Starting phenix.real_space_refine on Sun Aug 9 15:48:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9phf_71647/08_2026/9phf_71647.cif Found real_map, /net/cci-nas-00/data/ceres_data/9phf_71647/08_2026/9phf_71647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9phf_71647/08_2026/9phf_71647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9phf_71647/08_2026/9phf_71647.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9phf_71647/08_2026/9phf_71647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9phf_71647/08_2026/9phf_71647.map" } resolution = 2.2 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= 0.002 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: 5 Type Number sf(0) Gaussians Ca 21 9.91 5 S 63 5.16 5 C 21889 2.51 5 N 5901 2.21 5 O 7147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35021 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5000 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 607} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 5.05, per 1000 atoms: 0.14 Number of scatterers: 35021 At special positions: 0 Unit cell: (180.4, 180.4, 179.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 21 19.99 S 63 16.00 O 7147 8.00 N 5901 7.00 C 21889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.0 seconds 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8260 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 99 sheets defined 15.5% alpha, 46.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 246 through 251 removed outlier: 4.223A pdb=" N SER A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 251' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 465 through 474 Processing helix chain 'A' and resid 506 through 517 removed outlier: 3.871A pdb=" N VAL A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 552 through 561 Processing helix chain 'A' and resid 583 through 587 removed outlier: 3.692A pdb=" N ILE A 587 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 605 removed outlier: 3.692A pdb=" N HIS A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 732 through 734 No H-bonds generated for 'chain 'A' and resid 732 through 734' Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'B' and resid 226 through 233 Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.223A pdb=" N SER B 250 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 251' Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 465 through 474 Processing helix chain 'B' and resid 506 through 517 removed outlier: 3.871A pdb=" N VAL B 510 " --> pdb=" O GLN B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 531 Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 583 through 587 removed outlier: 3.691A pdb=" N ILE B 587 " --> pdb=" O GLU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 605 removed outlier: 3.692A pdb=" N HIS B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 614 Processing helix chain 'B' and resid 732 through 734 No H-bonds generated for 'chain 'B' and resid 732 through 734' Processing helix chain 'B' and resid 764 through 769 Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 246 through 251 removed outlier: 4.223A pdb=" N SER C 250 " --> pdb=" O ASP C 246 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 246 through 251' Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 465 through 474 Processing helix chain 'C' and resid 506 through 517 removed outlier: 3.871A pdb=" N VAL C 510 " --> pdb=" O GLN C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 531 Processing helix chain 'C' and resid 552 through 561 Processing helix chain 'C' and resid 583 through 587 removed outlier: 3.692A pdb=" N ILE C 587 " --> pdb=" O GLU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 605 removed outlier: 3.692A pdb=" N HIS C 605 " --> pdb=" O GLN C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 614 Processing helix chain 'C' and resid 732 through 734 No H-bonds generated for 'chain 'C' and resid 732 through 734' Processing helix chain 'C' and resid 764 through 769 Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 246 through 251 removed outlier: 4.222A pdb=" N SER D 250 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 246 through 251' Processing helix chain 'D' and resid 271 through 278 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 465 through 474 Processing helix chain 'D' and resid 506 through 517 removed outlier: 3.871A pdb=" N VAL D 510 " --> pdb=" O GLN D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 531 Processing helix chain 'D' and resid 552 through 561 Processing helix chain 'D' and resid 583 through 587 removed outlier: 3.692A pdb=" N ILE D 587 " --> pdb=" O GLU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 605 removed outlier: 3.691A pdb=" N HIS D 605 " --> pdb=" O GLN D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 614 Processing helix chain 'D' and resid 732 through 734 No H-bonds generated for 'chain 'D' and resid 732 through 734' Processing helix chain 'D' and resid 764 through 769 Processing helix chain 'E' and resid 226 through 233 Processing helix chain 'E' and resid 246 through 251 removed outlier: 4.222A pdb=" N SER E 250 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 246 through 251' Processing helix chain 'E' and resid 271 through 278 Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 465 through 474 Processing helix chain 'E' and resid 506 through 517 removed outlier: 3.871A pdb=" N VAL E 510 " --> pdb=" O GLN E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 527 through 531 Processing helix chain 'E' and resid 552 through 561 Processing helix chain 'E' and resid 583 through 587 removed outlier: 3.693A pdb=" N ILE E 587 " --> pdb=" O GLU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 592 through 605 removed outlier: 3.692A pdb=" N HIS E 605 " --> pdb=" O GLN E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 614 Processing helix chain 'E' and resid 732 through 734 No H-bonds generated for 'chain 'E' and resid 732 through 734' Processing helix chain 'E' and resid 764 through 769 Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 246 through 251 removed outlier: 4.223A pdb=" N SER F 250 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN F 251 " --> pdb=" O SER F 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 246 through 251' Processing helix chain 'F' and resid 271 through 278 Processing helix chain 'F' and resid 285 through 290 Processing helix chain 'F' and resid 465 through 474 Processing helix chain 'F' and resid 506 through 517 removed outlier: 3.871A pdb=" N VAL F 510 " --> pdb=" O GLN F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 531 Processing helix chain 'F' and resid 552 through 561 Processing helix chain 'F' and resid 583 through 587 removed outlier: 3.692A pdb=" N ILE F 587 " --> pdb=" O GLU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 592 through 605 removed outlier: 3.691A pdb=" N HIS F 605 " --> pdb=" O GLN F 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 610 through 614 Processing helix chain 'F' and resid 732 through 734 No H-bonds generated for 'chain 'F' and resid 732 through 734' Processing helix chain 'F' and resid 764 through 769 Processing helix chain 'G' and resid 226 through 233 Processing helix chain 'G' and resid 246 through 251 removed outlier: 4.222A pdb=" N SER G 250 " --> pdb=" O ASP G 246 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN G 251 " --> pdb=" O SER G 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 246 through 251' Processing helix chain 'G' and resid 271 through 278 Processing helix chain 'G' and resid 285 through 290 Processing helix chain 'G' and resid 465 through 474 Processing helix chain 'G' and resid 506 through 517 removed outlier: 3.871A pdb=" N VAL G 510 " --> pdb=" O GLN G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 527 through 531 Processing helix chain 'G' and resid 552 through 561 Processing helix chain 'G' and resid 583 through 587 removed outlier: 3.692A pdb=" N ILE G 587 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 592 through 605 removed outlier: 3.691A pdb=" N HIS G 605 " --> pdb=" O GLN G 601 " (cutoff:3.500A) Processing helix chain 'G' and resid 610 through 614 Processing helix chain 'G' and resid 732 through 734 No H-bonds generated for 'chain 'G' and resid 732 through 734' Processing helix chain 'G' and resid 764 through 769 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 237 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 310 removed outlier: 5.395A pdb=" N VAL A 301 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR A 396 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET A 303 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG A 394 " --> pdb=" O MET A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 440 through 441 removed outlier: 4.546A pdb=" N ILE A 462 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 312 through 345 Processing sheet with id=AA5, first strand: chain 'A' and resid 420 through 425 removed outlier: 6.319A pdb=" N SER A 420 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 414 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 422 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR A 404 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER A 434 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 420 through 425 removed outlier: 6.319A pdb=" N SER A 420 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 414 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 422 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 406 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS A 487 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN A 485 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR A 410 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A 483 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE A 412 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU A 481 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 414 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A 479 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AA8, first strand: chain 'A' and resid 532 through 537 removed outlier: 9.151A pdb=" N ILE A 622 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N SER A 520 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE A 624 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR A 522 " --> pdb=" O ILE A 624 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 564 through 566 Processing sheet with id=AB1, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.268A pdb=" N ASP A 753 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 12.277A pdb=" N LYS A 655 " --> pdb=" O ASP A 753 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 629 through 631 removed outlier: 4.935A pdb=" N PHE A 751 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS A 686 " --> pdb=" O PHE A 751 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP A 753 " --> pdb=" O TYR A 684 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR A 684 " --> pdb=" O ASP A 753 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 641 through 642 removed outlier: 5.837A pdb=" N VAL A 739 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 738 " --> pdb=" O ASP A 699 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A 699 " --> pdb=" O LYS A 738 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 774 through 776 removed outlier: 7.060A pdb=" N ASP A 775 " --> pdb=" O LYS A 784 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS A 784 " --> pdb=" O LYS A 825 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 805 through 806 Processing sheet with id=AB6, first strand: chain 'A' and resid 805 through 806 removed outlier: 6.247A pdb=" N ALA A 837 " --> pdb=" O LYS A 848 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS A 848 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB8, first strand: chain 'B' and resid 299 through 310 removed outlier: 5.394A pdb=" N VAL B 301 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR B 396 