Starting phenix.real_space_refine on Tue May 5 03:56:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvo_42625/05_2026/8uvo_42625.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvo_42625/05_2026/8uvo_42625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uvo_42625/05_2026/8uvo_42625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvo_42625/05_2026/8uvo_42625.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvo_42625/05_2026/8uvo_42625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvo_42625/05_2026/8uvo_42625.cif" } resolution = 3.22 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= 0.003 sd= 0.692 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 138 5.16 5 C 16404 2.51 5 N 4656 2.21 5 O 4968 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26202 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4277 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 30, 'TRANS': 518} Chain breaks: 2 Chain: "B" Number of atoms: 4277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4277 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 30, 'TRANS': 518} Chain breaks: 2 Chain: "C" Number of atoms: 4277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4277 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 30, 'TRANS': 518} Chain breaks: 2 Chain: "D" Number of atoms: 4277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4277 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 30, 'TRANS': 518} Chain breaks: 2 Chain: "E" Number of atoms: 4277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4277 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 30, 'TRANS': 518} Chain breaks: 2 Chain: "F" Number of atoms: 4277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4277 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 30, 'TRANS': 518} Chain breaks: 2 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {'ADP': 2, 'XNU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {'ADP': 2, 'XNU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {'ADP': 2, 'XNU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {'ADP': 2, 'XNU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {'ADP': 2, 'XNU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {'ADP': 2, 'XNU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.83, per 1000 atoms: 0.22 Number of scatterers: 26202 At special positions: 0 Unit cell: (163.28, 152.88, 95.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 138 16.00 P 24 15.00 F 12 9.00 O 4968 8.00 N 4656 7.00 C 16404 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: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6132 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 12 sheets defined 62.7% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 210 through 226 removed outlier: 4.019A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 removed outlier: 4.493A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.680A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.663A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.611A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 335 removed outlier: 3.567A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.576A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.955A pdb=" N ARG A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 359' Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 386 through 389 removed outlier: 4.639A pdb=" N LYS A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.741A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.508A pdb=" N TRP A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.711A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.558A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.503A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 587 through 591 Processing helix chain 'A' and resid 598 through 611 removed outlier: 3.687A pdb=" N ASN A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 649 through 662 removed outlier: 3.945A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.580A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 715 Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.703A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 763 Processing helix chain 'B' and resid 210 through 226 removed outlier: 4.009A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.491A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.676A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.630A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.609A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 335 removed outlier: 3.624A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.577A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.963A pdb=" N ARG B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 359' Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 386 through 389 removed outlier: 4.640A pdb=" N LYS B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 397 through 403 Processing helix chain 'B' and resid 407 through 426 Processing helix chain 'B' and resid 438 through 444 removed outlier: 3.737A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.507A pdb=" N TRP B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.708A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 543 through 554 removed outlier: 3.563A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 554 " --> pdb=" O MET B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 587 through 591 Processing helix chain 'B' and resid 598 through 611 removed outlier: 3.690A pdb=" N ASN B 602 " --> pdb=" O ASP B 598 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 649 through 662 removed outlier: 3.949A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.585A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 715 Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.696A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 Processing helix chain 'C' and resid 210 through 226 removed outlier: 4.009A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.493A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.699A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.636A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.606A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 335 removed outlier: 3.588A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.579A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.956A pdb=" N ARG C 358 " --> pdb=" O ASP C 354 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG C 359 " --> pdb=" O PRO C 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 354 through 359' Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 386 through 389 removed outlier: 4.637A pdb=" N LYS C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'C' and resid 397 through 403 Processing helix chain 'C' and resid 407 through 426 Processing helix chain 'C' and resid 438 through 444 removed outlier: 3.746A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.521A pdb=" N TRP C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 499 removed outlier: 4.343A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.716A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 543 through 554 removed outlier: 3.558A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 554 " --> pdb=" O MET C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.500A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 587 through 591 Processing helix chain 'C' and resid 598 through 611 removed outlier: 3.683A pdb=" N ASN C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 649 through 662 removed outlier: 3.940A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.583A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 715 Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.693A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'D' and resid 210 through 226 removed outlier: 4.008A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.499A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 277 removed outlier: 3.683A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.665A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.611A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 335 removed outlier: 3.593A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.577A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.956A pdb=" N ARG D 358 " --> pdb=" O ASP D 354 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 359 " --> pdb=" O PRO D 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 354 through 359' Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 386 through 389 removed outlier: 4.637A pdb=" N LYS D 389 " --> pdb=" O LYS D 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 386 through 389' Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 407 through 426 Processing helix chain 'D' and resid 438 through 444 removed outlier: 3.741A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.511A pdb=" N TRP D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 506 removed outlier: 3.710A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.557A pdb=" N LEU D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.505A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 587 through 591 Processing helix chain 'D' and resid 598 through 611 removed outlier: 3.683A pdb=" N ASN D 602 " --> pdb=" O ASP D 598 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 649 through 662 removed outlier: 3.945A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.580A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 715 Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.703A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 763 Processing helix chain 'E' and resid 210 through 226 removed outlier: 4.011A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 4.495A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 271 through 277 removed outlier: 3.679A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.630A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.611A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 335 removed outlier: 3.591A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.576A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.959A pdb=" N ARG E 358 " --> pdb=" O ASP E 354 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG E 359 " --> pdb=" O PRO E 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 354 through 359' Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 386 through 389 removed outlier: 4.641A pdb=" N LYS E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 386 through 389' Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 407 through 426 Processing helix chain 'E' and resid 438 through 444 removed outlier: 3.737A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER E 444 " --> pdb=" O GLU E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.505A pdb=" N TRP E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.710A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.561A pdb=" N LEU E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 569 Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 587 through 591 Processing helix chain 'E' and resid 598 through 611 removed outlier: 3.690A pdb=" N ASN E 602 " --> pdb=" O ASP E 598 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 634 Processing helix chain 'E' and resid 649 through 662 removed outlier: 3.949A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.584A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 715 Processing helix chain 'E' and resid 732 through 743 removed outlier: 3.695A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 763 Processing helix chain 'F' and resid 210 through 226 removed outlier: 4.007A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.497A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 271 through 277 removed outlier: 3.692A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.637A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.607A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 335 removed outlier: 3.589A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.581A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.956A pdb=" N ARG F 358 " --> pdb=" O ASP F 354 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG F 359 " --> pdb=" O PRO F 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 354 through 359' Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 386 through 389 removed outlier: 4.634A pdb=" N LYS F 389 " --> pdb=" O LYS F 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 386 through 389' Processing helix chain 'F' and resid 397 through 403 Processing helix chain 'F' and resid 407 through 426 Processing helix chain 'F' and resid 438 through 444 removed outlier: 3.746A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.520A pdb=" N TRP F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 499 removed outlier: 4.362A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.716A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 554 removed outlier: 3.559A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU F 554 " --> pdb=" O MET F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 569 Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 587 through 591 Processing helix chain 'F' and resid 598 through 611 removed outlier: 3.685A pdb=" N ASN F 602 " --> pdb=" O ASP F 598 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 