc_start: 0.7717 (mtp) cc_final: 0.7364 (mtp) REVERT: C 282 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.6477 (mm-40) REVERT: C 305 LYS cc_start: 0.7734 (ptmm) cc_final: 0.7487 (ttmm) outliers start: 41 outliers final: 27 residues processed: 135 average time/residue: 0.4453 time to fit residues: 65.3763 Evaluate side-chains 133 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 282 GLN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 516 MET Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 516 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [87, 35, 67, 56, 110, 55, 94, 79, 36, 76, 37] chunk 87 optimal weight: 0.3980 chunk 35 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 0.0870 chunk 110 optimal weight: 0.0020 chunk 55 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 36 optimal weight: 0.0040 chunk 76 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.181281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.154353 restraints weight = 9033.305| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.55 r_work: 0.3598 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9144 Z= 0.084 Angle : 0.460 9.018 12386 Z= 0.235 Chirality : 0.042 0.139 1546 Planarity : 0.003 0.034 1624 Dihedral : 3.583 18.954 1254 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.52 % Allowed : 26.22 % Favored : 70.25 % 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: 1.58 (0.26), residues: 1200 helix: 1.88 (0.22), residues: 632 sheet: 1.53 (0.41), residues: 198 loop : -0.69 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 375 PHE 0.006 0.001 PHE B 368 HIS 0.003 0.000 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.08 ( 9144) covalent geometry : angle 0.45990 / 0.23 (12386) hydrogen bonds : bond 0.02412 / 1.70 ( 443) hydrogen bonds : angle 3.44413 / 2.48 ( 1302) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 318 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8073 (mt) REVERT: B 335 MET cc_start: 0.7563 (mtp) cc_final: 0.7236 (mtp) REVERT: B 377 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7762 (mp) REVERT: B 381 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7635 (tm-30) REVERT: B 516 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7209 (ttt) REVERT: D 243 LYS cc_start: 0.8181 (ptmt) cc_final: 0.7444 (ptpp) REVERT: D 282 GLN cc_start: 0.6688 (OUTLIER) cc_final: 0.6339 (mm-40) REVERT: D 305 LYS cc_start: 0.7728 (ptmm) cc_final: 0.7444 (ttmm) REVERT: A 318 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8080 (mt) REVERT: A 335 MET cc_start: 0.7594 (mtp) cc_final: 0.7280 (mtp) REVERT: A 380 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7368 (mm-30) REVERT: A 381 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7717 (tm-30) REVERT: C 305 LYS cc_start: 0.7644 (ptmm) cc_final: 0.7403 (ttmm) REVERT: C 375 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7531 (mtt90) outliers start: 36 outliers final: 19 residues processed: 134 average time/residue: 0.4496 time to fit residues: 65.4334 Evaluate side-chains 126 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 282 GLN Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 500 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [35, 78, 84, 94, 72, 71, 85, 14, 76, 51, 62] chunk 35 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.176892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.148257 restraints weight = 8904.793| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.62 r_work: 0.3508 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9144 Z= 0.132 Angle : 0.538 8.963 12386 Z= 0.271 Chirality : 0.044 0.177 1546 Planarity : 0.003 0.034 1624 Dihedral : 3.872 19.646 1254 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.13 % Allowed : 27.01 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.26), residues: 1200 helix: 1.57 (0.22), residues: 632 sheet: 1.33 (0.41), residues: 198 loop : -0.78 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 375 PHE 0.011 0.002 PHE A 508 HIS 0.002 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 ( 9144) covalent geometry : angle 0.53823 / 0.27 (12386) hydrogen bonds : bond 0.03240 / 2.26 ( 443) hydrogen bonds : angle 3.52037 / 2.52 ( 1302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2853.32 seconds wall clock time: 49 minutes 22.73 seconds (2962.73 seconds total)