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N MET B 303 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG B 394 " --> pdb=" O MET B 303 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 440 through 441 removed outlier: 4.547A pdb=" N ILE B 462 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 420 through 425 removed outlier: 6.319A pdb=" N SER B 420 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 414 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 422 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR B 404 " --> pdb=" O SER B 434 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER B 434 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 420 through 425 removed outlier: 6.319A pdb=" N SER B 420 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 414 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 422 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B 406 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS B 487 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN B 485 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR B 410 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR B 483 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE B 412 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B 481 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU B 414 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 479 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AC4, first strand: chain 'B' and resid 532 through 537 removed outlier: 9.150A pdb=" N ILE B 622 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER B 520 " --> pdb=" O ILE B 622 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE B 624 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR B 522 " --> pdb=" O ILE B 624 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 564 through 566 Processing sheet with id=AC6, first strand: chain 'B' and resid 629 through 631 removed outlier: 6.269A pdb=" N ASP B 753 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 12.277A pdb=" N LYS B 655 " --> pdb=" O ASP B 753 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 629 through 631 removed outlier: 4.935A pdb=" N PHE B 751 " --> pdb=" O LYS B 686 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS B 686 " --> pdb=" O PHE B 751 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP B 753 " --> pdb=" O TYR B 684 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR B 684 " --> pdb=" O ASP B 753 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 641 through 642 removed outlier: 5.837A pdb=" N VAL B 739 " --> pdb=" O ALA B 667 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 738 " --> pdb=" O ASP B 699 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 699 " --> pdb=" O LYS B 738 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 774 through 776 removed outlier: 7.060A pdb=" N ASP B 775 " --> pdb=" O LYS B 784 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS B 784 " --> pdb=" O LYS B 825 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 805 through 806 Processing sheet with id=AD2, first strand: chain 'B' and resid 805 through 806 removed outlier: 6.247A pdb=" N ALA B 837 " --> pdb=" O LYS B 848 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS B 848 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 234 through 237 Processing sheet with id=AD4, first strand: chain 'C' and resid 299 through 310 removed outlier: 5.395A pdb=" N VAL C 301 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR C 396 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET C 303 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG C 394 " --> pdb=" O MET C 303 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 440 through 441 removed outlier: 4.546A pdb=" N ILE C 462 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 420 through 425 removed outlier: 6.319A pdb=" N SER C 420 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU C 414 " --> pdb=" O SER C 420 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA C 422 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR C 404 " --> pdb=" O SER C 434 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER C 434 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 420 through 425 removed outlier: 6.319A pdb=" N SER C 420 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU C 414 " --> pdb=" O SER C 420 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA C 422 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU C 406 " --> pdb=" O LYS C 487 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS C 487 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN C 485 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR C 410 " --> pdb=" O THR C 483 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR C 483 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE C 412 " --> pdb=" O LEU C 481 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU C 481 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 414 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU C 479 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 492 through 493 Processing sheet with id=AD9, first strand: chain 'C' and resid 532 through 537 removed outlier: 9.151A pdb=" N ILE C 622 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N SER C 520 " --> pdb=" O ILE C 622 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE C 624 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR C 522 " --> pdb=" O ILE C 624 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 564 through 566 Processing sheet with id=AE2, first strand: chain 'C' and resid 629 through 631 removed outlier: 6.268A pdb=" N ASP C 753 " --> pdb=" O LYS C 655 " (cutoff:3.500A) removed outlier: 12.278A pdb=" N LYS C 655 " --> pdb=" O ASP C 753 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 629 through 631 removed outlier: 4.935A pdb=" N PHE C 751 " --> pdb=" O LYS C 686 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS C 686 " --> pdb=" O PHE C 751 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP C 753 " --> pdb=" O TYR C 684 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR C 684 " --> pdb=" O ASP C 753 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 641 through 642 removed outlier: 5.837A pdb=" N VAL C 739 " --> pdb=" O ALA C 667 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 738 " --> pdb=" O ASP C 699 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP C 699 " --> pdb=" O LYS C 738 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 774 through 776 removed outlier: 7.059A pdb=" N ASP C 775 " --> pdb=" O LYS C 784 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS C 784 " --> pdb=" O LYS C 825 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 805 through 806 Processing sheet with id=AE7, first strand: chain 'C' and resid 805 through 806 removed outlier: 6.246A pdb=" N ALA C 837 " --> pdb=" O LYS C 848 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS C 848 " --> pdb=" O ALA C 837 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 234 through 237 Processing sheet with id=AE9, first strand: chain 'D' and resid 299 through 310 removed outlier: 5.395A pdb=" N VAL D 301 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR D 396 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET D 303 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG D 394 " --> pdb=" O MET D 303 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 440 through 441 removed outlier: 4.546A pdb=" N ILE D 462 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 420 through 425 removed outlier: 6.318A pdb=" N SER D 420 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU D 414 " --> pdb=" O SER D 420 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA D 422 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR D 404 " --> pdb=" O SER D 434 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER D 434 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 420 through 425 removed outlier: 6.318A pdb=" N SER D 420 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU D 414 " --> pdb=" O SER D 420 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA D 422 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU D 406 " --> pdb=" O LYS D 487 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS D 487 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN D 485 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR D 410 " --> pdb=" O THR D 483 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR D 483 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE D 412 " --> pdb=" O LEU D 481 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU D 481 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU D 414 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU D 479 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 492 through 493 Processing sheet with id=AF5, first strand: chain 'D' and resid 532 through 537 removed outlier: 9.151A pdb=" N ILE D 622 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N SER D 520 " --> pdb=" O ILE D 622 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE D 624 " --> pdb=" O SER D 520 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR D 522 " --> pdb=" O ILE D 624 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 564 through 566 Processing sheet with id=AF7, first strand: chain 'D' and resid 629 through 631 removed outlier: 6.269A pdb=" N ASP D 753 " --> pdb=" O LYS D 655 " (cutoff:3.500A) removed outlier: 12.278A pdb=" N LYS D 655 " --> pdb=" O ASP D 753 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 629 through 631 removed outlier: 4.935A pdb=" N PHE D 751 " --> pdb=" O LYS D 686 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS D 686 " --> pdb=" O PHE D 751 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP D 753 " --> pdb=" O TYR D 684 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR D 684 " --> pdb=" O ASP D 753 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 641 through 642 removed outlier: 5.837A pdb=" N VAL D 739 " --> pdb=" O ALA D 667 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS D 738 " --> pdb=" O ASP D 699 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP D 699 " --> pdb=" O LYS D 738 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 774 through 776 removed outlier: 7.060A pdb=" N ASP D 775 " --> pdb=" O LYS D 784 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS D 784 " --> pdb=" O LYS D 825 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 805 through 806 Processing sheet with id=AG3, first strand: chain 'D' and resid 805 through 806 removed outlier: 6.247A pdb=" N ALA D 837 " --> pdb=" O LYS D 848 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS D 848 " --> pdb=" O ALA D 837 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 234 through 237 Processing sheet with id=AG5, first strand: chain 'E' and resid 299 through 310 removed outlier: 5.395A pdb=" N VAL E 301 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR E 396 " --> pdb=" O VAL E 301 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET E 303 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG E 394 " --> pdb=" O MET E 303 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 440 through 441 removed outlier: 4.546A pdb=" N ILE E 462 " --> pdb=" O LEU E 389 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 420 through 425 removed outlier: 6.318A pdb=" N SER E 420 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU E 414 " --> pdb=" O SER E 420 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA E 422 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR E 404 " --> pdb=" O SER E 434 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER E 434 " --> pdb=" O TYR E 404 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 420 through 425 removed outlier: 6.318A pdb=" N SER E 420 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU E 414 " --> pdb=" O SER E 420 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA E 422 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU E 406 " --> pdb=" O LYS E 487 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS E 487 " --> pdb=" O LEU E 406 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN E 485 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR E 410 " --> pdb=" O THR E 483 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR E 483 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE E 412 " --> pdb=" O LEU E 481 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU E 481 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU E 414 " --> pdb=" O LEU E 479 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU E 479 " --> pdb=" O LEU E 414 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 492 through 493 Processing sheet with id=AH1, first strand: chain 'E' and resid 532 through 537 removed outlier: 9.151A pdb=" N ILE E 622 " --> pdb=" O SER E 518 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N SER E 520 " --> pdb=" O ILE E 622 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE E 624 " --> pdb=" O SER E 520 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR E 522 " --> pdb=" O ILE E 624 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 564 through 566 Processing sheet with id=AH3, first strand: chain 'E' and resid 629 through 631 removed outlier: 6.268A pdb=" N ASP E 753 " --> pdb=" O LYS E 655 " (cutoff:3.500A) removed outlier: 12.277A pdb=" N LYS E 655 " --> pdb=" O ASP E 753 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 629 through 631 removed outlier: 4.935A pdb=" N PHE E 751 " --> pdb=" O LYS E 686 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS E 686 " --> pdb=" O PHE E 751 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP E 753 " --> pdb=" O TYR E 684 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR E 684 " --> pdb=" O ASP E 753 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 641 through 642 removed outlier: 5.837A pdb=" N VAL E 739 " --> pdb=" O ALA E 667 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 738 " --> pdb=" O ASP E 699 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP E 699 " --> pdb=" O LYS E 738 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 774 through 776 removed outlier: 7.060A pdb=" N ASP E 775 " --> pdb=" O LYS E 784 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS E 784 " --> pdb=" O LYS E 825 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 805 through 806 Processing sheet with id=AH8, first strand: chain 'E' and resid 805 through 806 removed outlier: 6.246A pdb=" N ALA E 837 " --> pdb=" O LYS E 848 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS E 848 " --> pdb=" O ALA E 837 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 234 through 237 Processing sheet with id=AI1, first strand: chain 'F' and resid 299 through 310 removed outlier: 5.395A pdb=" N VAL F 301 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR F 396 " --> pdb=" O VAL F 301 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET F 303 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG F 394 " --> pdb=" O MET F 303 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 440 through 441 removed outlier: 4.546A pdb=" N ILE F 462 " --> pdb=" O LEU F 389 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 420 through 425 removed outlier: 6.319A pdb=" N SER F 420 " --> pdb=" O LEU F 414 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU F 414 " --> pdb=" O SER F 420 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA F 422 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR F 404 " --> pdb=" O SER F 434 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER F 434 " --> pdb=" O TYR F 404 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 420 through 425 removed outlier: 6.319A pdb=" N SER F 420 " --> pdb=" O LEU F 414 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU F 414 " --> pdb=" O SER F 420 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA F 422 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU F 406 " --> pdb=" O LYS F 487 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS F 487 " --> pdb=" O LEU F 406 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN F 485 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR F 410 " --> pdb=" O THR F 483 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR F 483 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE F 412 " --> pdb=" O LEU F 481 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU F 481 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU F 414 " --> pdb=" O LEU F 479 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU F 479 " --> pdb=" O LEU F 414 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 492 through 493 Processing sheet with id=AI6, first strand: chain 'F' and resid 532 through 537 removed outlier: 9.151A pdb=" N ILE F 622 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N SER F 520 " --> pdb=" O ILE F 622 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE F 624 " --> pdb=" O SER F 520 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR F 522 " --> pdb=" O ILE F 624 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 564 through 566 Processing sheet with id=AI8, first strand: chain 'F' and resid 629 through 631 removed outlier: 6.268A pdb=" N ASP F 753 " --> pdb=" O LYS F 655 " (cutoff:3.500A) removed outlier: 12.278A pdb=" N LYS F 655 " --> pdb=" O ASP F 753 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 629 through 631 removed outlier: 4.935A pdb=" N PHE F 751 " --> pdb=" O LYS F 686 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS F 686 " --> pdb=" O PHE F 751 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP F 753 " --> pdb=" O TYR F 684 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR F 684 " --> pdb=" O ASP F 753 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 641 through 642 removed outlier: 5.837A pdb=" N VAL F 739 " --> pdb=" O ALA F 667 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS F 738 " --> pdb=" O ASP F 699 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP F 699 " --> pdb=" O LYS F 738 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 774 through 776 removed outlier: 7.059A pdb=" N ASP F 775 " --> pdb=" O LYS F 784 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS F 784 " --> pdb=" O LYS F 825 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'F' and resid 805 through 806 Processing sheet with id=AJ4, first strand: chain 'F' and resid 805 through 806 removed outlier: 6.247A pdb=" N ALA F 837 " --> pdb=" O LYS F 848 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS F 848 " --> pdb=" O ALA F 837 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'G' and resid 234 through 237 Processing sheet with id=AJ6, first strand: chain 'G' and resid 299 through 310 removed outlier: 5.394A pdb=" N VAL G 301 " --> pdb=" O TYR G 396 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR G 396 " --> pdb=" O VAL G 301 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N MET G 303 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG G 394 " --> pdb=" O MET G 303 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'G' and resid 440 through 441 removed outlier: 4.546A pdb=" N ILE G 462 " --> pdb=" O LEU G 389 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'G' and resid 420 through 425 removed outlier: 6.319A pdb=" N SER G 420 " --> pdb=" O LEU G 414 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU G 414 " --> pdb=" O SER G 420 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA G 422 " --> pdb=" O PHE G 412 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR G 404 " --> pdb=" O SER G 434 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER G 434 " --> pdb=" O TYR G 404 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'G' and resid 420 through 425 removed outlier: 6.319A pdb=" N SER G 420 " --> pdb=" O LEU G 414 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU G 414 " --> pdb=" O SER G 420 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA G 422 " --> pdb=" O PHE G 412 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU G 406 " --> pdb=" O LYS G 487 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS G 487 " --> pdb=" O LEU G 406 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN G 485 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR G 410 " --> pdb=" O THR G 483 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR G 483 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE G 412 " --> pdb=" O LEU G 481 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU G 481 " --> pdb=" O PHE G 412 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU G 414 " --> pdb=" O LEU G 479 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU G 479 " --> pdb=" O LEU G 414 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'G' and resid 492 through 493 Processing sheet with id=AK2, first strand: chain 'G' and resid 532 through 537 removed outlier: 9.150A pdb=" N ILE G 622 " --> pdb=" O SER G 518 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N SER G 520 " --> pdb=" O ILE G 622 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE G 624 " --> pdb=" O SER G 520 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR G 522 " --> pdb=" O ILE G 624 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'G' and resid 564 through 566 Processing sheet with id=AK4, first strand: chain 'G' and resid 629 through 631 removed outlier: 6.268A pdb=" N ASP G 753 " --> pdb=" O LYS G 655 " (cutoff:3.500A) removed outlier: 12.277A pdb=" N LYS G 655 " --> pdb=" O ASP G 753 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'G' and resid 629 through 631 removed outlier: 4.935A pdb=" N PHE G 751 " --> pdb=" O LYS G 686 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS G 686 " --> pdb=" O PHE G 751 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP G 753 " --> pdb=" O TYR G 684 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR G 684 " --> pdb=" O ASP G 753 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'G' and resid 641 through 642 removed outlier: 5.837A pdb=" N VAL G 739 " --> pdb=" O ALA G 667 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS G 738 " --> pdb=" O ASP G 699 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP G 699 " --> pdb=" O LYS G 738 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'G' and resid 774 through 776 removed outlier: 7.060A pdb=" N ASP G 775 " --> pdb=" O LYS G 784 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS G 784 " --> pdb=" O LYS G 825 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 805 through 806 Processing sheet with id=AK9, first strand: chain 'G' and resid 805 through 806 removed outlier: 6.247A pdb=" N ALA G 837 " --> pdb=" O LYS G 848 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS G 848 " --> pdb=" O ALA G 837 " (cutoff:3.500A) 1561 hydrogen bonds defined for protein. 