634 Processing helix chain 'F' and resid 649 through 662 removed outlier: 3.945A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.583A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 715 Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.693A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 763 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 3.578A pdb=" N PHE A 267 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 347 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 469 through 470 removed outlier: 4.392A pdb=" N GLU A 470 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 643 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 270 removed outlier: 3.578A pdb=" N PHE B 267 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 347 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 469 through 470 removed outlier: 4.397A pdb=" N GLU B 470 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE B 643 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 270 removed outlier: 3.572A pdb=" N PHE C 267 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 347 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 469 through 470 removed outlier: 4.427A pdb=" N GLU C 470 " --> pdb=" O PHE C 539 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE C 643 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 270 removed outlier: 3.578A pdb=" N PHE D 267 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR D 347 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 469 through 470 removed outlier: 4.395A pdb=" N GLU D 470 " --> pdb=" O PHE D 539 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D 643 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 270 removed outlier: 3.580A pdb=" N PHE E 267 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR E 347 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 469 through 470 removed outlier: 4.386A pdb=" N GLU E 470 " --> pdb=" O PHE E 539 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE E 643 " --> pdb=" O LEU E 515 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 265 through 270 removed outlier: 3.576A pdb=" N PHE F 267 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR F 347 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 469 through 470 removed outlier: 4.409A pdb=" N GLU F 470 " --> pdb=" O PHE F 539 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE F 643 " --> pdb=" O LEU F 515 " (cutoff:3.500A) 1327 hydrogen bonds defined for protein. 3801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.29 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4543 1.31 - 1.44: 6329 1.44 - 1.57: 15504 1.57 - 1.70: 48 1.70 - 1.83: 234 Bond restraints: 26658 Sorted by residual: bond pdb=" C22 XNU A 903 " pdb=" C23 XNU A 903 " ideal model delta sigma weight residual 1.532 1.347 0.185 2.00e-02 2.50e+03 8.52e+01 bond pdb=" C22 XNU D 903 " pdb=" C23 XNU D 903 " ideal model delta sigma weight residual 1.532 1.348 0.184 2.00e-02 2.50e+03 8.49e+01 bond pdb=" C22 XNU B 903 " pdb=" C23 XNU B 903 " ideal model delta sigma weight residual 1.532 1.348 0.184 2.00e-02 2.50e+03 8.49e+01 bond pdb=" C22 XNU F 903 " pdb=" C23 XNU F 903 " ideal model delta sigma weight residual 1.532 1.348 0.184 2.00e-02 2.50e+03 8.44e+01 bond pdb=" C22 XNU C 903 " pdb=" C23 XNU C 903 " ideal model delta sigma weight residual 1.532 1.349 0.183 2.00e-02 2.50e+03 8.40e+01 ... (remaining 26653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 34687 1.66 - 3.31: 997 3.31 - 4.97: 232 4.97 - 6.62: 78 6.62 - 8.28: 24 Bond angle restraints: 36018 Sorted by residual: angle pdb=" C GLY D 481 " pdb=" N LEU D 482 " pdb=" CA LEU D 482 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C GLY B 481 " pdb=" N LEU B 482 " pdb=" CA LEU B 482 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C GLY E 481 " pdb=" N LEU E 482 " pdb=" CA LEU E 482 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C GLY F 481 " pdb=" N LEU F 482 " pdb=" CA LEU F 482 " ideal model delta sigma weight residual 121.54 127.74 -6.20 1.91e+00 2.74e-01 1.05e+01 angle pdb=" C GLY A 481 " pdb=" N LEU A 482 " pdb=" CA LEU A 482 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 ... (remaining 36013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.50: 15725 30.50 - 61.00: 595 61.00 - 91.50: 78 91.50 - 122.00: 3 122.00 - 152.50: 27 Dihedral angle restraints: 16428 sinusoidal: 6984 harmonic: 9444 Sorted by residual: dihedral pdb=" CA ALA A 297 " pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta harmonic sigma weight residual 180.00 126.22 53.78 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA ALA E 297 " pdb=" C ALA E 297 " pdb=" N PRO E 298 " pdb=" CA PRO E 298 " ideal model delta harmonic sigma weight residual 180.00 126.27 53.73 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA ALA F 297 " pdb=" C ALA F 297 " pdb=" N PRO F 298 " pdb=" CA PRO F 298 " ideal model delta harmonic sigma weight residual 180.00 126.29 53.71 0 5.00e+00 4.00e-02 1.15e+02 ... (remaining 16425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2498 0.029 - 0.059: 920 0.059 - 0.088: 346 0.088 - 0.117: 168 0.117 - 0.147: 52 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CA ILE F 371 " pdb=" N ILE F 371 " pdb=" C ILE F 371 " pdb=" CB ILE F 371 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA ILE C 371 " pdb=" N ILE C 371 " pdb=" C ILE C 371 " pdb=" CB ILE C 371 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE D 371 " pdb=" N ILE D 371 " pdb=" C ILE D 371 " pdb=" CB ILE D 371 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 3981 not shown) Planarity restraints: 4710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 271 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO C 272 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 272 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 272 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 271 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO F 272 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO F 272 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 272 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 271 " -0.045 5.00e-02 4.00e+02 6.83e-02 7.46e+00 pdb=" N PRO D 272 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 272 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 272 " -0.038 5.00e-02 4.00e+02 ... (remaining 4707 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 66 2.34 - 2.98: 13872 2.98 - 3.62: 41138 3.62 - 4.26: 58774 4.26 - 4.90: 98456 Nonbonded interactions: 212306 Sorted by model distance: nonbonded pdb=" C21 XNU F 903 " pdb=" C22 XNU F 903 " model vdw 1.696 3.860 nonbonded pdb=" C21 XNU B 903 " pdb=" C22 XNU B 903 " model vdw 1.697 3.860 nonbonded pdb=" C21 XNU E 903 " pdb=" C22 XNU E 903 " model vdw 1.697 3.860 nonbonded pdb=" C21 XNU A 903 " pdb=" C22 XNU A 903 " model vdw 1.697 3.860 nonbonded pdb=" C21 XNU C 903 " pdb=" C22 XNU C 903 " model vdw 1.697 3.860 ... (remaining 212301 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.770 Find NCS groups from input model: 0.240 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.007 0.185 26658 Z= 0.321 Angle : 0.737 8.277 36018 Z= 0.351 Chirality : 0.040 0.147 3984 Planarity : 0.005 0.069 4710 Dihedral : 17.203 152.504 10296 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.03 % 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: 0.19 (0.16), residues: 3258 helix: 1.15 (0.13), residues: 1728 sheet: -2.04 (0.29), residues: 354 loop : -0.58 (0.20), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 560 TYR 0.005 0.001 TYR F 517 PHE 0.007 0.001 PHE B 506 TRP 0.004 0.001 TRP A 454 HIS 0.003 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00658 (26658) covalent geometry : angle 0.73727 (36018) hydrogen bonds : bond 0.16735 ( 1327) hydrogen bonds : angle 5.82543 ( 3801) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 825 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8564 (pttt) REVERT: A 253 LEU cc_start: 0.8428 (tp) cc_final: 0.8182 (tp) REVERT: A 317 HIS cc_start: 0.7114 (t-90) cc_final: 0.6535 (t70) REVERT: A 319 GLU cc_start: 0.7556 (pp20) cc_final: 0.7345 (tm-30) REVERT: A 366 GLU cc_start: 0.8690 (mp0) cc_final: 0.8018 (mp0) REVERT: A 388 MET cc_start: 0.9219 (tpp) cc_final: 0.8409 (mtt) REVERT: A 415 CYS cc_start: 0.8826 (t) cc_final: 0.8581 (t) REVERT: A 460 ASN cc_start: 0.9012 (p0) cc_final: 0.8616 (p0) REVERT: A 486 LYS cc_start: 0.8455 (mtpp) cc_final: 0.7955 (mtmm) REVERT: A 508 MET cc_start: 0.8696 (tmm) cc_final: 0.8431 (tmm) REVERT: A 561 GLU cc_start: 0.8552 (tt0) cc_final: 0.8283 (tt0) REVERT: A 577 ASP cc_start: 0.8452 (t0) cc_final: 0.8080 (t0) REVERT: A 578 GLU cc_start: 0.8688 (mt-10) cc_final: 0.7765 (mt-10) REVERT: A 615 LYS cc_start: 0.9259 (pttt) cc_final: 0.8742 (ptmm) REVERT: A 616 ASN cc_start: 0.7791 (t0) cc_final: 0.7232 (t0) REVERT: A 649 ASP cc_start: 0.8289 (t70) cc_final: 0.7977 (t0) REVERT: A 712 GLU cc_start: 0.7951 (tp30) cc_final: 0.7670 (tm-30) REVERT: A 756 GLU cc_start: 0.8379 (tp30) cc_final: 0.7725 (pt0) REVERT: B 205 ASP cc_start: 0.8586 (t0) cc_final: 0.8032 (t0) REVERT: B 217 LYS cc_start: 0.8073 (tmtt) cc_final: 0.7809 (ttpt) REVERT: B 236 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8598 (pttt) REVERT: B 253 LEU cc_start: 0.8693 (tp) cc_final: 0.8429 (tp) REVERT: B 270 ASN cc_start: 0.8071 (t0) cc_final: 0.7798 (t0) REVERT: B 304 ASP cc_start: 0.8829 (t0) cc_final: 0.8554 (t0) REVERT: B 305 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7925 (mm-30) REVERT: B 317 HIS cc_start: 0.6896 (t-90) cc_final: 0.6230 (t70) REVERT: B 366 GLU cc_start: 0.8587 (mp0) cc_final: 0.8085 (mp0) REVERT: B 388 MET cc_start: 0.9033 (tpp) cc_final: 0.8456 (mtp) REVERT: B 460 ASN cc_start: 0.9068 (p0) cc_final: 0.8794 (p0) REVERT: B 486 LYS cc_start: 0.8688 (mtpp) cc_final: 0.8166 (mtmm) REVERT: B 508 MET cc_start: 0.8633 (tmm) cc_final: 0.8215 (tmm) REVERT: B 561 GLU cc_start: 0.8599 (tt0) cc_final: 0.8368 (tt0) REVERT: B 578 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8015 (mt-10) REVERT: B 607 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7249 (mm-30) REVERT: B 615 LYS cc_start: 0.9183 (pttt) cc_final: 0.8691 (ptmm) REVERT: B 649 ASP cc_start: 0.8053 (t70) cc_final: 0.7775 (t0) REVERT: B 712 GLU cc_start: 0.8023 (tp30) cc_final: 0.7788 (tm-30) REVERT: B 752 ILE cc_start: 0.8887 (tt) cc_final: 0.8375 (tt) REVERT: B 756 GLU cc_start: 0.8408 (tp30) cc_final: 0.7819 (pt0) REVERT: C 217 LYS cc_start: 0.8114 (tmtt) cc_final: 0.7844 (ttpt) REVERT: C 236 LYS cc_start: 0.9138 (mmmt) cc_final: 0.8640 (pttt) REVERT: C 253 LEU cc_start: 0.8680 (tp) cc_final: 0.8421 (tp) REVERT: C 317 HIS cc_start: 0.6909 (t-90) cc_final: 0.6204 (t70) REVERT: C 366 GLU cc_start: 0.8563 (mp0) cc_final: 0.8059 (mp0) REVERT: C 388 MET cc_start: 0.9108 (tpp) cc_final: 0.8311 (mtt) REVERT: C 508 MET cc_start: 0.8503 (tmm) cc_final: 0.8103 (tmm) REVERT: C 550 MET cc_start: 0.8563 (tpp) cc_final: 0.8351 (mmt) REVERT: C 561 GLU cc_start: 0.8549 (tt0) cc_final: 0.8306 (tt0) REVERT: C 577 ASP cc_start: 0.8386 (t0) cc_final: 0.7930 (t0) REVERT: C 578 GLU cc_start: 0.8665 (mt-10) cc_final: 0.7824 (mt-10) REVERT: C 607 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7531 (mm-30) REVERT: C 615 LYS cc_start: 0.9319 (pttt) cc_final: 0.8791 (ptmm) REVERT: C 678 MET cc_start: 0.6684 (ttt) cc_final: 0.6435 (ttm) REVERT: C 752 ILE cc_start: 0.8819 (tt) cc_final: 0.8294 (tt) REVERT: C 756 GLU cc_start: 0.8410 (tp30) cc_final: 0.7839 (pt0) REVERT: D 236 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8571 (pttt) REVERT: D 253 LEU cc_start: 0.8493 (tp) cc_final: 0.8241 (tp) REVERT: D 317 HIS cc_start: 0.7061 (t-90) cc_final: 0.6250 (t70) REVERT: D 366 GLU cc_start: 0.8693 (mp0) cc_final: 0.8021 (mp0) REVERT: D 388 MET cc_start: 0.9178 (tpp) cc_final: 0.8389 (mtt) REVERT: D 415 CYS cc_start: 0.8850 (t) cc_final: 0.8602 (t) REVERT: D 460 ASN cc_start: 0.8993 (p0) cc_final: 0.8595 (p0) REVERT: D 486 LYS cc_start: 0.8491 (mtpp) cc_final: 0.7987 (mtmm) REVERT: D 508 MET cc_start: 0.8668 (tmm) cc_final: 0.8429 (tmm) REVERT: D 561 GLU cc_start: 0.8575 (tt0) cc_final: 0.8310 (tt0) REVERT: D 577 ASP cc_start: 0.8456 (t0) cc_final: 0.8087 (t0) REVERT: D 578 GLU cc_start: 0.8689 (mt-10) cc_final: 0.7773 (mt-10) REVERT: D 616 ASN cc_start: 0.7858 (t0) cc_final: 0.7296 (t0) REVERT: D 712 GLU cc_start: 0.7955 (tp30) cc_final: 0.7673 (tm-30) REVERT: D 752 ILE cc_start: 0.8583 (tt) cc_final: 0.8188 (tt) REVERT: D 756 GLU cc_start: 0.8368 (tp30) cc_final: 0.7717 (pt0) REVERT: E 205 ASP cc_start: 0.8583 (t0) cc_final: 0.8011 (t0) REVERT: E 217 LYS cc_start: 0.8076 (tmtt) cc_final: 0.7809 (ttpt) REVERT: E 236 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8591 (pttt) REVERT: E 253 LEU cc_start: 0.8701 (tp) cc_final: 0.8440 (tp) REVERT: E 270 ASN cc_start: 0.8074 (t0) cc_final: 0.7805 (t0) REVERT: E 304 ASP cc_start: 0.8840 (t0) cc_final: 0.8558 (t0) REVERT: E 305 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7928 (mm-30) REVERT: E 317 HIS cc_start: 0.6849 (t-90) cc_final: 0.6116 (t70) REVERT: E 366 GLU cc_start: 0.8578 (mp0) cc_final: 0.8066 (mp0) REVERT: E 388 MET cc_start: 0.9006 (tpp) cc_final: 0.8405 (mtp) REVERT: E 460 ASN cc_start: 0.9051 (p0) cc_final: 0.8722 (p0) REVERT: E 486 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8153 (mtmm) REVERT: E 508 MET cc_start: 0.8606 (tmm) cc_final: 0.8204 (tmm) REVERT: E 561 GLU cc_start: 0.8589 (tt0) cc_final: 0.8361 (tt0) REVERT: E 578 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8025 (mt-10) REVERT: E 607 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7212 (mm-30) REVERT: E 615 LYS cc_start: 0.9196 (pttt) cc_final: 0.8702 (ptmm) REVERT: E 649 ASP cc_start: 0.8059 (t70) cc_final: 0.7782 (t0) REVERT: E 712 GLU cc_start: 0.8070 (tp30) cc_final: 0.7786 (tm-30) REVERT: E 752 ILE cc_start: 0.8884 (tt) cc_final: 0.8369 (tt) REVERT: E 756 GLU cc_start: 0.8426 (tp30) cc_final: 0.7843 (pt0) REVERT: F 217 LYS cc_start: 0.8045 (tmtt) cc_final: 0.7770 (ttpt) REVERT: F 236 LYS cc_start: 0.9120 (mmmt) cc_final: 0.8583 (pttt) REVERT: F 253 LEU cc_start: 0.8540 (tp) cc_final: 0.8282 (tp) REVERT: F 317 HIS cc_start: 0.6914 (t-90) cc_final: 0.6471 (t-90) REVERT: F 366 GLU cc_start: 0.8595 (mp0) cc_final: 0.8045 (mp0) REVERT: F 388 MET cc_start: 0.9187 (tpp) cc_final: 0.8340 (mtt) REVERT: F 508 MET cc_start: 0.8524 (tmm) cc_final: 0.8090 (tmm) REVERT: F 561 GLU cc_start: 0.8518 (tt0) cc_final: 0.8270 (tt0) REVERT: F 577 ASP cc_start: 0.8491 (t0) cc_final: 0.7976 (t0) REVERT: F 578 GLU cc_start: 0.8661 (mt-10) cc_final: 0.7740 (mt-10) REVERT: F 607 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7485 (mm-30) REVERT: F 615 LYS cc_start: 0.9314 (pttt) cc_final: 0.8784 (ptmm) REVERT: F 678 MET cc_start: 0.6663 (ttt) cc_final: 0.6410 (ttm) REVERT: F 752 ILE cc_start: 0.8717 (tt) cc_final: 0.8205 (tt) REVERT: F 756 GLU cc_start: 0.8423 (tp30) cc_final: 0.7821 (pt0) outliers start: 0 outliers final: 0 residues processed: 825 average time/residue: 0.1967 time to fit residues: 248.1559 Evaluate side-chains 644 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 644 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 226 HIS ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 458 GLN C 215 GLN C 226 HIS ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN C 404 HIS C 458 GLN C 533 ASN D 215 GLN D 226 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN E 226 HIS ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS E 458 GLN E 533 ASN F 215 GLN F 226 HIS ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN F 404 HIS F 458 GLN F 533 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.134973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108701 restraints weight = 40335.809| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.80 r_work: 0.3183 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26658 Z= 0.155 Angle : 0.757 7.218 36018 Z= 0.365 Chirality : 0.045 0.195 3984 Planarity : 0.006 0.067 4710 Dihedral : 12.917 152.729 3786 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.01 % Allowed : 12.39 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.03 (0.15), residues: 3258 helix: 0.85 (0.12), residues: 1776 sheet: -1.94 (0.28), residues: 354 loop : -0.61 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 349 TYR 0.011 0.002 TYR E 244 PHE 0.014 0.001 PHE B 682 TRP 0.005 0.001 TRP B 476 HIS 0.003 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00353 (26658) covalent geometry : angle 0.75724 (36018) hydrogen bonds : bond 0.04551 ( 1327) hydrogen bonds : angle 4.89764 ( 3801) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 682 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.9018 (mmmt) cc_final: 0.8500 (pttt) REVERT: A 273 GLU cc_start: 0.8113 (pp20) cc_final: 0.7673 (tp30) REVERT: A 317 HIS cc_start: 0.6916 (t-90) cc_final: 0.6309 (t-90) REVERT: A 319 GLU cc_start: 0.7528 (pp20) cc_final: 0.7218 (tm-30) REVERT: A 366 GLU cc_start: 0.8855 (mp0) cc_final: 0.8174 (mp0) REVERT: A 388 MET cc_start: 0.9333 (tpp) cc_final: 0.8364 (mtt) REVERT: A 458 GLN cc_start: 0.7728 (tt0) cc_final: 0.7122 (tt0) REVERT: A 460 ASN cc_start: 0.9043 (p0) cc_final: 0.8623 (p0) REVERT: A 486 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8038 (mtmm) REVERT: A 488 GLU cc_start: 0.8529 (tp30) cc_final: 0.8267 (tp30) REVERT: A 577 ASP cc_start: 0.8448 (t0) cc_final: 0.7897 (t0) REVERT: A 578 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7812 (mt-10) REVERT: A 607 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7808 (mm-30) REVERT: A 616 ASN cc_start: 0.7531 (t0) cc_final: 0.6911 (t0) REVERT: A 649 ASP cc_start: 0.8219 (t70) cc_final: 0.7941 (t0) REVERT: A 712 GLU cc_start: 0.7948 (tp30) cc_final: 0.7674 (tm-30) REVERT: A 756 GLU cc_start: 0.8325 (tp30) cc_final: 0.7514 (pt0) REVERT: B 205 ASP cc_start: 0.8503 (t0) cc_final: 0.7928 (t0) REVERT: B 236 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8467 (pttt) REVERT: B 253 LEU cc_start: 0.8251 (tp) cc_final: 0.7818 (tp) REVERT: B 305 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8000 (mm-30) REVERT: B 317 HIS cc_start: 0.6862 (t-90) cc_final: 0.6229 (t-90) REVERT: B 366 GLU cc_start: 0.8851 (mp0) cc_final: 0.8308 (mp0) REVERT: B 388 MET cc_start: 0.9147 (tpp) cc_final: 0.8224 (mtp) REVERT: B 491 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8488 (tt0) REVERT: B 578 GLU cc_start: 0.8634 (mt-10) cc_final: 0.7987 (mt-10) REVERT: B 607 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7760 (mm-30) REVERT: B 615 LYS cc_start: 0.8959 (pttt) cc_final: 0.8459 (ptmm) REVERT: B 649 ASP cc_start: 0.8130 (t70) cc_final: 0.7902 (t0) REVERT: B 712 GLU cc_start: 0.8052 (tp30) cc_final: 0.7794 (tm-30) REVERT: B 752 ILE cc_start: 0.8679 (tt) cc_final: 0.8275 (tt) REVERT: B 756 GLU cc_start: 0.8467 (tp30) cc_final: 0.7671 (pt0) REVERT: C 236 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8442 (pttt) REVERT: C 253 LEU cc_start: 0.8219 (tp) cc_final: 0.7978 (tp) REVERT: C 317 HIS cc_start: 0.6846 (t-90) cc_final: 0.6385 (t-90) REVERT: C 366 GLU cc_start: 0.8869 (mp0) cc_final: 0.8323 (mp0) REVERT: C 388 MET cc_start: 0.9244 (tpp) cc_final: 0.8506 (mtp) REVERT: C 491 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8165 (tt0) REVERT: C 578 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7959 (mt-10) REVERT: C 607 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7902 (mm-30) REVERT: C 615 LYS cc_start: 0.9092 (pttt) cc_final: 0.8600 (ptmm) REVERT: C 696 LYS cc_start: 0.8070 (tttt) cc_final: 0.7647 (tptm) REVERT: C 740 MET cc_start: 0.8446 (mmm) cc_final: 0.8182 (mmm) REVERT: C 752 ILE cc_start: 0.8583 (tt) cc_final: 0.8149 (tt) REVERT: C 756 GLU cc_start: 0.8455 (tp30) cc_final: 0.7794 (pt0) REVERT: D 236 LYS cc_start: 0.9029 (mmmt) cc_final: 0.8510 (pttt) REVERT: D 273 GLU cc_start: 0.8127 (pp20) cc_final: 0.7695 (tp30) REVERT: D 317 HIS cc_start: 0.6922 (t-90) cc_final: 0.6367 (t-90) REVERT: D 366 GLU cc_start: 0.8859 (mp0) cc_final: 0.8178 (mp0) REVERT: D 388 MET cc_start: 0.9329 (tpp) cc_final: 0.8359 (mtt) REVERT: D 458 GLN cc_start: 0.7703 (tt0) cc_final: 0.7101 (tt0) REVERT: D 460 ASN cc_start: 0.9036 (p0) cc_final: 0.8610 (p0) REVERT: D 486 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8033 (mtmm) REVERT: D 488 GLU cc_start: 0.8533 (tp30) cc_final: 0.8266 (tp30) REVERT: D 577 ASP cc_start: 0.8449 (t0) cc_final: 0.7894 (t0) REVERT: D 578 GLU cc_start: 0.8599 (mt-10) cc_final: 0.7820 (mt-10) REVERT: D 607 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7815 (mm-30) REVERT: D 615 LYS cc_start: 0.8698 (ptpt) cc_final: 0.8283 (ptmm) REVERT: D 616 ASN cc_start: 0.7510 (t0) cc_final: 0.6907 (t0) REVERT: D 712 GLU cc_start: 0.7963 (tp30) cc_final: 0.7682 (tm-30) REVERT: D 756 GLU cc_start: 0.8329 (tp30) cc_final: 0.7518 (pt0) REVERT: E 205 ASP cc_start: 0.8474 (t0) cc_final: 0.7871 (t0) REVERT: E 236 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8461 (pttt) REVERT: E 253 LEU cc_start: 0.8248 (tp) cc_final: 0.7817 (tp) REVERT: E 317 HIS cc_start: 0.6880 (t-90) cc_final: 0.6280 (t-90) REVERT: E 366 GLU cc_start: 0.8852 (mp0) cc_final: 0.8313 (mp0) REVERT: E 388 MET cc_start: 0.9143 (tpp) cc_final: 0.8200 (mtp) REVERT: E 491 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8464 (tt0) REVERT: E 578 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8001 (mt-10) REVERT: E 607 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7755 (mm-30) REVERT: E 615 LYS cc_start: 0.8956 (pttt) cc_final: 0.8457 (ptmm) REVERT: E 649 ASP cc_start: 0.8138 (t70) cc_final: 0.7907 (t0) REVERT: E 712 GLU cc_start: 0.8059 (tp30) cc_final: 0.7799 (tm-30) REVERT: E 752 ILE cc_start: 0.8683 (tt) cc_final: 0.8276 (tt) REVERT: E 756 GLU cc_start: 0.8468 (tp30) cc_final: 0.7669 (pt0) REVERT: F 236 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8452 (pttt) REVERT: F 253 LEU cc_start: 0.8211 (tp) cc_final: 0.7985 (tp) REVERT: F 317 HIS cc_start: 0.6849 (t-90) cc_final: 0.6398 (t-90) REVERT: F 366 GLU cc_start: 0.8866 (mp0) cc_final: 0.8344 (mp0) REVERT: F 388 MET cc_start: 0.9237 (tpp) cc_final: 0.8522 (mtp) REVERT: F 491 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8182 (tt0) REVERT: F 550 MET cc_start: 0.8535 (mmt) cc_final: 0.8279 (mmt) REVERT: F 561 GLU cc_start: 0.8335 (tt0) cc_final: 0.8047 (tt0) REVERT: F 578 GLU cc_start: 0.8564 (mt-10) cc_final: 0.7972 (mt-10) REVERT: F 607 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7907 (mm-30) REVERT: F 615 LYS cc_start: 0.9105 (pttt) cc_final: 0.8664 (ptmm) REVERT: F 696 LYS cc_start: 0.8073 (tttt) cc_final: 0.7654 (tptm) REVERT: F 752 ILE cc_start: 0.8592 (tt) cc_final: 0.8154 (tt) REVERT: F 756 GLU cc_start: 0.8454 (tp30) cc_final: 0.7791 (pt0) outliers start: 55 outliers final: 34 residues processed: 699 average time/residue: 0.1769 time to fit residues: 196.8975 Evaluate side-chains 644 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 610 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 695 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 695 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 276 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 404 HIS B 533 ASN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN C 404 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN E 404 HIS E 538 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN F 404 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107713 restraints weight = 40679.762| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.94 r_work: 0.3071 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26658 Z= 0.147 Angle : 0.720 7.062 36018 Z= 0.346 Chirality : 0.044 0.171 3984 Planarity : 0.006 0.066 4710 Dihedral : 12.616 152.545 3786 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.85 % Allowed : 14.66 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.15 (0.15), residues: 3258 helix: 0.81 (0.12), residues: 1776 sheet: -2.05 (0.26), residues: 354 loop : -0.73 (0.21), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 635 TYR 0.011 0.001 TYR B 244 PHE 0.022 0.001 PHE A 758 TRP 0.005 0.001 TRP D 454 HIS 0.005 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00341 (26658) covalent geometry : angle 0.71982 (36018) hydrogen bonds : bond 0.03860 ( 1327) hydrogen bonds : angle 4.73947 ( 3801) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 649 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.9006 (mmmt) cc_final: 0.8457 (pttt) REVERT: A 273 GLU cc_start: 0.8159 (pp20) cc_final: 0.7686 (tp30) REVERT: A 317 HIS cc_start: 0.6945 (t-90) cc_final: 0.6359 (t-90) REVERT: A 319 GLU cc_start: 0.7547 (pp20) cc_final: 0.7177 (tm-30) REVERT: A 349 ARG cc_start: 0.7927 (mmt-90) cc_final: 0.7613 (tpp80) REVERT: A 366 GLU cc_start: 0.8815 (mp0) cc_final: 0.8189 (mp0) REVERT: A 388 MET cc_start: 0.9365 (tpp) cc_final: 0.8481 (ttm) REVERT: A 404 HIS cc_start: 0.8963 (t70) cc_final: 0.8664 (t70) REVERT: A 458 GLN cc_start: 0.7616 (tt0) cc_final: 0.7029 (tt0) REVERT: A 460 ASN cc_start: 0.9041 (p0) cc_final: 0.8806 (p0) REVERT: A 486 LYS cc_start: 0.8434 (mtpp) cc_final: 0.7942 (mtmm) REVERT: A 488 GLU cc_start: 0.8495 (tp30) cc_final: 0.8245 (tp30) REVERT: A 550 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8204 (mpp) REVERT: A 577 ASP cc_start: 0.8452 (t0) cc_final: 0.7969 (t0) REVERT: A 578 GLU cc_start: 0.8588 (mt-10) cc_final: 0.7824 (mt-10) REVERT: A 607 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7752 (mm-30) REVERT: A 616 ASN cc_start: 0.7575 (t0) cc_final: 0.6917 (t0) REVERT: A 630 ASP cc_start: 0.8074 (t0) cc_final: 0.7819 (t0) REVERT: A 649 ASP cc_start: 0.8138 (t70) cc_final: 0.7828 (t0) REVERT: A 712 GLU cc_start: 0.7942 (tp30) cc_final: 0.7663 (tm-30) REVERT: A 741 ARG cc_start: 0.8247 (mtm180) cc_final: 0.7867 (mtp-110) REVERT: A 755 TYR cc_start: 0.6868 (m-10) cc_final: 0.6594 (m-10) REVERT: A 756 GLU cc_start: 0.8351 (tp30) cc_final: 0.7525 (pt0) REVERT: B 205 ASP cc_start: 0.8536 (t0) cc_final: 0.7974 (t0) REVERT: B 236 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8467 (pttt) REVERT: B 253 LEU cc_start: 0.8239 (tp) cc_final: 0.7798 (tp) REVERT: B 304 ASP cc_start: 0.8860 (t0) cc_final: 0.8609 (t0) REVERT: B 305 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7942 (mm-30) REVERT: B 317 HIS cc_start: 0.6951 (t-90) cc_final: 0.6336 (t-90) REVERT: B 366 GLU cc_start: 0.8846 (mp0) cc_final: 0.8323 (mp0) REVERT: B 388 MET cc_start: 0.9173 (tpp) cc_final: 0.8108 (mtp) REVERT: B 451 ASP cc_start: 0.8361 (m-30) cc_final: 0.7974 (m-30) REVERT: B 491 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8407 (tt0) REVERT: B 578 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 607 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7678 (mm-30) REVERT: B 615 LYS cc_start: 0.8982 (pttt) cc_final: 0.8610 (ptmm) REVERT: B 649 ASP cc_start: 0.8129 (t70) cc_final: 0.7898 (t0) REVERT: B 712 GLU cc_start: 0.7995 (tp30) cc_final: 