4074 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: 8.20 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9393 1.33 - 1.45: 7157 1.45 - 1.57: 19094 1.57 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 35770 Sorted by residual: bond pdb=" CB GLN D 485 " pdb=" CG GLN D 485 " ideal model delta sigma weight residual 1.520 1.426 0.094 3.00e-02 1.11e+03 9.74e+00 bond pdb=" CB GLN C 485 " pdb=" CG GLN C 485 " ideal model delta sigma weight residual 1.520 1.426 0.094 3.00e-02 1.11e+03 9.72e+00 bond pdb=" CB GLN A 485 " pdb=" CG GLN A 485 " ideal model delta sigma weight residual 1.520 1.427 0.093 3.00e-02 1.11e+03 9.63e+00 bond pdb=" CB GLN B 485 " pdb=" CG GLN B 485 " ideal model delta sigma weight residual 1.520 1.427 0.093 3.00e-02 1.11e+03 9.62e+00 bond pdb=" CB GLN E 485 " pdb=" CG GLN E 485 " ideal model delta sigma weight residual 1.520 1.427 0.093 3.00e-02 1.11e+03 9.54e+00 ... (remaining 35765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 42366 1.59 - 3.17: 5086 3.17 - 4.76: 850 4.76 - 6.35: 152 6.35 - 7.93: 42 Bond angle restraints: 48496 Sorted by residual: angle pdb=" C VAL D 573 " pdb=" N ASN D 574 " pdb=" CA ASN D 574 " ideal model delta sigma weight residual 120.87 128.80 -7.93 1.69e+00 3.50e-01 2.20e+01 angle pdb=" C VAL F 573 " pdb=" N ASN F 574 " pdb=" CA ASN F 574 " ideal model delta sigma weight residual 120.87 128.79 -7.92 1.69e+00 3.50e-01 2.20e+01 angle pdb=" C VAL B 573 " pdb=" N ASN B 574 " pdb=" CA ASN B 574 " ideal model delta sigma weight residual 120.87 128.79 -7.92 1.69e+00 3.50e-01 2.19e+01 angle pdb=" C VAL G 573 " pdb=" N ASN G 574 " pdb=" CA ASN G 574 " ideal model delta sigma weight residual 120.87 128.79 -7.92 1.69e+00 3.50e-01 2.19e+01 angle pdb=" OE1 GLN G 473 " pdb=" CD GLN G 473 " pdb=" NE2 GLN G 473 " ideal model delta sigma weight residual 122.60 118.14 4.46 1.00e+00 1.00e+00 1.99e+01 ... (remaining 48491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 19350 16.57 - 33.14: 1685 33.14 - 49.71: 221 49.71 - 66.28: 136 66.28 - 82.86: 42 Dihedral angle restraints: 21434 sinusoidal: 8526 harmonic: 12908 Sorted by residual: dihedral pdb=" CA ASN A 345 " pdb=" C ASN A 345 " pdb=" N ASP A 346 " pdb=" CA ASP A 346 " ideal model delta harmonic sigma weight residual 180.00 150.75 29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ASN C 345 " pdb=" C ASN C 345 " pdb=" N ASP C 346 " pdb=" CA ASP C 346 " ideal model delta harmonic sigma weight residual 180.00 150.76 29.24 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ASN F 345 " pdb=" C ASN F 345 " pdb=" N ASP F 346 " pdb=" CA ASP F 346 " ideal model delta harmonic sigma weight residual 180.00 150.76 29.24 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 21431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4085 0.079 - 0.157: 981 0.157 - 0.236: 84 0.236 - 0.314: 15 0.314 - 0.393: 8 Chirality restraints: 5173 Sorted by residual: chirality pdb=" CA LYS D 347 " pdb=" N LYS D 347 " pdb=" C LYS D 347 " pdb=" CB LYS D 347 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA LYS B 347 " pdb=" N LYS B 347 " pdb=" C LYS B 347 " pdb=" CB LYS B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA LYS A 347 " pdb=" N LYS A 347 " pdb=" C LYS A 347 " pdb=" CB LYS A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 5170 not shown) Planarity restraints: 6377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 736 " -0.030 2.00e-02 2.50e+03 1.93e-02 6.52e+00 pdb=" CG PHE E 736 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE E 736 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE E 736 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE E 736 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE E 736 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 736 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 736 " 0.030 2.00e-02 2.50e+03 1.92e-02 6.45e+00 pdb=" CG PHE B 736 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 736 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 736 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 736 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 736 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 736 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 736 " -0.030 2.00e-02 2.50e+03 1.92e-02 6.45e+00 pdb=" CG PHE F 736 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE F 736 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE F 736 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE F 736 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE F 736 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 736 " -0.012 2.00e-02 2.50e+03 ... (remaining 6374 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2652 2.75 - 3.29: 34660 3.29 - 3.82: 62377 3.82 - 4.36: 80177 4.36 - 4.90: 132053 Nonbonded interactions: 311919 Sorted by model distance: nonbonded pdb=" OE2 GLU G 230 " pdb="CA CA G1001 " model vdw 2.210 2.510 nonbonded pdb=" OE2 GLU A 230 " pdb="CA CA A1001 " model vdw 2.210 2.510 nonbonded pdb=" OE2 GLU C 230 " pdb="CA CA C1001 " model vdw 2.210 2.510 nonbonded pdb=" OE2 GLU E 230 " pdb="CA CA E1001 " model vdw 2.210 2.510 nonbonded pdb=" OE2 GLU F 230 " pdb="CA CA F1001 " model vdw 2.210 2.510 ... (remaining 311914 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 28.210 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- 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 : 0.006 0.094 35770 Z= 0.341 Angle : 1.116 7.933 48496 Z= 0.670 Chirality : 0.066 0.393 5173 Planarity : 0.008 0.072 6377 Dihedral : 13.956 82.855 13174 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 3.85 % 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: -0.21 (0.12), residues: 4410 helix: -1.10 (0.18), residues: 504 sheet: 0.85 (0.14), residues: 1204 loop : -0.37 (0.11), residues: 2702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 394 TYR 0.032 0.006 TYR D 296 PHE 0.037 0.008 PHE C 751 TRP 0.027 0.005 TRP E 806 HIS 0.011 0.002 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.34 (35770) covalent geometry : angle 1.11640 / 0.67 (48496) hydrogen bonds : bond 0.15075 / 10.08 ( 1498) hydrogen bonds : angle 7.78114 / 5.46 ( 4074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 341 LYS cc_start: 0.7813 (tttm) cc_final: 0.7586 (tttm) REVERT: D 341 LYS cc_start: 0.7629 (tttm) cc_final: 0.7400 (tttm) REVERT: D 351 PHE cc_start: 0.7862 (t80) cc_final: 0.7629 (t80) REVERT: E 322 MET cc_start: 0.8230 (mmt) cc_final: 0.7900 (mmt) REVERT: G 280 MET cc_start: 0.9291 (mtm) cc_final: 0.8902 (mtp) REVERT: G 341 LYS cc_start: 0.7751 (tttm) cc_final: 0.7313 (tttm) outliers start: 0 outliers final: 0 residues processed: 491 average time/residue: 0.7276 time to fit residues: 429.9585 Evaluate side-chains 323 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A 392 ASN A 433 ASN A 473 GLN A 852 HIS B 240 GLN B 392 ASN B 433 ASN B 473 GLN C 240 GLN C 392 ASN C 433 ASN C 473 GLN D 240 GLN D 392 ASN D 473 GLN D 660 ASN E 392 ASN E 433 ASN E 473 GLN F 240 GLN F 392 ASN F 433 ASN F 473 GLN G 240 GLN G 392 ASN G 433 ASN G 473 GLN G 640 GLN G 660 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.139547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.078927 restraints weight = 51442.914| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.14 r_work: 0.2761 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 35770 Z= 0.178 Angle : 0.650 6.049 48496 Z= 0.359 Chirality : 0.047 0.160 5173 Planarity : 0.004 0.052 6377 Dihedral : 6.544 26.394 4739 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.20 % Allowed : 6.71 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.00 (0.12), residues: 4410 helix: 0.51 (0.22), residues: 525 sheet: -0.07 (0.13), residues: 1442 loop : 0.06 (0.12), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 682 TYR 0.022 0.002 TYR D 666 PHE 0.017 0.002 PHE G 349 TRP 0.012 0.001 TRP A 361 HIS 0.007 0.001 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (35770) covalent geometry : angle 0.65026 / 0.36 (48496) hydrogen bonds : bond 0.04567 / 3.05 ( 1498) hydrogen bonds : angle 6.42925 / 4.50 ( 4074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 363 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8573 (mttt) cc_final: 0.8098 (mtpm) REVERT: A 555 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8243 (mt-10) REVERT: A 643 ASN cc_start: 0.8797 (t0) cc_final: 0.8412 (t0) REVERT: A 645 TYR cc_start: 0.8349 (m-80) cc_final: 0.7683 (m-80) REVERT: A 658 ARG cc_start: 0.8770 (ttp-170) cc_final: 0.8448 (tmm-80) REVERT: A 682 ARG cc_start: 0.7778 (mtt90) cc_final: 0.7448 (mtt90) REVERT: A 763 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8584 (pm20) REVERT: A 823 MET cc_start: 0.8293 (mmm) cc_final: 0.7830 (mmt) REVERT: B 217 MET cc_start: 0.8152 (mtp) cc_final: 0.7909 (mtp) REVERT: B 324 LYS cc_start: 0.8530 (mttt) cc_final: 0.8069 (mtpm) REVERT: B 356 LYS cc_start: 0.8228 (tttm) cc_final: 0.8009 (tttm) REVERT: B 555 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8171 (mt-10) REVERT: B 643 ASN cc_start: 0.8788 (t0) cc_final: 0.8398 (t0) REVERT: C 217 MET cc_start: 0.8068 (mtp) cc_final: 0.7834 (mtp) REVERT: C 324 LYS cc_start: 0.8643 (mttt) cc_final: 0.8271 (mtpm) REVERT: C 352 GLU cc_start: 0.8582 (pt0) cc_final: 0.8151 (pt0) REVERT: C 371 GLU cc_start: 0.8261 (tt0) cc_final: 0.8024 (tt0) REVERT: C 555 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8325 (mt-10) REVERT: C 643 ASN cc_start: 0.8841 (t0) cc_final: 0.8307 (t0) REVERT: C 645 TYR cc_start: 0.8320 (m-80) cc_final: 0.7760 (m-80) REVERT: C 660 ASN cc_start: 0.8581 (m-40) cc_final: 0.8353 (m110) REVERT: C 823 MET cc_start: 0.7762 (mpp) cc_final: 0.7166 (mmp) REVERT: C 842 ASN cc_start: 0.8390 (t0) cc_final: 0.8137 (t160) REVERT: D 324 LYS cc_start: 0.8625 (mttt) cc_final: 0.8147 (mtpp) REVERT: D 352 GLU cc_start: 0.8589 (pt0) cc_final: 0.8382 (pt0) REVERT: D 371 GLU cc_start: 0.8320 (tt0) cc_final: 0.8103 (tt0) REVERT: D 530 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6574 (pm20) REVERT: D 555 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8304 (mt-10) REVERT: D 643 ASN cc_start: 0.8955 (t0) cc_final: 0.8628 (t0) REVERT: E 322 MET cc_start: 0.8251 (mmt) cc_final: 0.7884 (mmt) REVERT: E 324 LYS cc_start: 0.8580 (mttt) cc_final: 0.8097 (mtpm) REVERT: E 337 ASP cc_start: 0.8444 (m-30) cc_final: 0.8038 (t0) REVERT: E 338 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8383 (mm) REVERT: E 643 ASN cc_start: 0.8919 (t0) cc_final: 0.8316 (t0) REVERT: E 645 TYR cc_start: 0.8325 (m-80) cc_final: 0.7920 (m-80) REVERT: E 669 LYS cc_start: 0.8703 (mppt) cc_final: 0.8260 (mppt) REVERT: E 842 ASN cc_start: 0.8524 (t0) cc_final: 0.8320 (t160) REVERT: F 217 MET cc_start: 0.8162 (mtp) cc_final: 0.7933 (mtp) REVERT: F 352 GLU cc_start: 0.8549 (pt0) cc_final: 0.8283 (pt0) REVERT: F 363 ASN cc_start: 0.8496 (t0) cc_final: 0.8292 (t0) REVERT: F 373 GLU cc_start: 0.8169 (tp30) cc_final: 0.7931 (tp30) REVERT: F 555 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8276 (mt-10) REVERT: F 643 ASN cc_start: 0.8783 (t0) cc_final: 0.8352 (t0) REVERT: F 645 TYR cc_start: 0.8279 (m-80) cc_final: 0.7665 (m-80) REVERT: F 660 ASN cc_start: 0.8625 (m-40) cc_final: 0.8389 (m110) REVERT: F 668 ILE cc_start: 0.9387 (mm) cc_final: 0.9171 (mp) REVERT: G 217 MET cc_start: 0.8155 (mtp) cc_final: 0.7830 (mtp) REVERT: G 324 LYS cc_start: 0.8620 (mttt) cc_final: 0.8132 (mtpp) REVERT: G 710 LYS cc_start: 0.9085 (ttmm) cc_final: 0.8650 (mptt) REVERT: G 823 MET cc_start: 0.7527 (mpp) cc_final: 0.6795 (mmp) outliers start: 46 outliers final: 9 residues processed: 386 average time/residue: 0.6291 time to fit residues: 297.4659 Evaluate side-chains 326 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 315 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 530 GLU Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 287 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 162 optimal weight: 0.8980 chunk 192 optimal weight: 4.9990 chunk 391 optimal weight: 10.0000 chunk 420 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 chunk 223 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 232 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 732 ASN B 640 GLN C 640 GLN C 732 ASN D 433 ASN D 640 GLN D 732 ASN F 732 ASN G 640 GLN G 732 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.136596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.074092 restraints weight = 51487.855| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.24 r_work: 0.2676 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 35770 Z= 0.343 Angle : 0.675 7.220 48496 Z= 0.369 Chirality : 0.049 0.184 5173 Planarity : 0.004 0.051 6377 Dihedral : 6.199 26.868 4739 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.16 % Allowed : 6.71 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.21 (0.12), residues: 4410 helix: 0.55 (0.22), residues: 525 sheet: -0.30 (0.13), residues: 1435 loop : -0.06 (0.12), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 535 TYR 0.025 0.002 TYR F 441 PHE 0.019 0.002 PHE A 581 TRP 0.010 0.001 TRP B 344 HIS 0.008 0.001 HIS C 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.34 (35770) covalent geometry : angle 0.67547 / 0.37 (48496) hydrogen bonds : bond 0.04888 / 3.27 ( 1498) hydrogen bonds : angle 6.20512 / 4.34 ( 4074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 335 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8984 (mtpp) cc_final: 0.8555 (tttp) REVERT: A 352 GLU cc_start: 0.8533 (pt0) cc_final: 0.8299 (pt0) REVERT: A 371 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7817 (tt0) REVERT: A 555 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8297 (mt-10) REVERT: A 640 GLN cc_start: 0.9172 (mt0) cc_final: 0.8964 (mp10) REVERT: A 643 ASN cc_start: 0.8792 (t0) cc_final: 0.8309 (t0) REVERT: A 682 ARG cc_start: 0.7792 (mtt90) cc_final: 0.7296 (mtt90) REVERT: A 763 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8519 (pm20) REVERT: A 823 MET cc_start: 0.8247 (mmm) cc_final: 0.7878 (mmt) REVERT: A 842 ASN cc_start: 0.8420 (t0) cc_final: 0.8038 (t160) REVERT: B 217 MET cc_start: 0.8346 (mtp) cc_final: 0.8092 (mtp) REVERT: B 555 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8254 (mt-10) REVERT: B 643 ASN cc_start: 0.8752 (t0) cc_final: 0.8147 (t0) REVERT: C 217 MET cc_start: 0.8142 (mtp) cc_final: 0.7933 (mtp) REVERT: C 287 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8533 (p0) REVERT: C 337 ASP cc_start: 0.8425 (t0) cc_final: 0.8142 (t0) REVERT: C 555 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8419 (mt-10) REVERT: C 621 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8190 (ttmm) REVERT: C 643 ASN cc_start: 0.8879 (t0) cc_final: 0.8267 (t0) REVERT: C 645 TYR cc_start: 0.8343 (m-80) cc_final: 0.7735 (m-80) REVERT: C 660 ASN cc_start: 0.8661 (m-40) cc_final: 0.8333 (m110) REVERT: C 710 LYS cc_start: 0.9238 (tttt) cc_final: 0.8913 (mptp) REVERT: C 823 MET cc_start: 0.7737 (mpp) cc_final: 0.7245 (mmp) REVERT: C 842 ASN cc_start: 0.8417 (t0) cc_final: 0.8120 (t160) REVERT: D 310 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8557 (tttp) REVERT: D 324 LYS cc_start: 0.8667 (mttt) cc_final: 0.8172 (mtpp) REVERT: D 352 GLU cc_start: 0.8512 (pt0) cc_final: 0.8126 (pt0) REVERT: D 371 GLU cc_start: 0.8372 (tt0) cc_final: 0.8164 (tt0) REVERT: D 555 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8350 (mt-10) REVERT: D 640 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: D 643 ASN cc_start: 0.8945 (t0) cc_final: 0.8461 (t0) REVERT: D 710 LYS cc_start: 0.8968 (mttt) cc_final: 0.8684 (mptt) REVERT: E 310 LYS cc_start: 0.8945 (mtpp) cc_final: 0.8517 (tttp) REVERT: E 337 ASP cc_start: 0.8379 (m-30) cc_final: 0.7992 (t0) REVERT: E 338 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8369 (mm) REVERT: E 635 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8242 (ptmm) REVERT: E 643 ASN cc_start: 0.8872 (t0) cc_final: 0.8207 (t0) REVERT: E 669 LYS cc_start: 0.8709 (mppt) cc_final: 0.8199 (mppt) REVERT: E 710 LYS cc_start: 0.9131 (tttt) cc_final: 0.8863 (mptt) REVERT: E 763 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8238 (pm20) REVERT: E 842 ASN cc_start: 0.8536 (t0) cc_final: 0.8275 (t160) REVERT: F 310 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8600 (tttp) REVERT: F 363 ASN cc_start: 0.8552 (t0) cc_final: 0.8331 (t0) REVERT: F 371 GLU cc_start: 0.8343 (tt0) cc_final: 0.7834 (tt0) REVERT: F 525 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8370 (mt) REVERT: F 643 ASN cc_start: 0.8794 (t0) cc_final: 0.8389 (t0) REVERT: F 645 TYR cc_start: 0.8148 (m-80) cc_final: 0.7781 (m-80) REVERT: F 823 MET cc_start: 0.8221 (mmp) cc_final: 0.7917 (mmp) REVERT: G 217 MET cc_start: 0.8258 (mtp) cc_final: 0.7941 (mtp) REVERT: G 352 GLU cc_start: 0.7736 (pm20) cc_final: 0.7503 (pm20) REVERT: G 643 ASN cc_start: 0.8717 (t0) cc_final: 0.8471 (t0) REVERT: G 669 LYS cc_start: 0.8764 (mppt) cc_final: 0.8359 (mppt) REVERT: G 763 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8319 (pm20) REVERT: G 823 MET cc_start: 0.7535 (mpp) cc_final: 0.6816 (mmp) outliers start: 83 outliers final: 34 residues processed: 391 average time/residue: 0.6887 time to fit residues: 326.1986 Evaluate side-chains 348 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 309 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 621 LYS Chi-restraints excluded: chain C residue 725 MET Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 640 GLN Chi-restraints excluded: chain D residue 647 ASP Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 525 LEU Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 456 ASP Chi-restraints excluded: chain F residue 517 VAL Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 647 ASP Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 456 ASP Chi-restraints excluded: chain G residue 485 GLN Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 668 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 78 optimal weight: 2.9990 chunk 388 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 320 optimal weight: 2.9990 chunk 352 optimal weight: 1.9990 chunk 258 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 732 ASN B 640 GLN B 732 ASN C 640 GLN C 732 ASN D 732 ASN E 485 GLN ** E 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 732 ASN G 640 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.138105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.076525 restraints weight = 51206.103| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.25 r_work: 0.2724 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 35770 Z= 0.211 Angle : 0.589 7.020 48496 Z= 0.324 Chirality : 0.046 0.157 5173 Planarity : 0.004 0.054 6377 Dihedral : 5.743 25.152 4739 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.77 % Allowed : 7.52 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.26 (0.12), residues: 4410 helix: 0.79 (0.23), residues: 518 sheet: -0.47 (0.13), residues: 1477 loop : -0.05 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 535 TYR 0.021 0.001 TYR F 441 PHE 0.015 0.002 PHE E 349 TRP 0.011 0.001 TRP E 361 HIS 0.008 0.001 HIS B 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (35770) covalent geometry : angle 0.58863 / 0.32 (48496) hydrogen bonds : bond 0.04083 / 2.74 ( 1498) hydrogen bonds : angle 6.06625 / 4.24 ( 4074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 324 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8522 (tttp) REVERT: A 352 GLU cc_start: 0.8506 (pt0) cc_final: 0.8150 (pt0) REVERT: A 371 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7706 (tt0) REVERT: A 555 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8326 (mt-10) REVERT: A 643 ASN cc_start: 0.8750 (t0) cc_final: 0.8159 (t0) REVERT: A 682 ARG cc_start: 0.7696 (mtt90) cc_final: 0.7312 (mtt90) REVERT: A 763 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8462 (pm20) REVERT: A 823 MET cc_start: 0.8269 (mmm) cc_final: 0.7929 (mmt) REVERT: A 842 ASN cc_start: 0.8301 (t0) cc_final: 0.7919 (t160) REVERT: B 530 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6733 (pm20) REVERT: B 555 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8160 (mt-10) REVERT: B 643 ASN cc_start: 0.8799 (t0) cc_final: 0.8284 (t0) REVERT: C 287 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8630 (p0) REVERT: C 371 GLU cc_start: 0.8204 (tt0) cc_final: 0.7933 (tt0) REVERT: C 555 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8468 (mt-10) REVERT: C 621 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8213 (ttmm) REVERT: C 643 ASN cc_start: 0.8864 (t0) cc_final: 0.8257 (t0) REVERT: C 823 MET cc_start: 0.7668 (mpp) cc_final: 0.7180 (mmp) REVERT: C 842 ASN cc_start: 0.8410 (t0) cc_final: 0.8112 (t160) REVERT: D 310 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8448 (tttp) REVERT: D 312 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8747 (mt-10) REVERT: D 324 LYS cc_start: 0.8637 (mttt) cc_final: 0.8122 (mtpp) REVERT: D 555 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8304 (mt-10) REVERT: D 635 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8202 (ptmm) REVERT: D 643 ASN cc_start: 0.9018 (t0) cc_final: 0.8464 (t0) REVERT: D 710 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8635 (mptt) REVERT: D 763 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8276 (pm20) REVERT: E 337 ASP cc_start: 0.8268 (m-30) cc_final: 0.7907 (t0) REVERT: E 338 LEU cc_start: 0.8571 (mp) cc_final: 0.8289 (mm) REVERT: E 635 LYS cc_start: 0.8404 (ttpp) cc_final: 0.8003 (ptmm) REVERT: E 643 ASN cc_start: 0.8857 (t0) cc_final: 0.8192 (t0) REVERT: E 669 LYS cc_start: 0.8692 (mppt) cc_final: 0.8175 (mppt) REVERT: E 710 LYS cc_start: 0.9027 (tttt) cc_final: 0.8743 (mptt) REVERT: E 763 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8263 (pm20) REVERT: E 842 ASN cc_start: 0.8586 (t0) cc_final: 0.8296 (t160) REVERT: F 310 LYS cc_start: 0.9010 (mtpp) cc_final: 0.8604 (tttp) REVERT: F 322 MET cc_start: 0.8463 (mmt) cc_final: 0.8059 (mmt) REVERT: F 363 ASN cc_start: 0.8593 (t0) cc_final: 0.8292 (t0) REVERT: F 371 GLU cc_start: 0.8290 (tt0) cc_final: 0.7851 (tt0) REVERT: F 643 ASN cc_start: 0.8716 (t0) cc_final: 0.8302 (t0) REVERT: F 645 TYR cc_start: 0.8170 (m-80) cc_final: 0.7853 (m-80) REVERT: F 660 ASN cc_start: 0.8536 (m110) cc_final: 0.8093 (m110) REVERT: F 763 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8303 (pm20) REVERT: F 823 MET cc_start: 0.8238 (mmp) cc_final: 0.7927 (mmp) REVERT: G 217 MET cc_start: 0.8325 (mtp) cc_final: 0.8032 (mtp) REVERT: G 643 ASN cc_start: 0.8798 (t0) cc_final: 0.8180 (t0) REVERT: G 669 LYS cc_start: 0.8750 (mppt) cc_final: 0.8348 (mppt) REVERT: G 763 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8358 (pm20) REVERT: G 823 MET cc_start: 0.7500 (mpp) cc_final: 0.6826 (mmp) REVERT: G 842 ASN cc_start: 0.8295 (t0) cc_final: 0.7988 (t160) outliers start: 68 outliers final: 29 residues processed: 364 average time/residue: 0.6204 time to fit residues: 275.4731 Evaluate side-chains 339 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 306 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 621 LYS Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 710 LYS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 725 MET Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 456 ASP Chi-restraints excluded: chain F residue 485 GLN Chi-restraints excluded: chain F residue 517 VAL Chi-restraints excluded: chain F residue 647 ASP Chi-restraints excluded: chain F residue 725 MET Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 668 ILE Chi-restraints excluded: chain G residue 725 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 248 optimal weight: 30.0000 chunk 426 optimal weight: 8.9990 chunk 304 optimal weight: 8.9990 chunk 264 optimal weight: 7.9990 chunk 232 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 337 optimal weight: 1.9990 chunk 332 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN A 732 ASN B 640 GLN B 732 ASN C 640 GLN D 732 ASN F 732 ASN G 485 GLN G 640 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.136897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074599 restraints weight = 51342.774| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.25 r_work: 0.2681 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 35770 Z= 0.295 Angle : 0.621 8.000 48496 Z= 0.338 Chirality : 0.047 0.181 5173 Planarity : 0.004 0.052 6377 Dihedral : 5.705 26.396 4739 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.93 % Allowed : 8.40 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.37 (0.12), residues: 4410 helix: 0.65 (0.23), residues: 525 sheet: -0.56 (0.13), residues: 1477 loop : -0.10 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 658 TYR 0.023 0.002 TYR F 441 PHE 0.017 0.002 PHE A 581 TRP 0.010 0.001 TRP D 344 HIS 0.008 0.001 HIS B 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.30 (35770) covalent geometry : angle 0.62108 / 0.34 (48496) hydrogen bonds : bond 0.04328 / 2.90 ( 1498) hydrogen bonds : angle 6.03109 / 4.22 ( 4074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 309 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8985 (mtpp) cc_final: 0.8520 (tttp) REVERT: A 352 GLU cc_start: 0.8507 (pt0) cc_final: 0.8128 (pt0) REVERT: A 371 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7764 (tt0) REVERT: A 555 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8322 (mt-10) REVERT: A 643 ASN cc_start: 0.8788 (t0) cc_final: 0.8165 (t0) REVERT: A 682 ARG cc_start: 0.7725 (mtt90) cc_final: 0.7391 (mtt90) REVERT: A 823 MET cc_start: 0.8371 (mmm) cc_final: 0.8005 (mmt) REVERT: A 842 ASN cc_start: 0.8274 (t0) cc_final: 0.7860 (t160) REVERT: B 530 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: B 555 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8200 (mt-10) REVERT: B 643 ASN cc_start: 0.8843 (t0) cc_final: 0.8309 (t0) REVERT: B 729 THR cc_start: 0.6454 (OUTLIER) cc_final: 0.6225 (p) REVERT: C 287 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8626 (p0) REVERT: C 371 GLU cc_start: 0.8272 (tt0) cc_final: 0.8049 (tt0) REVERT: C 555 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8480 (mt-10) REVERT: C 621 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8104 (tptt) REVERT: C 643 ASN cc_start: 0.8930 (t0) cc_final: 0.8319 (t0) REVERT: C 823 MET cc_start: 0.7683 (mpp) cc_final: 0.7230 (mmp) REVERT: C 842 ASN cc_start: 0.8316 (t0) cc_final: 0.7982 (t160) REVERT: D 555 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8308 (mt-10) REVERT: D 635 LYS cc_start: 0.8357 (ttpp) cc_final: 0.7958 (ptmm) REVERT: D 643 ASN cc_start: 0.8984 (t0) cc_final: 0.8531 (t0) REVERT: D 710 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8690 (mptt) REVERT: D 763 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8259 (pm20) REVERT: E 310 LYS cc_start: 0.8929 (mtpp) cc_final: 0.8544 (tttp) REVERT: E 322 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8294 (mmt) REVERT: E 337 ASP cc_start: 0.8280 (m-30) cc_final: 0.7888 (t0) REVERT: E 338 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8306 (mm) REVERT: E 341 LYS cc_start: 0.8162 (tttm) cc_final: 0.7837 (tptm) REVERT: E 356 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8157 (tttp) REVERT: E 371 GLU cc_start: 0.8383 (tt0) cc_final: 0.7682 (tm-30) REVERT: E 643 ASN cc_start: 0.8906 (t0) cc_final: 0.8226 (t0) REVERT: E 669 LYS cc_start: 0.8755 (mppt) cc_final: 0.8196 (mppt) REVERT: E 710 LYS cc_start: 0.9018 (tttt) cc_final: 0.8757 (mptt) REVERT: E 763 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8334 (tt0) REVERT: E 842 ASN cc_start: 0.8545 (t0) cc_final: 0.8271 (t160) REVERT: F 322 MET cc_start: 0.8583 (mmt) cc_final: 0.8214 (mmt) REVERT: F 337 ASP cc_start: 0.8236 (t0) cc_final: 0.7992 (t0) REVERT: F 363 ASN cc_start: 0.8583 (t0) cc_final: 0.8291 (t0) REVERT: F 371 GLU cc_start: 0.8261 (tt0) cc_final: 0.7835 (tt0) REVERT: F 643 ASN cc_start: 0.8773 (t0) cc_final: 0.8369 (t0) REVERT: F 645 TYR cc_start: 0.8202 (m-80) cc_final: 0.7883 (m-80) REVERT: F 660 ASN cc_start: 0.8534 (m110) cc_final: 0.8122 (m110) REVERT: F 823 MET cc_start: 0.8203 (mmp) cc_final: 0.7966 (mmp) REVERT: G 643 ASN cc_start: 0.8840 (t0) cc_final: 0.8471 (t0) REVERT: G 669 LYS cc_start: 0.8795 (mppt) cc_final: 0.8420 (mppt) REVERT: G 763 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8354 (pm20) REVERT: G 823 MET cc_start: 0.7480 (mpp) cc_final: 0.6797 (mmp) REVERT: G 842 ASN cc_start: 0.8368 (t0) cc_final: 0.8051 (t160) outliers start: 74 outliers final: 41 residues processed: 358 average time/residue: 0.5608 time to fit residues: 246.8600 Evaluate side-chains 347 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 298 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 621 LYS Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 725 MET Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 710 LYS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain E residue 725 MET Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 456 ASP Chi-restraints excluded: chain F residue 485 GLN Chi-restraints excluded: chain F residue 517 VAL Chi-restraints excluded: chain F residue 533 GLU Chi-restraints excluded: chain F residue 647 ASP Chi-restraints excluded: chain F residue 656 THR Chi-restraints excluded: chain F residue 725 MET Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 456 ASP Chi-restraints excluded: chain G residue 485 GLN Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 587 ILE Chi-restraints excluded: chain G residue 656 THR Chi-restraints excluded: chain G residue 668 ILE Chi-restraints excluded: chain G residue 725 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 115 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 404 optimal weight: 0.9990 chunk 329 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 347 optimal weight: 2.9990 chunk 171 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 66 optimal weight: 0.4980 chunk 103 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 GLN A 732 ASN B 640 GLN B 732 ASN D 732 ASN F 732 ASN F 842 ASN G 485 GLN G 640 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.138298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.076206 restraints weight = 51186.899| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.04 r_work: 0.2719 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35770 Z= 0.182 Angle : 0.563 8.331 48496 Z= 0.309 Chirality : 0.045 0.183 5173 Planarity : 0.004 0.052 6377 Dihedral : 5.413 24.842 4739 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.61 % Allowed : 8.82 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.26 (0.12), residues: 4410 helix: 0.85 (0.24), residues: 518 sheet: -0.49 (0.13), residues: 1435 loop : -0.07 (0.12), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 658 TYR 0.020 0.001 TYR A 441 PHE 0.022 0.002 PHE B 351 TRP 0.010 0.001 TRP E 344 HIS 0.008 0.001 HIS B 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (35770) covalent geometry : angle 0.56297 / 0.31 (48496) hydrogen bonds : bond 0.03786 / 2.54 ( 1498) hydrogen bonds : angle 5.95642 / 4.16 ( 4074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 309 time to evaluate : 1.408 Fit side-chains revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8957 (mtpp) cc_final: 0.8492 (tttp) REVERT: A 371 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7624 (tt0) REVERT: A 525 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8118 (mm) REVERT: A 555 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8278 (mt-10) REVERT: A 640 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: A 643 ASN cc_start: 0.8755 (t0) cc_final: 0.8123 (t0) REVERT: A 682 ARG cc_start: 0.7617 (mtt90) cc_final: 0.7379 (mtt90) REVERT: A 760 LYS cc_start: 0.8413 (mmtt) cc_final: 0.8114 (mmmt) REVERT: A 823 MET cc_start: 0.8401 (mmm) cc_final: 0.7999 (mmp) REVERT: A 842 ASN cc_start: 0.8260 (t0) cc_final: 0.7822 (t160) REVERT: B 356 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8144 (tttp) REVERT: B 555 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8096 (mt-10) REVERT: B 640 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8075 (mp10) REVERT: B 643 ASN cc_start: 0.8820 (t0) cc_final: 0.8274 (t0) REVERT: B 729 THR cc_start: 0.6414 (OUTLIER) cc_final: 0.6186 (p) REVERT: C 287 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8583 (p0) REVERT: C 322 MET cc_start: 0.8297 (mmt) cc_final: 0.7971 (mmt) REVERT: C 371 GLU cc_start: 0.8178 (tt0) cc_final: 0.7846 (tt0) REVERT: C 621 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8054 (tptt) REVERT: C 643 ASN cc_start: 0.8943 (t0) cc_final: 0.8317 (t0) REVERT: C 742 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7998 (mptt) REVERT: C 823 MET cc_start: 0.7707 (mpp) cc_final: 0.7256 (mmp) REVERT: C 842 ASN cc_start: 0.8322 (t0) cc_final: 0.7994 (t160) REVERT: D 310 LYS cc_start: 0.8840 (mtpp) cc_final: 0.8589 (tttp) REVERT: D 555 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8260 (mt-10) REVERT: D 643 ASN cc_start: 0.8861 (t0) cc_final: 0.8390 (t0) REVERT: D 710 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8663 (mptt) REVERT: D 763 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8287 (pm20) REVERT: E 310 LYS cc_start: 0.8890 (mtpp) cc_final: 0.8523 (tttp) REVERT: E 322 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8021 (mmt) REVERT: E 337 ASP cc_start: 0.8223 (m-30) cc_final: 0.7884 (t0) REVERT: E 356 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8142 (tttp) REVERT: E 371 GLU cc_start: 0.8279 (tt0) cc_final: 0.7943 (tt0) REVERT: E 635 LYS cc_start: 0.8263 (ttpp) cc_final: 0.7902 (ptmm) REVERT: E 643 ASN cc_start: 0.9060 (t0) cc_final: 0.8516 (t0) REVERT: E 842 ASN cc_start: 0.8566 (t0) cc_final: 0.8287 (t160) REVERT: F 310 LYS cc_start: 0.8935 (mtpp) cc_final: 0.8564 (tttp) REVERT: F 322 MET cc_start: 0.8379 (mmt) cc_final: 0.7971 (mmt) REVERT: F 337 ASP cc_start: 0.8153 (t0) cc_final: 0.7811 (t0) REVERT: F 363 ASN cc_start: 0.8567 (t0) cc_final: 0.8266 (t0) REVERT: F 371 GLU cc_start: 0.8193 (tt0) cc_final: 0.7758 (tt0) REVERT: F 643 ASN cc_start: 0.8797 (t0) cc_final: 0.8438 (t0) REVERT: F 763 GLU cc_start: 0.8669 (tt0) cc_final: 0.8323 (pm20) REVERT: F 823 MET cc_start: 0.8254 (mmp) cc_final: 0.7949 (mmp) REVERT: G 310 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8438 (tptp) REVERT: G 643 ASN cc_start: 0.8837 (t0) cc_final: 0.8439 (t0) REVERT: G 669 LYS cc_start: 0.8746 (mppt) cc_final: 0.8356 (mppt) REVERT: G 692 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7347 (m) REVERT: G 763 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8434 (pm20) REVERT: G 823 MET cc_start: 0.7479 (mpp) cc_final: 0.6808 (mmp) REVERT: G 842 ASN cc_start: 0.8371 (t0) cc_final: 0.8092 (t160) outliers start: 62 outliers final: 30 residues processed: 345 average time/residue: 0.6377 time to fit residues: 270.4655 Evaluate side-chains 335 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 293 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 621 LYS Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 742 LYS Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 710 LYS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain E residue 725 MET Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 456 ASP Chi-restraints excluded: chain F residue 485 GLN Chi-restraints excluded: chain F residue 517 VAL Chi-restraints excluded: chain F residue 656 THR Chi-restraints excluded: chain F residue 725 MET Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 587 ILE Chi-restraints excluded: chain G residue 656 THR Chi-restraints excluded: chain G residue 692 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 171 optimal weight: 20.0000 chunk 310 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 201 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 330 optimal weight: 8.9990 chunk 208 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 732 ASN B 732 ASN D 732 ASN E 646 GLN E 660 ASN F 732 ASN G 640 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.138313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.076325 restraints weight = 51442.249| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.13 r_work: 0.2744 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35770 Z= 0.185 Angle : 0.556 8.269 48496 Z= 0.305 Chirality : 0.045 0.195 5173 Planarity : 0.004 0.053 6377 Dihedral : 5.297 24.889 4739 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.54 % Allowed : 9.19 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.25 (0.12), residues: 4410 helix: 0.95 (0.24), residues: 511 sheet: -0.49 (0.13), residues: 1428 loop : -0.08 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 658 TYR 0.016 0.001 TYR F 441 PHE 0.026 0.001 PHE C 351 TRP 0.010 0.001 TRP D 344 HIS 0.009 0.001 HIS B 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (35770) covalent geometry : angle 0.55557 / 0.30 (48496) hydrogen bonds : bond 0.03720 / 2.50 ( 1498) hydrogen bonds : angle 5.86614 / 4.11 ( 4074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 317 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8504 (tttp) REVERT: A 351 PHE cc_start: 0.8298 (t80) cc_final: 0.7948 (t80) REVERT: A 371 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7649 (tt0) REVERT: A 555 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8352 (mt-10) REVERT: A 640 GLN cc_start: 0.8888 (mt0) cc_final: 0.8197 (mp10) REVERT: A 643 ASN cc_start: 0.8708 (t0) cc_final: 0.8066 (t0) REVERT: A 682 