0.7740 (tm-30) REVERT: B 752 ILE cc_start: 0.8688 (tt) cc_final: 0.8258 (tt) REVERT: B 755 TYR cc_start: 0.6896 (m-10) cc_final: 0.6652 (m-10) REVERT: B 756 GLU cc_start: 0.8499 (tp30) cc_final: 0.7677 (pt0) REVERT: B 763 GLN cc_start: 0.6234 (OUTLIER) cc_final: 0.5845 (tp-100) REVERT: C 236 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8460 (pttt) REVERT: C 253 LEU cc_start: 0.8143 (tp) cc_final: 0.7852 (tp) REVERT: C 275 MET cc_start: 0.8895 (mmm) cc_final: 0.8652 (mmm) REVERT: C 317 HIS cc_start: 0.6939 (t-90) cc_final: 0.6564 (t-90) REVERT: C 366 GLU cc_start: 0.8813 (mp0) cc_final: 0.8301 (mp0) REVERT: C 388 MET cc_start: 0.9257 (tpp) cc_final: 0.8399 (mtp) REVERT: C 491 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8147 (tm-30) REVERT: C 577 ASP cc_start: 0.8404 (t0) cc_final: 0.7909 (t0) REVERT: C 578 GLU cc_start: 0.8514 (mt-10) cc_final: 0.7721 (mt-10) REVERT: C 607 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7938 (mm-30) REVERT: C 615 LYS cc_start: 0.9036 (pttt) cc_final: 0.8658 (ptmt) REVERT: C 696 LYS cc_start: 0.8059 (tttt) cc_final: 0.7658 (tptm) REVERT: C 756 GLU cc_start: 0.8501 (tp30) cc_final: 0.7780 (pt0) REVERT: C 763 GLN cc_start: 0.6160 (OUTLIER) cc_final: 0.5765 (tp-100) REVERT: D 236 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8464 (pttt) REVERT: D 273 GLU cc_start: 0.8207 (pp20) cc_final: 0.7738 (tp30) REVERT: D 317 HIS cc_start: 0.6930 (t-90) cc_final: 0.6398 (t-90) REVERT: D 319 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6942 (tm-30) REVERT: D 349 ARG cc_start: 0.7926 (mmt-90) cc_final: 0.7602 (tpp80) REVERT: D 366 GLU cc_start: 0.8824 (mp0) cc_final: 0.8191 (mp0) REVERT: D 388 MET cc_start: 0.9373 (tpp) cc_final: 0.8479 (ttm) REVERT: D 404 HIS cc_start: 0.8970 (t70) cc_final: 0.8676 (t70) REVERT: D 451 ASP cc_start: 0.8253 (m-30) cc_final: 0.8039 (m-30) REVERT: D 458 GLN cc_start: 0.7609 (tt0) cc_final: 0.7027 (tt0) REVERT: D 460 ASN cc_start: 0.9038 (p0) cc_final: 0.8800 (p0) REVERT: D 486 LYS cc_start: 0.8455 (mtpp) cc_final: 0.7966 (mtmm) REVERT: D 488 GLU cc_start: 0.8493 (tp30) cc_final: 0.8242 (tp30) REVERT: D 550 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8203 (mpp) REVERT: D 577 ASP cc_start: 0.8444 (t0) cc_final: 0.7959 (t0) REVERT: D 578 GLU cc_start: 0.8538 (mt-10) cc_final: 0.7815 (mt-10) REVERT: D 607 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7748 (mm-30) REVERT: D 615 LYS cc_start: 0.8485 (ptpt) cc_final: 0.8160 (ptmm) REVERT: D 616 ASN cc_start: 0.7560 (t0) cc_final: 0.6901 (t0) REVERT: D 712 GLU cc_start: 0.7948 (tp30) cc_final: 0.7668 (tm-30) REVERT: D 741 ARG cc_start: 0.8231 (mtm180) cc_final: 0.7853 (mtp-110) REVERT: D 755 TYR cc_start: 0.6890 (m-10) cc_final: 0.6618 (m-10) REVERT: D 756 GLU cc_start: 0.8351 (tp30) cc_final: 0.7525 (pt0) REVERT: E 205 ASP cc_start: 0.8530 (t0) cc_final: 0.7968 (t0) REVERT: E 236 LYS cc_start: 0.9114 (mmmt) cc_final: 0.8500 (pttt) REVERT: E 253 LEU cc_start: 0.8225 (tp) cc_final: 0.7782 (tp) REVERT: E 317 HIS cc_start: 0.6791 (t-90) cc_final: 0.6219 (t-90) REVERT: E 366 GLU cc_start: 0.8845 (mp0) cc_final: 0.8297 (mp0) REVERT: E 388 MET cc_start: 0.9176 (tpp) cc_final: 0.8141 (mtp) REVERT: E 410 ASP cc_start: 0.8379 (m-30) cc_final: 0.8024 (m-30) REVERT: E 451 ASP cc_start: 0.8357 (m-30) cc_final: 0.7974 (m-30) REVERT: E 491 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8407 (tt0) REVERT: E 578 GLU cc_start: 0.8617 (mt-10) cc_final: 0.7943 (mt-10) REVERT: E 607 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7695 (mm-30) REVERT: E 615 LYS cc_start: 0.8985 (pttt) cc_final: 0.8605 (ptmm) REVERT: E 649 ASP cc_start: 0.8140 (t70) cc_final: 0.7904 (t0) REVERT: E 712 GLU cc_start: 0.8010 (tp30) cc_final: 0.7754 (tm-30) REVERT: E 752 ILE cc_start: 0.8692 (tt) cc_final: 0.8263 (tt) REVERT: E 755 TYR cc_start: 0.6900 (m-10) cc_final: 0.6657 (m-10) REVERT: E 756 GLU cc_start: 0.8497 (tp30) cc_final: 0.7673 (pt0) REVERT: E 763 GLN cc_start: 0.6222 (OUTLIER) cc_final: 0.5854 (tp-100) REVERT: F 236 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8462 (pttt) REVERT: F 253 LEU cc_start: 0.8150 (tp) cc_final: 0.7844 (tp) REVERT: F 317 HIS cc_start: 0.6898 (t-90) cc_final: 0.6529 (t-90) REVERT: F 366 GLU cc_start: 0.8804 (mp0) cc_final: 0.8296 (mp0) REVERT: F 388 MET cc_start: 0.9280 (tpp) cc_final: 0.8434 (mtp) REVERT: F 561 GLU cc_start: 0.8325 (tt0) cc_final: 0.8051 (tt0) REVERT: F 577 ASP cc_start: 0.8405 (t0) cc_final: 0.7937 (t0) REVERT: F 578 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7734 (mt-10) REVERT: F 607 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7925 (mm-30) REVERT: F 615 LYS cc_start: 0.9025 (pttt) cc_final: 0.8635 (ptmt) REVERT: F 696 LYS cc_start: 0.8078 (tttt) cc_final: 0.7678 (tptm) REVERT: F 756 GLU cc_start: 0.8535 (tp30) cc_final: 0.7845 (pt0) outliers start: 78 outliers final: 42 residues processed: 683 average time/residue: 0.1791 time to fit residues: 194.9005 Evaluate side-chains 647 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 600 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 415 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 695 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 522 CYS Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 763 GLN Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 695 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 84 optimal weight: 0.0970 chunk 286 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 141 optimal weight: 0.0770 chunk 126 optimal weight: 0.0060 chunk 245 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.3352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 538 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN C 404 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN F 404 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.137454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110633 restraints weight = 40024.240| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.97 r_work: 0.3195 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26658 Z= 0.124 Angle : 0.701 6.846 36018 Z= 0.337 Chirality : 0.044 0.185 3984 Planarity : 0.005 0.065 4710 Dihedral : 12.378 166.267 3786 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.22 % Allowed : 15.90 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.14 (0.15), residues: 3258 helix: 0.83 (0.12), residues: 1812 sheet: -2.02 (0.27), residues: 336 loop : -0.86 (0.20), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.011 0.001 TYR B 244 PHE 0.021 0.001 PHE E 758 TRP 0.005 0.001 TRP C 476 HIS 0.006 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00278 (26658) covalent geometry : angle 0.70120 (36018) hydrogen bonds : bond 0.03574 ( 1327) hydrogen bonds : angle 4.64242 ( 3801) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 624 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8513 (pttt) REVERT: A 273 GLU cc_start: 0.8176 (pp20) cc_final: 0.7782 (tp30) REVERT: A 317 HIS cc_start: 0.6883 (t-90) cc_final: 0.6318 (t-90) REVERT: A 349 ARG cc_start: 0.7797 (mmt-90) cc_final: 0.7553 (tpp80) REVERT: A 366 GLU cc_start: 0.8709 (mp0) cc_final: 0.8054 (mp0) REVERT: A 404 HIS cc_start: 0.8960 (t70) cc_final: 0.8646 (t70) REVERT: A 449 MET cc_start: 0.7360 (tpt) cc_final: 0.7150 (tpt) REVERT: A 458 GLN cc_start: 0.7710 (tt0) cc_final: 0.7123 (tt0) REVERT: A 486 LYS cc_start: 0.8437 (mtpp) cc_final: 0.8186 (mttm) REVERT: A 488 GLU cc_start: 0.8511 (tp30) cc_final: 0.8288 (tp30) REVERT: A 550 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8166 (mpp) REVERT: A 577 ASP cc_start: 0.8392 (t0) cc_final: 0.7943 (t0) REVERT: A 578 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7761 (mt-10) REVERT: A 607 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7704 (mm-30) REVERT: A 615 LYS cc_start: 0.7954 (ptmm) cc_final: 0.7562 (ptmm) REVERT: A 616 ASN cc_start: 0.7592 (t0) cc_final: 0.6947 (t0) REVERT: A 630 ASP cc_start: 0.8032 (t0) cc_final: 0.7670 (t0) REVERT: A 712 GLU cc_start: 0.7921 (tp30) cc_final: 0.7632 (tm-30) REVERT: A 741 ARG cc_start: 0.8150 (mtm180) cc_final: 0.7759 (mtp-110) REVERT: A 755 TYR cc_start: 0.6841 (m-10) cc_final: 0.6540 (m-10) REVERT: A 756 GLU cc_start: 0.8384 (tp30) cc_final: 0.7590 (pt0) REVERT: A 763 GLN cc_start: 0.5833 (OUTLIER) cc_final: 0.5456 (tp-100) REVERT: B 205 ASP cc_start: 0.8566 (t0) cc_final: 0.7957 (t0) REVERT: B 236 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8502 (pttt) REVERT: B 253 LEU cc_start: 0.8230 (tp) cc_final: 0.7755 (tp) REVERT: B 304 ASP cc_start: 0.8898 (t0) cc_final: 0.8653 (t0) REVERT: B 305 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7952 (mm-30) REVERT: B 317 HIS cc_start: 0.6774 (t-90) cc_final: 0.6216 (t-90) REVERT: B 327 GLN cc_start: 0.8460 (tp40) cc_final: 0.8187 (tp-100) REVERT: B 366 GLU cc_start: 0.8859 (mp0) cc_final: 0.8191 (mp0) REVERT: B 388 MET cc_start: 0.9157 (tpp) cc_final: 0.8226 (mtp) REVERT: B 491 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8378 (tt0) REVERT: B 578 GLU cc_start: 0.8625 (mt-10) cc_final: 0.7967 (mt-10) REVERT: B 607 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7706 (mm-30) REVERT: B 649 ASP cc_start: 0.8122 (t70) cc_final: 0.7887 (t0) REVERT: B 712 GLU cc_start: 0.7988 (tp30) cc_final: 0.7733 (tm-30) REVERT: B 752 ILE cc_start: 0.8700 (tt) cc_final: 0.8269 (tt) REVERT: B 756 GLU cc_start: 0.8521 (tp30) cc_final: 0.7682 (pt0) REVERT: B 763 GLN cc_start: 0.6228 (OUTLIER) cc_final: 0.5806 (tp-100) REVERT: C 236 LYS cc_start: 0.9099 (mmmt) cc_final: 0.8479 (pttt) REVERT: C 253 LEU cc_start: 0.8169 (tp) cc_final: 0.7855 (tp) REVERT: C 275 MET cc_start: 0.8897 (mmm) cc_final: 0.8662 (mmm) REVERT: C 317 HIS cc_start: 0.6987 (t-90) cc_final: 0.6646 (t-90) REVERT: C 366 GLU cc_start: 0.8806 (mp0) cc_final: 0.8271 (mp0) REVERT: C 427 MET cc_start: 0.5185 (ppp) cc_final: 0.4942 (ppp) REVERT: C 491 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8154 (tm-30) REVERT: C 578 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7927 (mt-10) REVERT: C 607 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7982 (mm-30) REVERT: C 741 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7633 (mtm110) REVERT: C 756 GLU cc_start: 0.8441 (tp30) cc_final: 0.7699 (pt0) REVERT: D 236 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8525 (pttt) REVERT: D 273 GLU cc_start: 0.8180 (pp20) cc_final: 0.7786 (tp30) REVERT: D 317 HIS cc_start: 0.6851 (t-90) cc_final: 0.6339 (t-90) REVERT: D 349 ARG cc_start: 0.7808 (mmt-90) cc_final: 0.7554 (tpp80) REVERT: D 366 GLU cc_start: 0.8716 (mp0) cc_final: 0.8058 (mp0) REVERT: D 404 HIS cc_start: 0.8961 (t70) cc_final: 0.8669 (t70) REVERT: D 458 GLN cc_start: 0.7706 (tt0) cc_final: 0.7127 (tt0) REVERT: D 486 LYS cc_start: 0.8454 (mtpp) cc_final: 0.7985 (mtmm) REVERT: D 488 GLU cc_start: 0.8510 (tp30) cc_final: 0.8284 (tp30) REVERT: D 550 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8170 (mpp) REVERT: D 577 ASP cc_start: 0.8388 (t0) cc_final: 0.7940 (t0) REVERT: D 578 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7779 (mt-10) REVERT: D 607 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7700 (mm-30) REVERT: D 615 LYS cc_start: 0.8413 (ptpt) cc_final: 0.8078 (ptmm) REVERT: D 616 ASN cc_start: 0.7633 (t0) cc_final: 0.6999 (t0) REVERT: D 712 GLU cc_start: 0.7936 (tp30) cc_final: 0.7641 (tm-30) REVERT: D 741 ARG cc_start: 0.8146 (mtm180) cc_final: 0.7756 (mtp-110) REVERT: D 755 TYR cc_start: 0.6836 (m-10) cc_final: 0.6539 (m-10) REVERT: D 756 GLU cc_start: 0.8386 (tp30) cc_final: 0.7595 (pt0) REVERT: D 763 GLN cc_start: 0.5828 (OUTLIER) cc_final: 0.5457 (tp-100) REVERT: E 205 ASP cc_start: 0.8558 (t0) cc_final: 0.7954 (t0) REVERT: E 236 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8497 (pttt) REVERT: E 253 LEU cc_start: 0.8214 (tp) cc_final: 0.7751 (tp) REVERT: E 317 HIS cc_start: 0.6776 (t-90) cc_final: 0.6242 (t-90) REVERT: E 327 GLN cc_start: 0.8470 (tp40) cc_final: 0.8196 (tp-100) REVERT: E 366 GLU cc_start: 0.8859 (mp0) cc_final: 0.8189 (mp0) REVERT: E 388 MET cc_start: 0.9176 (tpp) cc_final: 0.8248 (mtp) REVERT: E 451 ASP cc_start: 0.8357 (m-30) cc_final: 0.8007 (m-30) REVERT: E 491 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8428 (tt0) REVERT: E 578 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7904 (mt-10) REVERT: E 607 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7693 (mm-30) REVERT: E 712 GLU cc_start: 0.7990 (tp30) cc_final: 0.7734 (tm-30) REVERT: E 752 ILE cc_start: 0.8701 (tt) cc_final: 0.8255 (tt) REVERT: E 756 GLU cc_start: 0.8516 (tp30) cc_final: 0.7672 (pt0) REVERT: E 763 GLN cc_start: 0.6172 (OUTLIER) cc_final: 0.5754 (tp-100) REVERT: F 236 LYS cc_start: 0.9099 (mmmt) cc_final: 0.8475 (pttt) REVERT: F 253 LEU cc_start: 0.8168 (tp) cc_final: 0.7842 (tp) REVERT: F 317 HIS cc_start: 0.6922 (t-90) cc_final: 0.6614 (t-90) REVERT: F 366 GLU cc_start: 0.8808 (mp0) cc_final: 0.8294 (mp0) REVERT: F 427 MET cc_start: 0.5167 (ppp) cc_final: 0.4924 (ppp) REVERT: F 486 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8156 (mtmm) REVERT: F 578 GLU cc_start: 0.8525 (mt-10) cc_final: 0.7904 (mt-10) REVERT: F 607 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8002 (mm-30) REVERT: F 608 MET cc_start: 0.8709 (mtp) cc_final: 0.8414 (ttm) REVERT: F 696 LYS cc_start: 0.8102 (tttt) cc_final: 0.7684 (tptm) REVERT: F 741 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7538 (mtm110) REVERT: F 756 GLU cc_start: 0.8493 (tp30) cc_final: 0.7790 (pt0) outliers start: 88 outliers final: 51 residues processed: 665 average time/residue: 0.1765 time to fit residues: 187.3785 Evaluate side-chains 647 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 590 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 415 CYS Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 695 CYS Chi-restraints excluded: chain D residue 763 GLN Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 763 GLN Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 695 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 304 optimal weight: 0.6980 chunk 248 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 233 optimal weight: 0.0040 chunk 114 optimal weight: 7.9990 chunk 294 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN C 404 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN F 404 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.134060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107542 restraints weight = 40417.875| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.89 r_work: 0.3168 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26658 Z= 0.157 Angle : 0.705 7.015 36018 Z= 0.337 Chirality : 0.045 0.184 3984 Planarity : 0.005 0.065 4710 Dihedral : 12.237 171.168 3786 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.85 % Allowed : 17.00 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.01 (0.15), residues: 3258 helix: 1.02 (0.12), residues: 1752 sheet: -2.06 (0.26), residues: 354 loop : -0.80 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 358 TYR 0.011 0.001 TYR E 244 PHE 0.014 0.001 PHE E 758 TRP 0.007 0.001 TRP E 454 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00368 (26658) covalent geometry : angle 0.70494 (36018) hydrogen bonds : bond 0.03447 ( 1327) hydrogen bonds : angle 4.60108 ( 3801) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 615 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8564 (pttt) REVERT: A 273 GLU cc_start: 0.8282 (pp20) cc_final: 0.7835 (tp30) REVERT: A 317 HIS cc_start: 0.6982 (t-90) cc_final: 0.6427 (t-90) REVERT: A 366 GLU cc_start: 0.8700 (mp0) cc_final: 0.8068 (mp0) REVERT: A 404 HIS cc_start: 0.9011 (t70) cc_final: 0.8706 (t70) REVERT: A 451 ASP cc_start: 0.8257 (m-30) cc_final: 0.8040 (m-30) REVERT: A 458 GLN cc_start: 0.7580 (tt0) cc_final: 0.7000 (tt0) REVERT: A 486 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8238 (mttm) REVERT: A 488 GLU cc_start: 0.8533 (tp30) cc_final: 0.8286 (tp30) REVERT: A 550 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8076 (mpp) REVERT: A 577 ASP cc_start: 0.8453 (t0) cc_final: 0.8019 (t0) REVERT: A 578 GLU cc_start: 0.8546 (mt-10) cc_final: 0.7807 (mt-10) REVERT: A 607 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7780 (mm-30) REVERT: A 712 GLU cc_start: 0.7958 (tp30) cc_final: 0.7687 (tm-30) REVERT: A 752 ILE cc_start: 0.8702 (tt) cc_final: 0.8275 (tt) REVERT: A 755 TYR cc_start: 0.6997 (m-10) cc_final: 0.6774 (m-10) REVERT: A 756 GLU cc_start: 0.8406 (tp30) cc_final: 0.7584 (pt0) REVERT: A 763 GLN cc_start: 0.5875 (OUTLIER) cc_final: 0.5398 (tp-100) REVERT: B 205 ASP cc_start: 0.8626 (t0) cc_final: 0.7992 (t0) REVERT: B 236 LYS cc_start: 0.9110 (mmmt) cc_final: 0.8504 (pttt) REVERT: B 253 LEU cc_start: 0.8298 (tp) cc_final: 0.7803 (tp) REVERT: B 273 GLU cc_start: 0.8191 (pp20) cc_final: 0.7697 (tp30) REVERT: B 304 ASP cc_start: 0.8920 (t0) cc_final: 0.8663 (t0) REVERT: B 305 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7949 (mm-30) REVERT: B 317 HIS cc_start: 0.6848 (t-90) cc_final: 0.6343 (t-90) REVERT: B 366 GLU cc_start: 0.8828 (mp0) cc_final: 0.8141 (mp0) REVERT: B 388 MET cc_start: 0.9189 (tpp) cc_final: 0.8412 (tpp) REVERT: B 491 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8168 (tm-30) REVERT: B 578 GLU cc_start: 0.8618 (mt-10) cc_final: 0.7989 (mt-10) REVERT: B 607 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7690 (mm-30) REVERT: B 649 ASP cc_start: 0.8120 (t70) cc_final: 0.7883 (t0) REVERT: B 712 GLU cc_start: 0.8046 (tp30) cc_final: 0.7779 (tm-30) REVERT: B 752 ILE cc_start: 0.8758 (tt) cc_final: 0.8324 (tt) REVERT: B 755 TYR cc_start: 0.7005 (m-10) cc_final: 0.6796 (m-10) REVERT: B 756 GLU cc_start: 0.8531 (tp30) cc_final: 0.7706 (pt0) REVERT: C 236 LYS cc_start: 0.9101 (mmmt) cc_final: 0.8497 (pttt) REVERT: C 253 LEU cc_start: 0.8226 (tp) cc_final: 0.7904 (tp) REVERT: C 317 HIS cc_start: 0.6975 (t-90) cc_final: 0.6639 (t-90) REVERT: C 331 LEU cc_start: 0.7602 (mt) cc_final: 0.7389 (mt) REVERT: C 366 GLU cc_start: 0.8814 (mp0) cc_final: 0.8193 (mp0) REVERT: C 388 MET cc_start: 0.9287 (tpp) cc_final: 0.8702 (tpp) REVERT: C 427 MET cc_start: 0.5384 (ppp) cc_final: 0.4999 (ppp) REVERT: C 451 ASP cc_start: 0.8281 (m-30) cc_final: 0.7879 (m-30) REVERT: C 491 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8055 (tm-30) REVERT: C 577 ASP cc_start: 0.8443 (t0) cc_final: 0.7928 (t0) REVERT: C 578 GLU cc_start: 0.8584 (mt-10) cc_final: 0.7718 (mt-10) REVERT: C 607 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7997 (mm-30) REVERT: C 738 GLU cc_start: 0.8174 (tp30) cc_final: 0.7726 (tp30) REVERT: C 741 ARG cc_start: 0.7978 (mtm110) cc_final: 0.7576 (mtm110) REVERT: C 752 ILE cc_start: 0.8806 (tt) cc_final: 0.8352 (tt) REVERT: C 755 TYR cc_start: 0.6911 (m-10) cc_final: 0.6681 (m-10) REVERT: C 756 GLU cc_start: 0.8500 (tp30) cc_final: 0.7755 (pt0) REVERT: D 236 LYS cc_start: 0.9059 (mmmt) cc_final: 0.8575 (pttt) REVERT: D 273 GLU cc_start: 0.8313 (pp20) cc_final: 0.7870 (tp30) REVERT: D 317 HIS cc_start: 0.6927 (t-90) cc_final: 0.6425 (t-90) REVERT: D 366 GLU cc_start: 0.8718 (mp0) cc_final: 0.8074 (mp0) REVERT: D 404 HIS cc_start: 0.9021 (t70) cc_final: 0.8721 (t70) REVERT: D 451 ASP cc_start: 0.8155 (m-30) cc_final: 0.7412 (m-30) REVERT: D 458 GLN cc_start: 0.7579 (tt0) cc_final: 0.7005 (tt0) REVERT: D 486 LYS cc_start: 0.8498 (mtpp) cc_final: 0.8242 (mttm) REVERT: D 488 GLU cc_start: 0.8507 (tp30) cc_final: 0.8290 (tp30) REVERT: D 550 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8087 (mpp) REVERT: D 577 ASP cc_start: 0.8443 (t0) cc_final: 0.8008 (t0) REVERT: D 578 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7760 (mt-10) REVERT: D 607 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7789 (mm-30) REVERT: D 615 LYS cc_start: 0.8538 (ptpt) cc_final: 0.7917 (ptmm) REVERT: D 712 GLU cc_start: 0.7962 (tp30) cc_final: 0.7691 (tm-30) REVERT: D 752 ILE cc_start: 0.8703 (tt) cc_final: 0.8281 (tt) REVERT: D 755 TYR cc_start: 0.6998 (m-10) cc_final: 0.6777 (m-10) REVERT: D 756 GLU cc_start: 0.8409 (tp30) cc_final: 0.7587 (pt0) REVERT: D 763 GLN cc_start: 0.5885 (OUTLIER) cc_final: 0.5413 (tp-100) REVERT: E 205 ASP cc_start: 0.8631 (t0) cc_final: 0.7987 (t0) REVERT: E 236 LYS cc_start: 0.9091 (mmmt) cc_final: 0.8504 (pttt) REVERT: E 253 LEU cc_start: 0.8274 (tp) cc_final: 0.7779 (tp) REVERT: E 273 GLU cc_start: 0.8242 (pp20) cc_final: 0.7737 (tp30) REVERT: E 305 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8206 (mm-30) REVERT: E 317 HIS cc_start: 0.6838 (t-90) cc_final: 0.6358 (t-90) REVERT: E 366 GLU cc_start: 0.8856 (mp0) cc_final: 0.8177 (mp0) REVERT: E 491 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8181 (tm-30) REVERT: E 578 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8023 (mt-10) REVERT: E 607 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7671 (mm-30) REVERT: E 712 GLU cc_start: 0.8061 (tp30) cc_final: 0.7796 (tm-30) REVERT: E 738 GLU cc_start: 0.8404 (tp30) cc_final: 0.7978 (tp30) REVERT: E 752 ILE cc_start: 0.8759 (tt) cc_final: 0.8313 (tt) REVERT: E 755 TYR cc_start: 0.7011 (m-10) cc_final: 0.6807 (m-10) REVERT: E 756 GLU cc_start: 0.8531 (tp30) cc_final: 0.7699 (pt0) REVERT: F 236 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8501 (pttt) REVERT: F 253 LEU cc_start: 0.8240 (tp) cc_final: 0.7894 (tp) REVERT: F 317 HIS cc_start: 0.7048 (t-90) cc_final: 0.6754 (t-90) REVERT: F 366 GLU cc_start: 0.8806 (mp0) cc_final: 0.8199 (mp0) REVERT: F 388 MET cc_start: 0.9301 (tpp) cc_final: 0.8705 (tpp) REVERT: F 427 MET cc_start: 0.5403 (ppp) cc_final: 0.5013 (ppp) REVERT: F 451 ASP cc_start: 0.8290 (m-30) cc_final: 0.7910 (m-30) REVERT: F 491 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8155 (tm-30) REVERT: F 549 THR cc_start: 0.7682 (m) cc_final: 0.7266 (m) REVERT: F 577 ASP cc_start: 0.8437 (t0) cc_final: 0.7944 (t0) REVERT: F 578 GLU cc_start: 0.8575 (mt-10) cc_final: 0.7722 (mt-10) REVERT: F 607 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7994 (mm-30) REVERT: F 696 LYS cc_start: 0.8057 (tttt) cc_final: 0.7649 (tptm) REVERT: F 741 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7584 (mtm110) REVERT: F 752 ILE cc_start: 0.8819 (tt) cc_final: 0.8359 (tt) REVERT: F 755 TYR cc_start: 0.6935 (m-10) cc_final: 0.6707 (m-10) REVERT: F 756 GLU cc_start: 0.8544 (tp30) cc_final: 0.7813 (pt0) outliers start: 78 outliers final: 59 residues processed: 645 average time/residue: 0.1734 time to fit residues: 178.9363 Evaluate side-chains 642 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 579 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 415 CYS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 695 CYS Chi-restraints excluded: chain D residue 763 GLN Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 695 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 229 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 300 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 254 optimal weight: 30.0000 chunk 97 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 283 optimal weight: 7.9990 chunk 25 optimal weight: 0.0770 chunk 155 optimal weight: 7.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 404 HIS ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 404 HIS ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.108795 restraints weight = 40321.490| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 4.00 r_work: 0.3194 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26658 Z= 0.126 Angle : 0.700 7.526 36018 Z= 0.334 Chirality : 0.044 0.159 3984 Planarity : 0.005 0.065 4710 Dihedral : 12.149 174.125 3786 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.14 % Allowed : 18.09 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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 (0.15), residues: 3258 helix: 1.02 (0.12), residues: 1776 sheet: -2.04 (0.26), residues: 354 loop : -0.83 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 741 TYR 0.015 0.001 TYR E 244 PHE 0.011 0.001 PHE E 758 TRP 0.006 0.001 TRP E 454 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00288 (26658) covalent geometry : angle 0.69964 (36018) hydrogen bonds : bond 0.03352 ( 1327) hydrogen bonds : angle 4.55171 ( 3801) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 620 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8547 (pttt) REVERT: A 273 GLU cc_start: 0.8296 (pp20) cc_final: 0.7825 (tp30) REVERT: A 317 HIS cc_start: 0.6930 (t-90) cc_final: 0.6389 (t-90) REVERT: A 366 GLU cc_start: 0.8703 (mp0) cc_final: 0.8078 (mp0) REVERT: A 404 HIS cc_start: 0.8980 (t70) cc_final: 0.8673 (t70) REVERT: A 451 ASP cc_start: 0.8231 (m-30) cc_final: 0.8013 (m-30) REVERT: A 458 GLN cc_start: 0.7675 (tt0) cc_final: 0.7100 (tt0) REVERT: A 486 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8221 (mttm) REVERT: A 488 GLU cc_start: 0.8537 (tp30) cc_final: 0.8301 (tp30) REVERT: A 550 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8086 (mpp) REVERT: A 577 ASP cc_start: 0.8430 (t0) cc_final: 0.8028 (t0) REVERT: A 578 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7756 (mt-10) REVERT: A 607 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7766 (mm-30) REVERT: A 616 ASN cc_start: 0.7747 (t0) cc_final: 0.7088 (t0) REVERT: A 630 ASP cc_start: 0.8206 (t0) cc_final: 0.7992 (t0) REVERT: A 712 GLU cc_start: 0.7945 (tp30) cc_final: 0.7662 (tm-30) REVERT: A 755 TYR cc_start: 0.6917 (m-10) cc_final: 0.6634 (m-10) REVERT: A 756 GLU cc_start: 0.8411 (tp30) cc_final: 0.7613 (pt0) REVERT: A 763 GLN cc_start: 0.5733 (OUTLIER) cc_final: 0.5346 (tp-100) REVERT: B 205 ASP cc_start: 0.8637 (t0) cc_final: 0.7983 (t0) REVERT: B 236 LYS cc_start: 0.9096 (mmmt) cc_final: 0.8480 (pttt) REVERT: B 253 LEU cc_start: 0.8287 (tp) cc_final: 0.7809 (tp) REVERT: B 304 ASP cc_start: 0.8931 (t0) cc_final: 0.8681 (t0) REVERT: B 305 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7949 (mm-30) REVERT: B 317 HIS cc_start: 0.6812 (t-90) cc_final: 0.6186 (t-90) REVERT: B 366 GLU cc_start: 0.8816 (mp0) cc_final: 0.8137 (mp0) REVERT: B 388 MET cc_start: 0.9172 (tpp) cc_final: 0.8377 (tpp) REVERT: B 486 LYS cc_start: 0.8539 (mtpp) cc_final: 0.8273 (mttm) REVERT: B 491 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8209 (tm-30) REVERT: B 578 GLU cc_start: 0.8591 (mt-10) cc_final: 0.7952 (mt-10) REVERT: B 607 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7759 (mm-30) REVERT: B 649 ASP cc_start: 0.8126 (t70) cc_final: 0.7882 (t0) REVERT: B 712 GLU cc_start: 0.8034 (tp30) cc_final: 0.7768 (tm-30) REVERT: B 752 ILE cc_start: 0.8742 (tt) cc_final: 0.8343 (tt) REVERT: B 755 TYR cc_start: 0.6974 (m-10) cc_final: 0.6695 (m-10) REVERT: B 756 GLU cc_start: 0.8556 (tp30) cc_final: 0.7720 (pt0) REVERT: B 763 GLN cc_start: 0.6164 (OUTLIER) cc_final: 0.5744 (tp-100) REVERT: C 236 LYS cc_start: 0.9101 (mmmt) cc_final: 0.8496 (pttt) REVERT: C 253 LEU cc_start: 0.8190 (tp) cc_final: 0.7874 (tp) REVERT: C 317 HIS cc_start: 0.7043 (t-90) cc_final: 