ARG cc_start: 0.7586 (mtt90) cc_final: 0.7347 (mtt90) REVERT: A 760 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8188 (mmmt) REVERT: A 823 MET cc_start: 0.8337 (mmm) cc_final: 0.7950 (mmt) REVERT: B 352 GLU cc_start: 0.8254 (pt0) cc_final: 0.7971 (pt0) REVERT: B 356 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8141 (tttp) REVERT: B 555 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8208 (mt-10) REVERT: B 640 GLN cc_start: 0.8926 (mt0) cc_final: 0.8088 (mp10) REVERT: B 643 ASN cc_start: 0.8828 (t0) cc_final: 0.8277 (t0) REVERT: B 668 ILE cc_start: 0.9455 (mm) cc_final: 0.9228 (mt) REVERT: B 669 LYS cc_start: 0.9007 (mppt) cc_final: 0.8363 (mppt) REVERT: B 729 THR cc_start: 0.6471 (OUTLIER) cc_final: 0.6240 (p) REVERT: C 287 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8589 (p0) REVERT: C 621 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8097 (tptt) REVERT: C 643 ASN cc_start: 0.8963 (t0) cc_final: 0.8305 (t0) REVERT: C 742 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7985 (mptt) REVERT: C 823 MET cc_start: 0.7717 (mpp) cc_final: 0.7256 (mmp) REVERT: C 842 ASN cc_start: 0.8335 (t0) cc_final: 0.7999 (t160) REVERT: D 310 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8606 (tttp) REVERT: D 351 PHE cc_start: 0.8378 (t80) cc_final: 0.7989 (t80) REVERT: D 555 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8263 (mt-10) REVERT: D 643 ASN cc_start: 0.8824 (t0) cc_final: 0.8349 (t0) REVERT: D 710 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8665 (mptt) REVERT: D 763 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8327 (pm20) REVERT: E 310 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8544 (tttp) REVERT: E 322 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8044 (mmt) REVERT: E 334 ASN cc_start: 0.8367 (m-40) cc_final: 0.8037 (m-40) REVERT: E 337 ASP cc_start: 0.8210 (m-30) cc_final: 0.7849 (t0) REVERT: E 338 LEU cc_start: 0.8522 (mt) cc_final: 0.8178 (mm) REVERT: E 341 LYS cc_start: 0.8169 (tptp) cc_final: 0.7724 (tptp) REVERT: E 356 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8097 (tttp) REVERT: E 371 GLU cc_start: 0.8299 (tt0) cc_final: 0.7934 (tt0) REVERT: E 640 GLN cc_start: 0.9072 (mt0) cc_final: 0.8468 (mp10) REVERT: E 643 ASN cc_start: 0.9089 (t0) cc_final: 0.8534 (t0) REVERT: E 842 ASN cc_start: 0.8542 (t0) cc_final: 0.8249 (t160) REVERT: F 322 MET cc_start: 0.8425 (mmt) cc_final: 0.8035 (mmt) REVERT: F 337 ASP cc_start: 0.8140 (t0) cc_final: 0.7861 (t0) REVERT: F 363 ASN cc_start: 0.8584 (t0) cc_final: 0.8289 (t0) REVERT: F 371 GLU cc_start: 0.8244 (tt0) cc_final: 0.7815 (tt0) REVERT: F 640 GLN cc_start: 0.9135 (mt0) cc_final: 0.8312 (mp10) REVERT: F 643 ASN cc_start: 0.8816 (t0) cc_final: 0.8468 (t160) REVERT: F 763 GLU cc_start: 0.8663 (tt0) cc_final: 0.8366 (pm20) REVERT: F 823 MET cc_start: 0.8242 (mmp) cc_final: 0.7947 (mmp) REVERT: G 310 LYS cc_start: 0.8898 (mtpp) cc_final: 0.8446 (tptp) REVERT: G 341 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7482 (tptp) REVERT: G 643 ASN cc_start: 0.8871 (t0) cc_final: 0.8460 (t160) REVERT: G 669 LYS cc_start: 0.8720 (mppt) cc_final: 0.8322 (mppt) REVERT: G 692 THR cc_start: 0.7491 (OUTLIER) cc_final: 0.7188 (m) REVERT: G 763 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8437 (pm20) REVERT: G 823 MET cc_start: 0.7417 (mpp) cc_final: 0.6782 (mmp) REVERT: G 842 ASN cc_start: 0.8343 (t0) cc_final: 0.8107 (t160) outliers start: 59 outliers final: 29 residues processed: 353 average time/residue: 0.6200 time to fit residues: 269.3012 Evaluate side-chains 337 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 621 LYS Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 742 LYS Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 710 LYS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 456 ASP Chi-restraints excluded: chain F residue 485 GLN Chi-restraints excluded: chain F residue 517 VAL Chi-restraints excluded: chain F residue 656 THR Chi-restraints excluded: chain F residue 725 MET Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 485 GLN Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 656 THR Chi-restraints excluded: chain G residue 692 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 64 optimal weight: 0.9980 chunk 379 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 323 optimal weight: 0.5980 chunk 348 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 646 GLN A 732 ASN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 732 ASN F 732 ASN F 842 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.138525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.076101 restraints weight = 51349.647| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.99 r_work: 0.2765 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35770 Z= 0.178 Angle : 0.553 9.804 48496 Z= 0.302 Chirality : 0.045 0.204 5173 Planarity : 0.004 0.054 6377 Dihedral : 5.198 24.685 4739 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.38 % Allowed : 9.65 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.23 (0.12), residues: 4410 helix: 1.00 (0.24), residues: 511 sheet: -0.44 (0.13), residues: 1414 loop : -0.11 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 658 TYR 0.016 0.001 TYR F 441 PHE 0.025 0.002 PHE B 351 TRP 0.015 0.001 TRP D 361 HIS 0.009 0.001 HIS B 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (35770) covalent geometry : angle 0.55294 / 0.30 (48496) hydrogen bonds : bond 0.03643 / 2.44 ( 1498) hydrogen bonds : angle 5.79884 / 4.06 ( 4074) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 310 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8484 (tttp) REVERT: A 351 PHE cc_start: 0.8250 (t80) cc_final: 0.7895 (t80) REVERT: A 371 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7612 (tt0) REVERT: A 525 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8152 (mm) REVERT: A 555 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8281 (mt-10) REVERT: A 640 GLN cc_start: 0.8623 (mt0) cc_final: 0.7738 (mp10) REVERT: A 643 ASN cc_start: 0.8718 (t0) cc_final: 0.8296 (t0) REVERT: A 682 ARG cc_start: 0.7584 (mtt90) cc_final: 0.7360 (mtt90) REVERT: A 823 MET cc_start: 0.8328 (mmm) cc_final: 0.7984 (mmt) REVERT: B 356 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8145 (tttm) REVERT: B 555 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8168 (mt-10) REVERT: B 640 GLN cc_start: 0.8966 (mt0) cc_final: 0.8045 (mp10) REVERT: B 643 ASN cc_start: 0.8877 (t0) cc_final: 0.8244 (t0) REVERT: B 668 ILE cc_start: 0.9450 (mm) cc_final: 0.9189 (mt) REVERT: B 669 LYS cc_start: 0.8969 (mppt) cc_final: 0.8320 (mppt) REVERT: C 287 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8509 (p0) REVERT: C 322 MET cc_start: 0.8253 (mmt) cc_final: 0.7893 (mmt) REVERT: C 371 GLU cc_start: 0.8095 (tt0) cc_final: 0.7711 (tp30) REVERT: C 621 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8185 (ttmm) REVERT: C 643 ASN cc_start: 0.8964 (t0) cc_final: 0.8300 (t0) REVERT: C 742 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7960 (mptt) REVERT: C 823 MET cc_start: 0.7726 (mpp) cc_final: 0.7281 (mmp) REVERT: C 842 ASN cc_start: 0.8371 (t0) cc_final: 0.8049 (t160) REVERT: D 310 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8592 (tttp) REVERT: D 351 PHE cc_start: 0.8328 (t80) cc_final: 0.7955 (t80) REVERT: D 555 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8226 (mt-10) REVERT: D 640 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8585 (mp10) REVERT: D 643 ASN cc_start: 0.8844 (t0) cc_final: 0.8343 (t0) REVERT: D 710 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8685 (mptt) REVERT: D 763 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8347 (pm20) REVERT: E 310 LYS cc_start: 0.8893 (mtpp) cc_final: 0.8522 (tttp) REVERT: E 337 ASP cc_start: 0.8224 (m-30) cc_final: 0.7807 (t0) REVERT: E 338 LEU cc_start: 0.8586 (mt) cc_final: 0.8242 (mm) REVERT: E 341 LYS cc_start: 0.8217 (tptp) cc_final: 0.7736 (tptp) REVERT: E 342 LEU cc_start: 0.8580 (mp) cc_final: 0.8296 (mm) REVERT: E 356 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8079 (tttp) REVERT: E 371 GLU cc_start: 0.8200 (tt0) cc_final: 0.7496 (tm-30) REVERT: E 640 GLN cc_start: 0.9067 (mt0) cc_final: 0.8496 (mp10) REVERT: E 643 ASN cc_start: 0.9055 (t0) cc_final: 0.8484 (t0) REVERT: E 760 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8114 (mmmt) REVERT: E 842 ASN cc_start: 0.8581 (t0) cc_final: 0.8310 (t160) REVERT: F 310 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8647 (tttp) REVERT: F 322 MET cc_start: 0.8405 (mmt) cc_final: 0.8021 (mmt) REVERT: F 363 ASN cc_start: 0.8576 (t0) cc_final: 0.8277 (t0) REVERT: F 371 GLU cc_start: 0.8217 (tt0) cc_final: 0.7786 (tt0) REVERT: F 640 GLN cc_start: 0.9137 (mt0) cc_final: 0.8360 (mp10) REVERT: F 643 ASN cc_start: 0.8823 (t0) cc_final: 0.8450 (t160) REVERT: F 763 GLU cc_start: 0.8672 (tt0) cc_final: 0.8384 (pm20) REVERT: F 823 MET cc_start: 0.8218 (mmp) cc_final: 0.7961 (mmp) REVERT: G 341 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7497 (tptp) REVERT: G 356 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7955 (tttp) REVERT: G 643 ASN cc_start: 0.8864 (t0) cc_final: 0.8461 (t160) REVERT: G 669 LYS cc_start: 0.8701 (mppt) cc_final: 0.8297 (mppt) REVERT: G 692 THR cc_start: 0.7369 (OUTLIER) cc_final: 0.7034 (m) REVERT: G 763 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8444 (pm20) REVERT: G 823 MET cc_start: 0.7438 (mpp) cc_final: 0.6823 (mmp) REVERT: G 842 ASN cc_start: 0.8430 (t0) cc_final: 0.8156 (t160) outliers start: 53 outliers final: 31 residues processed: 345 average time/residue: 0.6049 time to fit residues: 257.1680 Evaluate side-chains 340 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 299 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 621 LYS Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 742 LYS Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 710 LYS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 456 ASP Chi-restraints excluded: chain F residue 485 GLN Chi-restraints excluded: chain F residue 517 VAL Chi-restraints excluded: chain F residue 656 THR Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 356 LYS Chi-restraints excluded: chain G residue 456 ASP Chi-restraints excluded: chain G residue 485 GLN Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 656 THR Chi-restraints excluded: chain G residue 692 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 29 optimal weight: 0.5980 chunk 375 optimal weight: 0.8980 chunk 401 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 285 optimal weight: 0.9980 chunk 394 optimal weight: 6.9990 chunk 274 optimal weight: 0.7980 chunk 61 optimal weight: 20.0000 chunk 404 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 732 ASN B 646 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 732 ASN F 646 GLN ** F 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.139564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.077571 restraints weight = 51296.140| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.99 r_work: 0.2805 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35770 Z= 0.146 Angle : 0.533 10.699 48496 Z= 0.292 Chirality : 0.044 0.211 5173 Planarity : 0.004 0.074 6377 Dihedral : 5.019 23.862 4739 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.22 % Allowed : 10.12 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.24 (0.12), residues: 4410 helix: 1.10 (0.24), residues: 511 sheet: -0.47 (0.13), residues: 1400 loop : -0.13 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 658 TYR 0.014 0.001 TYR C 684 PHE 0.029 0.001 PHE C 351 TRP 0.011 0.001 TRP C 344 HIS 0.009 0.001 HIS B 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (35770) covalent geometry : angle 0.53269 / 0.29 (48496) hydrogen bonds : bond 0.03408 / 2.28 ( 1498) hydrogen bonds : angle 5.68442 / 3.98 ( 4074) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 313 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 PHE cc_start: 0.8223 (t80) cc_final: 0.7889 (t80) REVERT: A 525 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8144 (mm) REVERT: A 555 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8284 (mt-10) REVERT: A 640 GLN cc_start: 0.8666 (mt0) cc_final: 0.7829 (mp10) REVERT: A 643 ASN cc_start: 0.8878 (t0) cc_final: 0.8490 (t0) REVERT: A 682 ARG cc_start: 0.7533 (mtt90) cc_final: 0.7316 (mtt90) REVERT: A 823 MET cc_start: 0.8280 (mmm) cc_final: 0.7982 (mmt) REVERT: B 356 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8182 (tttp) REVERT: B 555 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8158 (mt-10) REVERT: B 640 GLN cc_start: 0.9001 (mt0) cc_final: 0.8100 (mp10) REVERT: B 643 ASN cc_start: 0.8896 (t0) cc_final: 0.8318 (t0) REVERT: B 668 ILE cc_start: 0.9447 (mm) cc_final: 0.9192 (mt) REVERT: B 669 LYS cc_start: 0.8952 (mppt) cc_final: 0.8300 (mppt) REVERT: C 621 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8214 (ttmm) REVERT: C 640 GLN cc_start: 0.9149 (mt0) cc_final: 0.8278 (mp10) REVERT: C 643 ASN cc_start: 0.8941 (t0) cc_final: 0.8284 (t0) REVERT: C 682 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7498 (mtt90) REVERT: C 742 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7925 (mptt) REVERT: C 823 MET cc_start: 0.7724 (mpp) cc_final: 0.7304 (mmp) REVERT: C 842 ASN cc_start: 0.8355 (t0) cc_final: 0.8027 (t160) REVERT: D 310 LYS cc_start: 0.8826 (mtpp) cc_final: 0.8598 (tttp) REVERT: D 351 PHE cc_start: 0.8275 (t80) cc_final: 0.7928 (t80) REVERT: D 555 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8249 (mt-10) REVERT: D 640 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8570 (mp10) REVERT: D 643 ASN cc_start: 0.8838 (t0) cc_final: 0.8334 (t0) REVERT: D 693 ASP cc_start: 0.8865 (m-30) cc_final: 0.8211 (p0) REVERT: D 710 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8573 (mptt) REVERT: D 823 MET cc_start: 0.8071 (mmm) cc_final: 0.7802 (mpm) REVERT: E 310 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8558 (tttp) REVERT: E 322 MET cc_start: 0.8362 (mmt) cc_final: 0.7913 (mmt) REVERT: E 337 ASP cc_start: 0.8163 (m-30) cc_final: 0.7833 (t0) REVERT: E 341 LYS cc_start: 0.8187 (tptp) cc_final: 0.7712 (tptp) REVERT: E 356 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8130 (tttp) REVERT: E 371 GLU cc_start: 0.8076 (tt0) cc_final: 0.7769 (tt0) REVERT: E 640 GLN cc_start: 0.9011 (mt0) cc_final: 0.8457 (mp10) REVERT: E 643 ASN cc_start: 0.9039 (t0) cc_final: 0.8412 (t0) REVERT: E 760 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8207 (mmmt) REVERT: E 842 ASN cc_start: 0.8598 (t0) cc_final: 0.8324 (t160) REVERT: F 310 LYS cc_start: 0.8899 (mtpp) cc_final: 0.8621 (tttp) REVERT: F 322 MET cc_start: 0.8395 (mmt) cc_final: 0.8007 (mmt) REVERT: F 363 ASN cc_start: 0.8585 (t0) cc_final: 0.8266 (t0) REVERT: F 371 GLU cc_start: 0.8191 (tt0) cc_final: 0.7774 (tt0) REVERT: F 640 GLN cc_start: 0.9131 (mt0) cc_final: 0.8465 (mp10) REVERT: F 643 ASN cc_start: 0.8800 (t0) cc_final: 0.8435 (t160) REVERT: F 763 GLU cc_start: 0.8650 (tt0) cc_final: 0.8405 (pm20) REVERT: F 823 MET cc_start: 0.8188 (mmp) cc_final: 0.7935 (mmp) REVERT: G 310 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8628 (tptp) REVERT: G 341 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7581 (tptp) REVERT: G 356 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7957 (tttp) REVERT: G 640 GLN cc_start: 0.8973 (mp10) cc_final: 0.8163 (mp10) REVERT: G 643 ASN cc_start: 0.8873 (t0) cc_final: 0.8468 (t160) REVERT: G 669 LYS cc_start: 0.8659 (mppt) cc_final: 0.8238 (mppt) REVERT: G 692 THR cc_start: 0.7185 (OUTLIER) cc_final: 0.6807 (m) REVERT: G 823 MET cc_start: 0.7425 (mpp) cc_final: 0.6822 (mmp) REVERT: G 842 ASN cc_start: 0.8438 (t0) cc_final: 0.8186 (t160) outliers start: 47 outliers final: 26 residues processed: 346 average time/residue: 0.5773 time to fit residues: 247.7178 Evaluate side-chains 332 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 297 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 621 LYS Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 742 LYS Chi-restraints excluded: chain D residue 376 SER Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 710 LYS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 642 HIS Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 456 ASP Chi-restraints excluded: chain F residue 485 GLN Chi-restraints excluded: chain F residue 517 VAL Chi-restraints excluded: chain F residue 656 THR Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 356 LYS Chi-restraints excluded: chain G residue 456 ASP Chi-restraints excluded: chain G residue 485 GLN Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 656 THR Chi-restraints excluded: chain G residue 692 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 126 optimal weight: 7.9990 chunk 357 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 264 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 425 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 283 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 732 ASN A 842 ASN A 852 HIS ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 732 ASN E 330 ASN F 842 ASN G 378 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.137312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074110 restraints weight = 51394.903| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.97 r_work: 0.2723 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 35770 Z= 0.264 Angle : 0.598 10.139 48496 Z= 0.324 Chirality : 0.046 0.240 5173 Planarity : 0.004 0.081 6377 Dihedral : 5.251 25.576 4739 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.96 % Allowed : 10.56 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.26 (0.12), residues: 4410 helix: 0.87 (0.24), residues: 518 sheet: -0.39 (0.13), residues: 1421 loop : -0.15 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 658 TYR 0.022 0.002 TYR G 441 PHE 0.027 0.002 PHE B 351 TRP 0.011 0.001 TRP D 361 HIS 0.009 0.001 HIS B 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.26 (35770) covalent geometry : angle 0.59798 / 0.32 (48496) hydrogen bonds : bond 0.03993 / 2.68 ( 1498) hydrogen bonds : angle 5.74170 / 4.02 ( 4074) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 300 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8967 (mtpp) cc_final: 0.8596 (tttp) REVERT: A 351 PHE cc_start: 0.8288 (t80) cc_final: 0.7941 (t80) REVERT: A 371 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7654 (tt0) REVERT: A 555 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8333 (mt-10) REVERT: A 640 GLN cc_start: 0.8660 (mt0) cc_final: 0.7779 (mp10) REVERT: A 643 ASN cc_start: 0.8836 (t0) cc_final: 0.8434 (t0) REVERT: A 682 ARG cc_start: 0.7599 (mtt90) cc_final: 0.7376 (mtt90) REVERT: A 823 MET cc_start: 0.8285 (mmm) cc_final: 0.7945 (mmt) REVERT: B 356 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8162 (tttm) REVERT: B 555 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8228 (mt-10) REVERT: B 640 GLN cc_start: 0.8997 (mt0) cc_final: 0.8089 (mp10) REVERT: B 643 ASN cc_start: 0.8895 (t0) cc_final: 0.8325 (t0) REVERT: B 668 ILE cc_start: 0.9471 (mm) cc_final: 0.9159 (mt) REVERT: B 669 LYS cc_start: 0.8985 (mppt) cc_final: 0.8332 (mppt) REVERT: C 621 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8163 (ttmm) REVERT: C 640 GLN cc_start: 0.9152 (mt0) cc_final: 0.8271 (mp10) REVERT: C 643 ASN cc_start: 0.8938 (t0) cc_final: 0.8284 (t0) REVERT: C 682 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7548 (mtt90) REVERT: C 823 MET cc_start: 0.7709 (mpp) cc_final: 0.7274 (mmp) REVERT: C 842 ASN cc_start: 0.8350 (t0) cc_final: 0.8023 (t160) REVERT: D 310 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8597 (tttp) REVERT: D 351 PHE cc_start: 0.8307 (t80) cc_final: 0.7940 (t80) REVERT: D 555 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8280 (mt-10) REVERT: D 640 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8592 (mp10) REVERT: D 643 ASN cc_start: 0.8838 (t0) cc_final: 0.8354 (t0) REVERT: D 710 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8641 (mptt) REVERT: D 823 MET cc_start: 0.8026 (mmm) cc_final: 0.7530 (mpm) REVERT: E 322 MET cc_start: 0.8530 (mmt) cc_final: 0.7998 (mmt) REVERT: E 337 ASP cc_start: 0.8228 (m-30) cc_final: 0.7883 (t0) REVERT: E 356 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8177 (tttp) REVERT: E 371 GLU cc_start: 0.8259 (tt0) cc_final: 0.7889 (tt0) REVERT: E 619 ASP cc_start: 0.8058 (p0) cc_final: 0.7825 (p0) REVERT: E 640 GLN cc_start: 0.9007 (mt0) cc_final: 0.8442 (mp10) REVERT: E 643 ASN cc_start: 0.8999 (t0) cc_final: 0.8377 (t0) REVERT: E 842 ASN cc_start: 0.8536 (t0) cc_final: 0.8292 (t160) REVERT: F 310 LYS cc_start: 0.8926 (mtpp) cc_final: 0.8629 (tttp) REVERT: F 363 ASN cc_start: 0.8636 (t0) cc_final: 0.8320 (t0) REVERT: F 371 GLU cc_start: 0.8215 (tt0) cc_final: 0.7670 (tt0) REVERT: F 477 GLU cc_start: 0.7707 (pt0) cc_final: 0.7079 (tt0) REVERT: F 640 GLN cc_start: 0.9145 (mt0) cc_final: 0.8477 (mp10) REVERT: F 643 ASN cc_start: 0.8790 (t0) cc_final: 0.8446 (t160) REVERT: F 763 GLU cc_start: 0.8634 (tt0) cc_final: 0.8349 (pm20) REVERT: F 823 MET cc_start: 0.8225 (mmp) cc_final: 0.7893 (mmp) REVERT: G 310 LYS cc_start: 0.8988 (mtpp) cc_final: 0.8632 (tptp) REVERT: G 341 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7653 (tptp) REVERT: G 356 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7970 (tttp) REVERT: G 371 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7459 (tm-30) REVERT: G 643 ASN cc_start: 0.8833 (t0) cc_final: 0.8543 (t160) REVERT: G 669 LYS cc_start: 0.8704 (mppt) cc_final: 0.8300 (mppt) REVERT: G 692 THR cc_start: 0.7336 (OUTLIER) cc_final: 0.6980 (m) REVERT: G 823 MET cc_start: 0.7385 (mpp) cc_final: 0.6742 (mmp) outliers start: 37 outliers final: 25 residues processed: 328 average time/residue: 0.5973 time to fit residues: 241.0717 Evaluate side-chains 320 residues out of total 3864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 288 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 621 LYS Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 710 LYS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 456 ASP Chi-restraints excluded: chain F residue 485 GLN Chi-restraints excluded: chain F residue 517 VAL Chi-restraints excluded: chain F residue 656 THR Chi-restraints excluded: chain G residue 287 ASP Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 356 LYS Chi-restraints excluded: chain G residue 372 SER Chi-restraints excluded: chain G residue 456 ASP Chi-restraints excluded: chain G residue 485 GLN Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 656 THR Chi-restraints excluded: chain G residue 692 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 401 optimal weight: 1.9990 chunk 409 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 384 optimal weight: 0.6980 chunk 406 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 732 ASN A 842 ASN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN D 660 ASN D 732 ASN E 330 ASN G 378 GLN G 643 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.138845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.076402 restraints weight = 51235.612| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.98 r_work: 0.2774 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35770 Z= 0.166 Angle : 0.552 10.462 48496 Z= 0.301 Chirality : 0.044 0.239 5173 Planarity : 0.004 0.086 6377 Dihedral : 5.061 24.374 4739 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.07 % Allowed : 10.62 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.24 (0.12), residues: 4410 helix: 1.04 (0.24), residues: 511 sheet: -0.47 (0.13), residues: 1400 loop : -0.10 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 658 TYR 0.016 0.001 TYR C 684 PHE 0.027 0.001 PHE C 351 TRP 0.010 0.001 TRP D 361 HIS 0.008 0.001 HIS B 852 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (35770) covalent geometry : angle 0.55234 / 0.30 (48496) hydrogen bonds : bond 0.03539 / 2.37 ( 1498) hydrogen bonds : angle 5.70843 / 4.00 ( 4074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20990.36 seconds wall clock time: 356 minutes 23.58 seconds (21383.58 seconds total)