0.6572 (t70) REVERT: C 331 LEU cc_start: 0.7571 (mt) cc_final: 0.7353 (mt) REVERT: C 366 GLU cc_start: 0.8821 (mp0) cc_final: 0.8220 (mp0) REVERT: C 388 MET cc_start: 0.9283 (tpp) cc_final: 0.8669 (tpp) REVERT: C 427 MET cc_start: 0.5344 (ppp) cc_final: 0.4980 (ppp) REVERT: C 451 ASP cc_start: 0.8240 (m-30) cc_final: 0.7808 (m-30) REVERT: C 491 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8051 (tm-30) REVERT: C 550 MET cc_start: 0.8418 (mmt) cc_final: 0.8166 (mmt) REVERT: C 578 GLU cc_start: 0.8574 (mt-10) cc_final: 0.7937 (mt-10) REVERT: C 607 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8030 (mm-30) REVERT: C 741 ARG cc_start: 0.7923 (mtm110) cc_final: 0.7573 (mtm110) REVERT: C 752 ILE cc_start: 0.8804 (tt) cc_final: 0.8351 (tt) REVERT: C 755 TYR cc_start: 0.6850 (m-10) cc_final: 0.6596 (m-10) REVERT: C 756 GLU cc_start: 0.8481 (tp30) cc_final: 0.7730 (pt0) REVERT: D 213 LEU cc_start: 0.8252 (tp) cc_final: 0.7967 (tp) REVERT: D 236 LYS cc_start: 0.9051 (mmmt) cc_final: 0.8560 (pttt) REVERT: D 273 GLU cc_start: 0.8332 (pp20) cc_final: 0.7854 (tp30) REVERT: D 317 HIS cc_start: 0.7015 (t-90) cc_final: 0.6593 (t-90) REVERT: D 366 GLU cc_start: 0.8688 (mp0) cc_final: 0.8041 (mp0) REVERT: D 404 HIS cc_start: 0.8999 (t70) cc_final: 0.8699 (t70) REVERT: D 451 ASP cc_start: 0.8115 (m-30) cc_final: 0.7311 (m-30) REVERT: D 458 GLN cc_start: 0.7685 (tt0) cc_final: 0.7115 (tt0) REVERT: D 486 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8219 (mttm) REVERT: D 488 GLU cc_start: 0.8498 (tp30) cc_final: 0.8279 (tp30) REVERT: D 550 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8098 (mpp) REVERT: D 577 ASP cc_start: 0.8426 (t0) cc_final: 0.8026 (t0) REVERT: D 578 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7753 (mt-10) REVERT: D 607 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7746 (mm-30) REVERT: D 615 LYS cc_start: 0.8484 (ptpt) cc_final: 0.7933 (ptmm) REVERT: D 616 ASN cc_start: 0.7772 (t0) cc_final: 0.7115 (t0) REVERT: D 712 GLU cc_start: 0.7960 (tp30) cc_final: 0.7672 (tm-30) REVERT: D 755 TYR cc_start: 0.6908 (m-10) cc_final: 0.6592 (m-10) REVERT: D 756 GLU cc_start: 0.8411 (tp30) cc_final: 0.7617 (pt0) REVERT: D 763 GLN cc_start: 0.5741 (OUTLIER) cc_final: 0.5342 (tp-100) REVERT: E 205 ASP cc_start: 0.8634 (t0) cc_final: 0.7957 (t0) REVERT: E 236 LYS cc_start: 0.9094 (mmmt) cc_final: 0.8478 (pttt) REVERT: E 253 LEU cc_start: 0.8251 (tp) cc_final: 0.7779 (tp) REVERT: E 273 GLU cc_start: 0.8217 (pp20) cc_final: 0.7666 (tp30) REVERT: E 305 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8162 (mm-30) REVERT: E 317 HIS cc_start: 0.6817 (t-90) cc_final: 0.6352 (t-90) REVERT: E 366 GLU cc_start: 0.8821 (mp0) cc_final: 0.8136 (mp0) REVERT: E 486 LYS cc_start: 0.8510 (mtpp) cc_final: 0.8246 (mttm) REVERT: E 491 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8209 (tm-30) REVERT: E 578 GLU cc_start: 0.8605 (mt-10) cc_final: 0.7969 (mt-10) REVERT: E 607 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7739 (mm-30) REVERT: E 712 GLU cc_start: 0.8040 (tp30) cc_final: 0.7775 (tm-30) REVERT: E 752 ILE cc_start: 0.8743 (tt) cc_final: 0.8320 (tt) REVERT: E 755 TYR cc_start: 0.6981 (m-10) cc_final: 0.6705 (m-10) REVERT: E 756 GLU cc_start: 0.8554 (tp30) cc_final: 0.7715 (pt0) REVERT: E 763 GLN cc_start: 0.5962 (OUTLIER) cc_final: 0.5558 (tp-100) REVERT: F 236 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8495 (pttt) REVERT: F 253 LEU cc_start: 0.8200 (tp) cc_final: 0.7860 (tp) REVERT: F 275 MET cc_start: 0.8765 (mmm) cc_final: 0.8556 (mmm) REVERT: F 317 HIS cc_start: 0.7014 (t-90) cc_final: 0.6738 (t-90) REVERT: F 366 GLU cc_start: 0.8798 (mp0) cc_final: 0.8172 (mp0) REVERT: F 388 MET cc_start: 0.9309 (tpp) cc_final: 0.8707 (tpp) REVERT: F 427 MET cc_start: 0.5465 (ppp) cc_final: 0.5096 (ppp) REVERT: F 451 ASP cc_start: 0.8250 (m-30) cc_final: 0.7850 (m-30) REVERT: F 491 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8182 (tm-30) REVERT: F 549 THR cc_start: 0.7648 (m) cc_final: 0.7234 (m) REVERT: F 578 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7923 (mt-10) REVERT: F 607 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8040 (mm-30) REVERT: F 696 LYS cc_start: 0.8039 (tttt) cc_final: 0.7588 (tptm) REVERT: F 741 ARG cc_start: 0.7999 (mtm110) cc_final: 0.7568 (mtm110) REVERT: F 752 ILE cc_start: 0.8809 (tt) cc_final: 0.8353 (tt) REVERT: F 755 TYR cc_start: 0.6867 (m-10) cc_final: 0.6616 (m-10) REVERT: F 756 GLU cc_start: 0.8480 (tp30) cc_final: 0.7727 (pt0) outliers start: 86 outliers final: 60 residues processed: 649 average time/residue: 0.1668 time to fit residues: 174.5784 Evaluate side-chains 653 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 587 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 695 CYS Chi-restraints excluded: chain D residue 763 GLN Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 763 GLN Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 695 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 148 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 266 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 289 optimal weight: 0.0060 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 660 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS E 660 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.136780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110166 restraints weight = 40187.788| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.97 r_work: 0.3195 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26658 Z= 0.137 Angle : 0.699 7.525 36018 Z= 0.334 Chirality : 0.044 0.159 3984 Planarity : 0.005 0.065 4710 Dihedral : 12.150 174.125 3786 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.41 % Allowed : 19.52 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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 (0.15), residues: 3258 helix: 1.02 (0.12), residues: 1776 sheet: -2.04 (0.26), residues: 354 loop : -0.83 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 741 TYR 0.015 0.001 TYR E 244 PHE 0.011 0.001 PHE E 758 TRP 0.006 0.001 TRP E 454 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00298 (26658) covalent geometry : angle 0.69948 (36018) hydrogen bonds : bond 0.03352 ( 1327) hydrogen bonds : angle 4.55171 ( 3801) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 588 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.9037 (mmmt) cc_final: 0.8546 (pttt) REVERT: A 273 GLU cc_start: 0.8296 (pp20) cc_final: 0.7824 (tp30) REVERT: A 317 HIS cc_start: 0.6950 (t-90) cc_final: 0.6411 (t-90) REVERT: A 366 GLU cc_start: 0.8706 (mp0) cc_final: 0.8081 (mp0) REVERT: A 404 HIS cc_start: 0.8988 (t70) cc_final: 0.8682 (t70) REVERT: A 451 ASP cc_start: 0.8227 (m-30) cc_final: 0.8009 (m-30) REVERT: A 458 GLN cc_start: 0.7671 (tt0) cc_final: 0.7094 (tt0) REVERT: A 486 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8217 (mttm) REVERT: A 488 GLU cc_start: 0.8539 (tp30) cc_final: 0.8300 (tp30) REVERT: A 546 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7077 (tm-30) REVERT: A 550 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.7826 (mpp) REVERT: A 577 ASP cc_start: 0.8429 (t0) cc_final: 0.8027 (t0) REVERT: A 578 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7747 (mt-10) REVERT: A 607 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7769 (mm-30) REVERT: A 616 ASN cc_start: 0.7747 (t0) cc_final: 0.7088 (t0) REVERT: A 712 GLU cc_start: 0.7952 (tp30) cc_final: 0.7665 (tm-30) REVERT: A 755 TYR cc_start: 0.6863 (m-10) cc_final: 0.6639 (m-10) REVERT: A 756 GLU cc_start: 0.8408 (tp30) cc_final: 0.7612 (pt0) REVERT: A 763 GLN cc_start: 0.5753 (OUTLIER) cc_final: 0.5356 (tp-100) REVERT: B 205 ASP cc_start: 0.8646 (t0) cc_final: 0.7980 (t0) REVERT: B 236 LYS cc_start: 0.9084 (mmmt) cc_final: 0.8473 (pttt) REVERT: B 253 LEU cc_start: 0.8291 (tp) cc_final: 0.7809 (tp) REVERT: B 304 ASP cc_start: 0.8934 (t0) cc_final: 0.8682 (t0) REVERT: B 305 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7949 (mm-30) REVERT: B 317 HIS cc_start: 0.6818 (t-90) cc_final: 0.6195 (t-90) REVERT: B 366 GLU cc_start: 0.8797 (mp0) cc_final: 0.8130 (mp0) REVERT: B 388 MET cc_start: 0.9174 (tpp) cc_final: 0.8381 (tpp) REVERT: B 486 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8285 (mttm) REVERT: B 491 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8217 (tm-30) REVERT: B 578 GLU cc_start: 0.8575 (mt-10) cc_final: 0.7935 (mt-10) REVERT: B 607 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7756 (mm-30) REVERT: B 649 ASP cc_start: 0.8119 (t70) cc_final: 0.7873 (t0) REVERT: B 712 GLU cc_start: 0.8040 (tp30) cc_final: 0.7772 (tm-30) REVERT: B 752 ILE cc_start: 0.8728 (tt) cc_final: 0.8332 (tt) REVERT: B 755 TYR cc_start: 0.6902 (m-10) cc_final: 0.6691 (m-10) REVERT: B 756 GLU cc_start: 0.8554 (tp30) cc_final: 0.7718 (pt0) REVERT: B 763 GLN cc_start: 0.6170 (OUTLIER) cc_final: 0.5738 (tp-100) REVERT: C 236 LYS cc_start: 0.9098 (mmmt) cc_final: 0.8493 (pttt) REVERT: C 253 LEU cc_start: 0.8187 (tp) cc_final: 0.7867 (tp) REVERT: C 317 HIS cc_start: 0.7042 (t-90) cc_final: 0.6573 (t70) REVERT: C 331 LEU cc_start: 0.7567 (mt) cc_final: 0.7352 (mt) REVERT: C 366 GLU cc_start: 0.8827 (mp0) cc_final: 0.8228 (mp0) REVERT: C 388 MET cc_start: 0.9279 (tpp) cc_final: 0.8660 (tpp) REVERT: C 427 MET cc_start: 0.5341 (ppp) cc_final: 0.4979 (ppp) REVERT: C 451 ASP cc_start: 0.8242 (m-30) cc_final: 0.7809 (m-30) REVERT: C 491 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8056 (tm-30) REVERT: C 578 GLU cc_start: 0.8570 (mt-10) cc_final: 0.7932 (mt-10) REVERT: C 607 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8035 (mm-30) REVERT: C 738 GLU cc_start: 0.8186 (tp30) cc_final: 0.7833 (tp30) REVERT: C 741 ARG cc_start: 0.7939 (mtm110) cc_final: 0.7572 (mtm110) REVERT: C 752 ILE cc_start: 0.8806 (tt) cc_final: 0.8355 (tt) REVERT: C 755 TYR cc_start: 0.6850 (m-10) cc_final: 0.6601 (m-10) REVERT: C 756 GLU cc_start: 0.8482 (tp30) cc_final: 0.7733 (pt0) REVERT: D 213 LEU cc_start: 0.8256 (tp) cc_final: 0.7969 (tp) REVERT: D 236 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8552 (pttt) REVERT: D 273 GLU cc_start: 0.8327 (pp20) cc_final: 0.7850 (tp30) REVERT: D 317 HIS cc_start: 0.7023 (t-90) cc_final: 0.6603 (t-90) REVERT: D 366 GLU cc_start: 0.8677 (mp0) cc_final: 0.8030 (mp0) REVERT: D 404 HIS cc_start: 0.9001 (t70) cc_final: 0.8701 (t70) REVERT: D 451 ASP cc_start: 0.8113 (m-30) cc_final: 0.7312 (m-30) REVERT: D 458 GLN cc_start: 0.7673 (tt0) cc_final: 0.7103 (tt0) REVERT: D 486 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8210 (mttm) REVERT: D 488 GLU cc_start: 0.8497 (tp30) cc_final: 0.8276 (tp30) REVERT: D 550 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8086 (mpp) REVERT: D 577 ASP cc_start: 0.8428 (t0) cc_final: 0.8027 (t0) REVERT: D 578 GLU cc_start: 0.8549 (mt-10) cc_final: 0.7751 (mt-10) REVERT: D 607 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7745 (mm-30) REVERT: D 615 LYS cc_start: 0.8478 (ptpt) cc_final: 0.7927 (ptmm) REVERT: D 616 ASN cc_start: 0.7771 (t0) cc_final: 0.7115 (t0) REVERT: D 712 GLU cc_start: 0.7966 (tp30) cc_final: 0.7674 (tm-30) REVERT: D 752 ILE cc_start: 0.8720 (tt) cc_final: 0.8310 (tt) REVERT: D 755 TYR cc_start: 0.6846 (m-10) cc_final: 0.6606 (m-10) REVERT: D 756 GLU cc_start: 0.8413 (tp30) cc_final: 0.7616 (pt0) REVERT: D 763 GLN cc_start: 0.5744 (OUTLIER) cc_final: 0.5343 (tp-100) REVERT: E 205 ASP cc_start: 0.8643 (t0) cc_final: 0.7961 (t0) REVERT: E 236 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8474 (pttt) REVERT: E 253 LEU cc_start: 0.8246 (tp) cc_final: 0.7773 (tp) REVERT: E 273 GLU cc_start: 0.8209 (pp20) cc_final: 0.7662 (tp30) REVERT: E 305 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8156 (mm-30) REVERT: E 317 HIS cc_start: 0.6831 (t-90) cc_final: 0.6368 (t-90) REVERT: E 366 GLU cc_start: 0.8789 (mp0) cc_final: 0.8109 (mp0) REVERT: E 486 LYS cc_start: 0.8518 (mtpp) cc_final: 0.8254 (mttm) REVERT: E 491 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8208 (tm-30) REVERT: E 578 GLU cc_start: 0.8586 (mt-10) cc_final: 0.7952 (mt-10) REVERT: E 607 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7734 (mm-30) REVERT: E 712 GLU cc_start: 0.8038 (tp30) cc_final: 0.7774 (tm-30) REVERT: E 752 ILE cc_start: 0.8735 (tt) cc_final: 0.8312 (tt) REVERT: E 755 TYR cc_start: 0.6908 (m-10) cc_final: 0.6700 (m-10) REVERT: E 756 GLU cc_start: 0.8554 (tp30) cc_final: 0.7714 (pt0) REVERT: E 763 GLN cc_start: 0.5960 (OUTLIER) cc_final: 0.5545 (tp-100) REVERT: F 236 LYS cc_start: 0.9103 (mmmt) cc_final: 0.8495 (pttt) REVERT: F 253 LEU cc_start: 0.8189 (tp) cc_final: 0.7848 (tp) REVERT: F 275 MET cc_start: 0.8762 (mmm) cc_final: 0.8553 (mmm) REVERT: F 317 HIS cc_start: 0.7018 (t-90) cc_final: 0.6746 (t-90) REVERT: F 366 GLU cc_start: 0.8803 (mp0) cc_final: 0.8181 (mp0) REVERT: F 388 MET cc_start: 0.9303 (tpp) cc_final: 0.8695 (tpp) REVERT: F 427 MET cc_start: 0.5466 (ppp) cc_final: 0.5098 (ppp) REVERT: F 451 ASP cc_start: 0.8247 (m-30) cc_final: 0.7849 (m-30) REVERT: F 491 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8182 (tm-30) REVERT: F 549 THR cc_start: 0.7633 (m) cc_final: 0.7223 (m) REVERT: F 578 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7923 (mt-10) REVERT: F 607 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8053 (mm-30) REVERT: F 696 LYS cc_start: 0.8041 (tttt) cc_final: 0.7592 (tptm) REVERT: F 741 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7574 (mtm110) REVERT: F 752 ILE cc_start: 0.8808 (tt) cc_final: 0.8357 (tt) REVERT: F 755 TYR cc_start: 0.6870 (m-10) cc_final: 0.6623 (m-10) REVERT: F 756 GLU cc_start: 0.8480 (tp30) cc_final: 0.7730 (pt0) outliers start: 66 outliers final: 60 residues processed: 606 average time/residue: 0.1701 time to fit residues: 166.1506 Evaluate side-chains 650 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 584 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 695 CYS Chi-restraints excluded: chain D residue 763 GLN Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 763 GLN Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 695 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 256 optimal weight: 2.9990 chunk 258 optimal weight: 0.0270 chunk 242 optimal weight: 0.6980 chunk 293 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 chunk 166 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 3 optimal weight: 0.0870 chunk 299 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 255 optimal weight: 0.7980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109985 restraints weight = 40134.195| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.92 r_work: 0.3185 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26658 Z= 0.137 Angle : 0.699 7.525 36018 Z= 0.334 Chirality : 0.044 0.159 3984 Planarity : 0.005 0.065 4710 Dihedral : 12.149 174.125 3786 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.41 % Allowed : 19.55 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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 (0.15), residues: 3258 helix: 1.02 (0.12), residues: 1776 sheet: -2.04 (0.26), residues: 354 loop : -0.83 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 741 TYR 0.015 0.001 TYR E 244 PHE 0.011 0.001 PHE E 758 TRP 0.006 0.001 TRP E 454 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00298 (26658) covalent geometry : angle 0.69948 (36018) hydrogen bonds : bond 0.03352 ( 1327) hydrogen bonds : angle 4.55171 ( 3801) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 584 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8540 (pttt) REVERT: A 273 GLU cc_start: 0.8303 (pp20) cc_final: 0.7829 (tp30) REVERT: A 317 HIS cc_start: 0.6944 (t-90) cc_final: 0.6405 (t-90) REVERT: A 366 GLU cc_start: 0.8708 (mp0) cc_final: 0.8082 (mp0) REVERT: A 404 HIS cc_start: 0.8993 (t70) cc_final: 0.8689 (t70) REVERT: A 451 ASP cc_start: 0.8231 (m-30) cc_final: 0.8014 (m-30) REVERT: A 458 GLN cc_start: 0.7663 (tt0) cc_final: 0.7086 (tt0) REVERT: A 486 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8219 (mttm) REVERT: A 488 GLU cc_start: 0.8543 (tp30) cc_final: 0.8307 (tp30) REVERT: A 546 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7080 (tm-30) REVERT: A 550 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.7822 (mpp) REVERT: A 577 ASP cc_start: 0.8430 (t0) cc_final: 0.8028 (t0) REVERT: A 578 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7747 (mt-10) REVERT: A 607 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7771 (mm-30) REVERT: A 616 ASN cc_start: 0.7765 (t0) cc_final: 0.7105 (t0) REVERT: A 712 GLU cc_start: 0.7949 (tp30) cc_final: 0.7664 (tm-30) REVERT: A 755 TYR cc_start: 0.6866 (m-10) cc_final: 0.6643 (m-10) REVERT: A 756 GLU cc_start: 0.8410 (tp30) cc_final: 0.7611 (pt0) REVERT: A 763 GLN cc_start: 0.5758 (OUTLIER) cc_final: 0.5358 (tp-100) REVERT: B 205 ASP cc_start: 0.8653 (t0) cc_final: 0.7983 (t0) REVERT: B 236 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8472 (pttt) REVERT: B 253 LEU cc_start: 0.8287 (tp) cc_final: 0.7806 (tp) REVERT: B 304 ASP cc_start: 0.8936 (t0) cc_final: 0.8688 (t0) REVERT: B 305 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7952 (mm-30) REVERT: B 317 HIS cc_start: 0.6810 (t-90) cc_final: 0.6184 (t-90) REVERT: B 366 GLU cc_start: 0.8789 (mp0) cc_final: 0.8119 (mp0) REVERT: B 388 MET cc_start: 0.9175 (tpp) cc_final: 0.8386 (tpp) REVERT: B 486 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8281 (mttm) REVERT: B 491 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 578 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7940 (mt-10) REVERT: B 607 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7768 (mm-30) REVERT: B 649 ASP cc_start: 0.8123 (t70) cc_final: 0.7877 (t0) REVERT: B 712 GLU cc_start: 0.8034 (tp30) cc_final: 0.7770 (tm-30) REVERT: B 752 ILE cc_start: 0.8728 (tt) cc_final: 0.8328 (tt) REVERT: B 755 TYR cc_start: 0.6902 (m-10) cc_final: 0.6692 (m-10) REVERT: B 756 GLU cc_start: 0.8556 (tp30) cc_final: 0.7717 (pt0) REVERT: B 763 GLN cc_start: 0.6168 (OUTLIER) cc_final: 0.5735 (tp-100) REVERT: C 236 LYS cc_start: 0.9099 (mmmt) cc_final: 0.8495 (pttt) REVERT: C 253 LEU cc_start: 0.8187 (tp) cc_final: 0.7869 (tp) REVERT: C 317 HIS cc_start: 0.7048 (t-90) cc_final: 0.6582 (t70) REVERT: C 331 LEU cc_start: 0.7571 (mt) cc_final: 0.7355 (mt) REVERT: C 366 GLU cc_start: 0.8825 (mp0) cc_final: 0.8225 (mp0) REVERT: C 388 MET cc_start: 0.9282 (tpp) cc_final: 0.8668 (tpp) REVERT: C 427 MET cc_start: 0.5339 (ppp) cc_final: 0.4978 (ppp) REVERT: C 451 ASP cc_start: 0.8245 (m-30) cc_final: 0.7811 (m-30) REVERT: C 491 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8059 (tm-30) REVERT: C 578 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7935 (mt-10) REVERT: C 607 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8042 (mm-30) REVERT: C 738 GLU cc_start: 0.8188 (tp30) cc_final: 0.7836 (tp30) REVERT: C 741 ARG cc_start: 0.7943 (mtm110) cc_final: 0.7576 (mtm110) REVERT: C 752 ILE cc_start: 0.8814 (tt) cc_final: 0.8362 (tt) REVERT: C 755 TYR cc_start: 0.6861 (m-10) cc_final: 0.6612 (m-10) REVERT: C 756 GLU cc_start: 0.8484 (tp30) cc_final: 0.7734 (pt0) REVERT: D 213 LEU cc_start: 0.8260 (tp) cc_final: 0.7973 (tp) REVERT: D 236 LYS cc_start: 0.9034 (mmmt) cc_final: 0.8550 (pttt) REVERT: D 273 GLU cc_start: 0.8334 (pp20) cc_final: 0.7856 (tp30) REVERT: D 317 HIS cc_start: 0.7024 (t-90) cc_final: 0.6604 (t-90) REVERT: D 366 GLU cc_start: 0.8673 (mp0) cc_final: 0.8026 (mp0) REVERT: D 404 HIS cc_start: 0.9006 (t70) cc_final: 0.8707 (t70) REVERT: D 451 ASP cc_start: 0.8115 (m-30) cc_final: 0.7315 (m-30) REVERT: D 458 GLN cc_start: 0.7669 (tt0) cc_final: 0.7101 (tt0) REVERT: D 486 LYS cc_start: 0.8467 (mtpp) cc_final: 0.8210 (mttm) REVERT: D 488 GLU cc_start: 0.8499 (tp30) cc_final: 0.8281 (tp30) REVERT: D 546 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7084 (tm-30) REVERT: D 550 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.7828 (mpp) REVERT: D 577 ASP cc_start: 0.8428 (t0) cc_final: 0.8027 (t0) REVERT: D 578 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7748 (mt-10) REVERT: D 607 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7744 (mm-30) REVERT: D 615 LYS cc_start: 0.8484 (ptpt) cc_final: 0.7932 (ptmm) REVERT: D 616 ASN cc_start: 0.7782 (t0) cc_final: 0.7123 (t0) REVERT: D 712 GLU cc_start: 0.7961 (tp30) cc_final: 0.7672 (tm-30) REVERT: D 752 ILE cc_start: 0.8723 (tt) cc_final: 0.8312 (tt) REVERT: D 755 TYR cc_start: 0.6850 (m-10) cc_final: 0.6611 (m-10) REVERT: D 756 GLU cc_start: 0.8416 (tp30) cc_final: 0.7619 (pt0) REVERT: D 763 GLN cc_start: 0.5754 (OUTLIER) cc_final: 0.5349 (tp-100) REVERT: E 205 ASP cc_start: 0.8646 (t0) cc_final: 0.7968 (t0) REVERT: E 236 LYS cc_start: 0.9079 (mmmt) cc_final: 0.8471 (pttt) REVERT: E 253 LEU cc_start: 0.8238 (tp) cc_final: 0.7769 (tp) REVERT: E 273 GLU cc_start: 0.8219 (pp20) cc_final: 0.7671 (tp30) REVERT: E 305 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8164 (mm-30) REVERT: E 317 HIS cc_start: 0.6826 (t-90) cc_final: 0.6364 (t-90) REVERT: E 366 GLU cc_start: 0.8789 (mp0) cc_final: 0.8111 (mp0) REVERT: E 486 LYS cc_start: 0.8516 (mtpp) cc_final: 0.8253 (mttm) REVERT: E 491 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8212 (tm-30) REVERT: E 578 GLU cc_start: 0.8585 (mt-10) cc_final: 0.7950 (mt-10) REVERT: E 607 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7747 (mm-30) REVERT: E 712 GLU cc_start: 0.8037 (tp30) cc_final: 0.7773 (tm-30) REVERT: E 752 ILE cc_start: 0.8744 (tt) cc_final: 0.8318 (tt) REVERT: E 755 TYR cc_start: 0.6913 (m-10) cc_final: 0.6706 (m-10) REVERT: E 756 GLU cc_start: 0.8554 (tp30) cc_final: 0.7713 (pt0) REVERT: E 763 GLN cc_start: 0.5969 (OUTLIER) cc_final: 0.5553 (tp-100) REVERT: F 236 LYS cc_start: 0.9103 (mmmt) cc_final: 0.8497 (pttt) REVERT: F 253 LEU cc_start: 0.8191 (tp) cc_final: 0.7852 (tp) REVERT: F 275 MET cc_start: 0.8762 (mmm) cc_final: 0.8554 (mmm) REVERT: F 317 HIS cc_start: 0.7010 (t-90) cc_final: 0.6737 (t-90) REVERT: F 366 GLU cc_start: 0.8807 (mp0) cc_final: 0.8186 (mp0) REVERT: F 388 MET cc_start: 0.9310 (tpp) cc_final: 0.8712 (tpp) REVERT: F 427 MET cc_start: 0.5457 (ppp) cc_final: 0.5093 (ppp) REVERT: F 451 ASP cc_start: 0.8249 (m-30) cc_final: 0.7851 (m-30) REVERT: F 491 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8185 (tm-30) REVERT: F 549 THR cc_start: 0.7640 (m) cc_final: 0.7229 (m) REVERT: F 578 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7923 (mt-10) REVERT: F 607 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8054 (mm-30) REVERT: F 696 LYS cc_start: 0.8043 (tttt) cc_final: 0.7595 (tptm) REVERT: F 741 ARG cc_start: 0.8002 (mtm110) cc_final: 0.7577 (mtm110) REVERT: F 752 ILE cc_start: 0.8815 (tt) cc_final: 0.8361 (tt) REVERT: F 755 TYR cc_start: 0.6876 (m-10) cc_final: 0.6629 (m-10) REVERT: F 756 GLU cc_start: 0.8482 (tp30) cc_final: 0.7731 (pt0) outliers start: 66 outliers final: 60 residues processed: 602 average time/residue: 0.1666 time to fit residues: 161.6340 Evaluate side-chains 649 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 583 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 695 CYS Chi-restraints excluded: chain D residue 763 GLN Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 763 GLN Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 695 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 281 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 273 optimal weight: 0.0870 chunk 262 optimal weight: 6.9990 chunk 105 optimal weight: 0.0570 chunk 264 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN C 404 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN F 404 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.135874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109129 restraints weight = 40183.104| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.98 r_work: 0.3200 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26658 Z= 0.129 Angle : 0.712 8.418 36018 Z= 0.340 Chirality : 0.044 0.191 3984 Planarity : 0.005 0.064 4710 Dihedral : 12.067 176.863 3786 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.63 % Allowed : 19.33 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.02 (0.15), residues: 3258 helix: 1.03 (0.12), residues: 1776 sheet: -1.98 (0.26), residues: 354 loop : -0.83 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 741 TYR 0.017 0.001 TYR E 244 PHE 0.013 0.001 PHE B 742 TRP 0.006 0.001 TRP B 454 HIS 0.004 0.001 HIS F 226 Details of bonding type rmsd covalent geometry : bond 0.00297 (26658) covalent geometry : angle 0.71159 (36018) hydrogen bonds : bond 0.03304 ( 1327) hydrogen bonds : angle 4.52641 ( 3801) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 605 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.8384 (tp) cc_final: 0.8149 (tp) REVERT: A 236 LYS cc_start: 0.9074 (mmmt) cc_final: 0.8577 (pttt) REVERT: A 273 GLU cc_start: 0.8302 (pp20) cc_final: 0.7826 (tp30) REVERT: A 317 HIS cc_start: 0.6967 (t-90) cc_final: 0.6422 (t-90) REVERT: A 366 GLU cc_start: 0.8705 (mp0) cc_final: 0.8064 (mp0) REVERT: A 404 HIS cc_start: 0.8981 (t70) cc_final: 0.8695 (t70) REVERT: A 451 ASP cc_start: 0.8250 (m-30) cc_final: 0.8027 (m-30) REVERT: A 458 GLN cc_start: 0.7676 (tt0) cc_final: 0.7105 (tt0) REVERT: A 486 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8224 (mttm) REVERT: A 488 GLU cc_start: 0.8533 (tp30) cc_final: 0.8294 (tp30) REVERT: A 546 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7074 (tm-30) REVERT: A 550 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.7801 (mpp) REVERT: A 577 ASP cc_start: 0.8423 (t0) cc_final: 0.8033 (t0) REVERT: A 578 GLU cc_start: 0.8553 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 607 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7760 (mm-30) REVERT: A 712 GLU cc_start: 0.7947 (tp30) cc_final: 0.7663 (tm-30) REVERT: A 755 TYR cc_start: 0.6820 (m-10) cc_final: 0.6589 (m-10) REVERT: A 756 GLU cc_start: 0.8411 (tp30) cc_final: 0.7613 (pt0) REVERT: A 763 GLN cc_start: 0.5712 (OUTLIER) cc_final: 0.5308 (tp-100) REVERT: B 205 ASP cc_start: 0.8656 (t0) cc_final: 0.7982 (t0) REVERT: B 236 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8523 (pttt) REVERT: B 253 LEU cc_start: 0.8281 (tp) cc_final: 0.7815 (tp) REVERT: B 304 ASP cc_start: 0.8936 (t0) cc_final: 0.8681 (t0) REVERT: B 305 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7949 (mm-30) REVERT: B 317 HIS cc_start: 0.6821 (t-90) cc_final: 0.6198 (t-90) REVERT: B 366 GLU cc_start: 0.8780 (mp0) cc_final: 0.8102 (mp0) REVERT: B 491 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8209 (tm-30) REVERT: B 578 GLU cc_start: 0.8581 (mt-10) cc_final: 0.7940 (mt-10) REVERT: B 607 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 649 ASP cc_start: 0.8103 (t70) cc_final: 0.7877 (t0) REVERT: B 712 GLU cc_start: 0.8030 (tp30) cc_final: 0.7766 (tm-30) REVERT: B 738 GLU cc_start: 0.8422 (tp30) cc_final: 0.8070 (tp30) REVERT: B 752 ILE cc_start: 0.8737 (tt) cc_final: 0.8330 (tt) REVERT: B 756 GLU cc_start: 0.8556 (tp30) cc_final: 0.7718 (pt0) REVERT: B 763 GLN cc_start: 0.5972 (OUTLIER) cc_final: 0.5558 (tp-100) REVERT: C 236 LYS cc_start: 0.9098 (mmmt) cc_final: 0.8495 (pttt) REVERT: C 253 LEU cc_start: 0.8217 (tp) cc_final: 0.7883 (tp) REVERT: C 317 HIS cc_start: 0.7044 (t-90) cc_final: 0.6572 (t70) REVERT: C 366 GLU cc_start: 0.8798 (mp0) cc_final: 0.8199 (mp0) REVERT: C 388 MET cc_start: 0.9286 (tpp) cc_final: 0.8685 (tpp) REVERT: C 427 MET cc_start: 0.5170 (ppp) cc_final: 0.4836 (ppp) REVERT: C 451 ASP cc_start: 0.8254 (m-30) cc_final: 0.7812 (m-30) REVERT: C 486 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8156 (mtmm) REVERT: C 491 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8123 (tm-30) REVERT: C 578 GLU cc_start: 0.8584 (mt-10) cc_final: 0.7923 (mt-10) REVERT: C 607 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8039 (mm-30) REVERT: C 608 MET cc_start: 0.8773 (mtp) cc_final: 0.8449 (ttm) REVERT: C 741 ARG cc_start: 0.7893 (mtm110) cc_final: 0.7541 (mtm110) REVERT: C 752 ILE cc_start: 0.8814 (tt) cc_final: 0.8358 (tt) REVERT: C 755 TYR cc_start: 0.6848 (m-10) cc_final: 0.6598 (m-10) REVERT: C 756 GLU cc_start: 0.8486 (tp30) cc_final: 0.7735 (pt0) REVERT: D 213 LEU cc_start: 0.8249 (tp) cc_final: 0.7993 (tp) REVERT: D 218 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8394 (tm-30) REVERT: D 236 LYS cc_start: 0.9079 (mmmt) cc_final: 0.8590 (pttt) REVERT: D 273 GLU cc_start: 0.8301 (pp20) cc_final: 0.7824 (tp30) REVERT: D 317 HIS cc_start: 0.6924 (t-90) cc_final: 0.6488 (t-90) REVERT: D 319 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6959 (tm-30) REVERT: D 366 GLU cc_start: 0.8672 (mp0) cc_final: 0.8006 (mp0) REVERT: D 404 HIS cc_start: 0.8994 (t70) cc_final: 0.8716 (t70) REVERT: D 451 ASP cc_start: 0.8102 (m-30) cc_final: 0.7300 (m-30) REVERT: D 458 GLN cc_start: 0.7673 (tt0) cc_final: 0.7108 (tt0) REVERT: D 486 LYS cc_start: 0.8478 (mtpp) cc_final: 0.8217 (mttm) REVERT: D 546 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7086 (tm-30) REVERT: D 550 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.7819 (mpp) REVERT: D 577 ASP cc_start: 0.8419 (t0) cc_final: 0.8031 (t0) REVERT: D 578 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7745 (mt-10) REVERT: D 607 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7794 (mm-30) REVERT: D 615 LYS cc_start: 0.8478 (ptpt) cc_final: 0.7958 (ptmm) REVERT: D 616 ASN cc_start: 0.7801 (t0) cc_final: 0.7143 (t0) REVERT: D 712 GLU cc_start: 0.7954 (tp30) cc_final: 0.7667 (tm-30) REVERT: D 755 TYR cc_start: 0.6844 (m-10) cc_final: 0.6597 (m-10) REVERT: D 756 GLU cc_start: 0.8416 (tp30) cc_final: 0.7621 (pt0) REVERT: D 763 GLN cc_start: 0.5698 (OUTLIER) cc_final: 0.5351 (tp-100) REVERT: E 205 ASP cc_start: 0.8655 (t0) cc_final: 0.7971 (t0) REVERT: E 236 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8477 (pttt) REVERT: E 253 LEU cc_start: 0.8248 (tp) cc_final: 0.7772 (tp) REVERT: E 305 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8127 (mm-30) REVERT: E 317 HIS cc_start: 0.6875 (t-90) cc_final: 0.6428 (t-90) REVERT: E 366 GLU cc_start: 0.8778 (mp0) cc_final: 0.8099 (mp0) REVERT: E 388 MET cc_start: 0.9215 (tpp) cc_final: 0.8309 (mtp) REVERT: E 491 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8208 (tm-30) REVERT: E 578 GLU cc_start: 0.8583 (mt-10) cc_final: 0.7946 (mt-10) REVERT: E 607 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7723 (mm-30) REVERT: E 712 GLU cc_start: 0.8033 (tp30) cc_final: 0.7769 (tm-30) REVERT: E 738 GLU cc_start: 0.8391 (tp30) cc_final: 0.7951 (tp30) REVERT: E 752 ILE cc_start: 0.8746 (tt) cc_final: 0.8308 (tt) REVERT: E 756 GLU cc_start: 0.8553 (tp30) cc_final: 0.7711 (pt0) REVERT: E 763 GLN cc_start: 0.5951 (OUTLIER) cc_final: 0.5536 (tp-100) REVERT: F 236 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8500 (pttt) REVERT: F 253 LEU cc_start: 0.8192 (tp) cc_final: 0.7847 (tp) REVERT: F 275 MET cc_start: 0.8761 (mmm) cc_final: 0.8548 (mmm) REVERT: F 317 HIS cc_start: 0.7044 (t-90) cc_final: 0.6750 (t-90) REVERT: F 366 GLU cc_start: 0.8802 (mp0) cc_final: 0.8200 (mp0) REVERT: F 388 MET cc_start: 0.9309 (tpp) cc_final: 0.9044 (tpp) REVERT: F 427 MET cc_start: 0.5305 (ppp) cc_final: 0.4963 (ppp) REVERT: F 451 ASP cc_start: 0.8260 (m-30) cc_final: 0.7858 (m-30) REVERT: F 486 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8177 (mtmm) REVERT: F 491 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8166 (tm-30) REVERT: F 578 GLU cc_start: 0.8573 (mt-10) cc_final: 0.7930 (mt-10) REVERT: F 607 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8061 (mm-30) REVERT: F 696 LYS cc_start: 0.8008 (tttt) cc_final: 0.7558 (tptm) REVERT: F 741 ARG cc_start: 0.7985 (mtm110) cc_final: 0.7573 (mtm110) REVERT: F 752 ILE cc_start: 0.8816 (tt) cc_final: 0.8369 (tt) REVERT: F 755 TYR cc_start: 0.6860 (m-10) cc_final: 0.6611 (m-10) REVERT: F 756 GLU cc_start: 0.8482 (tp30) cc_final: 0.7733 (pt0) outliers start: 72 outliers final: 60 residues processed: 626 average time/residue: 0.1702 time to fit residues: 171.9137 Evaluate side-chains 654 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 588 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 695 CYS Chi-restraints excluded: chain D residue 763 GLN Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 763 GLN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 695 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 117 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 302 optimal weight: 0.9990 chunk 323 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 273 optimal weight: 0.4980 chunk 45 optimal weight: 0.1980 chunk 128 optimal weight: 0.9980 chunk 294 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.135893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109224 restraints weight = 40040.506| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.90 r_work: 0.3191 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26658 Z= 0.129 Angle : 0.712 8.418 36018 Z= 0.340 Chirality : 0.044 0.191 3984 Planarity : 0.005 0.064 4710 Dihedral : 12.067 176.863 3786 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.41 % Allowed : 19.66 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.02 (0.15), residues: 3258 helix: 1.03 (0.12), residues: 1776 sheet: -1.98 (0.26), residues: 354 loop : -0.83 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 741 TYR 0.017 0.001 TYR E 244 PHE 0.013 0.001 PHE B 742 TRP 0.006 0.001 TRP B 454 HIS 0.004 0.001 HIS F 226 Details of bonding type rmsd covalent geometry : bond 0.00297 (26658) covalent geometry : angle 0.71159 (36018) hydrogen bonds : bond 0.03304 ( 1327) hydrogen bonds : angle 4.52641 ( 3801) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 588 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.8373 (tp) cc_final: 0.8142 (tp) REVERT: A 236 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8569 (pttt) REVERT: A 273 GLU cc_start: 0.8302 (pp20) cc_final: 0.7825 (tp30) REVERT: A 317 HIS cc_start: 0.6965 (t-90) cc_final: 0.6417 (t-90) REVERT: A 366 GLU cc_start: 0.8708 (mp0) cc_final: 0.8069 (mp0) REVERT: A 404 HIS cc_start: 0.8979 (t70) cc_final: 0.8694 (t70) REVERT: A 451 ASP cc_start: 0.8244 (m-30) cc_final: 0.8021 (m-30) REVERT: A 458 GLN cc_start: 0.7665 (tt0) cc_final: 0.7094 (tt0) REVERT: A 486 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8224 (mttm) REVERT: A 488 GLU cc_start: 0.8535 (tp30) cc_final: 0.8299 (tp30) REVERT: A 546 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7078 (tm-30) REVERT: A 550 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.7792 (mpp) REVERT: A 577 ASP cc_start: 0.8435 (t0) cc_final: 0.8045 (t0) REVERT: A 578 GLU cc_start: 0.8557 (mt-10) cc_final: 0.7760 (mt-10) REVERT: A 607 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7771 (mm-30) REVERT: A 712 GLU cc_start: 0.7954 (tp30) cc_final: 0.7667 (tm-30) REVERT: A 752 ILE cc_start: 0.8717 (tt) cc_final: 0.8303 (tt) REVERT: A 755 TYR cc_start: 0.6825 (m-10) cc_final: 0.6596 (m-10) REVERT: A 756 GLU cc_start: 0.8413 (tp30) cc_final: 0.7612 (pt0) REVERT: A 763 GLN cc_start: 0.5708 (OUTLIER) cc_final: 0.5304 (tp-100) REVERT: B 205 ASP cc_start: 0.8664 (t0) cc_final: 0.7985 (t0) REVERT: B 236 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8522 (pttt) REVERT: B 253 LEU cc_start: 0.8259 (tp) cc_final: 0.7800 (tp) REVERT: B 304 ASP cc_start: 0.8934 (t0) cc_final: 0.8683 (t0) REVERT: B 305 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7948 (mm-30) REVERT: B 317 HIS cc_start: 0.6813 (t-90) cc_final: 0.6195 (t-90) REVERT: B 366 GLU cc_start: 0.8776 (mp0) cc_final: 0.8097 (mp0) REVERT: B 491 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8214 (tm-30) REVERT: B 578 GLU cc_start: 0.8582 (mt-10) cc_final: 0.7943 (mt-10) REVERT: B 607 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7753 (mm-30) REVERT: B 649 ASP cc_start: 0.8106 (t70) cc_final: 0.7880 (t0) REVERT: B 712 GLU cc_start: 0.8032 (tp30) cc_final: 0.7768 (tm-30) REVERT: B 738 GLU cc_start: 0.8318 (tp30) cc_final: 0.8071 (tp30) REVERT: B 752 ILE cc_start: 0.8741 (tt) cc_final: 0.8325 (tt) REVERT: B 756 GLU cc_start: 0.8556 (tp30) cc_final: 0.7717 (pt0) REVERT: B 763 GLN cc_start: 0.5980 (OUTLIER) cc_final: 0.5561 (tp-100) REVERT: C 236 LYS cc_start: 0.9099 (mmmt) cc_final: 0.8496 (pttt) REVERT: C 253 LEU cc_start: 0.8207 (tp) cc_final: 0.7878 (tp) REVERT: C 317 HIS cc_start: 0.7041 (t-90) cc_final: 0.6571 (t70) REVERT: C 366 GLU cc_start: 0.8797 (mp0) cc_final: 0.8196 (mp0) REVERT: C 388 MET cc_start: 0.9289 (tpp) cc_final: 0.8696 (tpp) REVERT: C 427 MET cc_start: 0.5177 (ppp) cc_final: 0.4842 (ppp) REVERT: C 451 ASP cc_start: 0.8255 (m-30) cc_final: 0.7815 (m-30) REVERT: C 486 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8158 (mtmm) REVERT: C 491 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8142 (tm-30) REVERT: C 578 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7915 (mt-10) REVERT: C 607 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8050 (mm-30) REVERT: C 608 MET cc_start: 0.8779 (mtp) cc_final: 0.8449 (ttm) REVERT: C 741 ARG cc_start: 0.7900 (mtm110) cc_final: 0.7552 (mtm110) REVERT: C 752 ILE cc_start: 0.8815 (tt) cc_final: 0.8358 (tt) REVERT: C 755 TYR cc_start: 0.6856 (m-10) cc_final: 0.6605 (m-10) REVERT: C 756 GLU cc_start: 0.8486 (tp30) cc_final: 0.7735 (pt0) REVERT: D 213 LEU cc_start: 0.8250 (tp) cc_final: 0.7996 (tp) REVERT: D 218 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8396 (tm-30) REVERT: D 236 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8587 (pttt) REVERT: D 273 GLU cc_start: 0.8302 (pp20) cc_final: 0.7826 (tp30) REVERT: D 317 HIS cc_start: 0.6933 (t-90) cc_final: 0.6493 (t-90) REVERT: D 319 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6960 (tm-30) REVERT: D 366 GLU cc_start: 0.8668 (mp0) cc_final: 0.8001 (mp0) REVERT: D 404 HIS cc_start: 0.8994 (t70) cc_final: 0.8715 (t70) REVERT: D 451 ASP cc_start: 0.8100 (m-30) cc_final: 0.7294 (m-30) REVERT: D 458 GLN cc_start: 0.7649 (tt0) cc_final: 0.7085 (tt0) REVERT: D 486 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8235 (mttm) REVERT: D 546 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7088 (tm-30) REVERT: D 550 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.7813 (mpp) REVERT: D 577 ASP cc_start: 0.8423 (t0) cc_final: 0.8034 (t0) REVERT: D 578 GLU cc_start: 0.8523 (mt-10) cc_final: 0.7740 (mt-10) REVERT: D 607 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7797 (mm-30) REVERT: D 615 LYS cc_start: 0.8475 (ptpt) cc_final: 0.7957 (ptmm) REVERT: D 616 ASN cc_start: 0.7807 (t0) cc_final: 0.7150 (t0) REVERT: D 712 GLU cc_start: 0.7958 (tp30) cc_final: 0.7670 (tm-30) REVERT: D 752 ILE cc_start: 0.8726 (tt) cc_final: 0.8313 (tt) REVERT: D 755 TYR cc_start: 0.6844 (m-10) cc_final: 0.6602 (m-10) REVERT: D 756 GLU cc_start: 0.8418 (tp30) cc_final: 0.7618 (pt0) REVERT: D 763 GLN cc_start: 0.5732 (OUTLIER) cc_final: 0.5371 (tp-100) REVERT: E 205 ASP cc_start: 0.8662 (t0) cc_final: 0.7972 (t0) REVERT: E 236 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8477 (pttt) REVERT: E 253 LEU cc_start: 0.8246 (tp) cc_final: 0.7772 (tp) REVERT: E 305 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8123 (mm-30) REVERT: E 317 HIS cc_start: 0.6878 (t-90) cc_final: 0.6432 (t-90) REVERT: E 366 GLU cc_start: 0.8775 (mp0) cc_final: 0.8099 (mp0) REVERT: E 388 MET cc_start: 0.9212 (tpp) cc_final: 0.8300 (mtp) REVERT: E 491 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8209 (tm-30) REVERT: E 578 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7936 (mt-10) REVERT: E 607 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7729 (mm-30) REVERT: E 712 GLU cc_start: 0.8037 (tp30) cc_final: 0.7772 (tm-30) REVERT: E 738 GLU cc_start: 0.8350 (tp30) cc_final: 0.7956 (tp30) REVERT: E 752 ILE cc_start: 0.8752 (tt) cc_final: 0.8308 (tt) REVERT: E 756 GLU cc_start: 0.8554 (tp30) cc_final: 0.7711 (pt0) REVERT: E 763 GLN cc_start: 0.5962 (OUTLIER) cc_final: 0.5542 (tp-100) REVERT: F 236 LYS cc_start: 0.9096 (mmmt) cc_final: 0.8495 (pttt) REVERT: F 253 LEU cc_start: 0.8184 (tp) cc_final: 0.7843 (tp) REVERT: F 275 MET cc_start: 0.8764 (mmm) cc_final: 0.8552 (mmm) REVERT: F 317 HIS cc_start: 0.7038 (t-90) cc_final: 0.6743 (t-90) REVERT: F 366 GLU cc_start: 0.8802 (mp0) cc_final: 0.8198 (mp0) REVERT: F 388 MET cc_start: 0.9315 (tpp) cc_final: 0.9052 (tpp) REVERT: F 427 MET cc_start: 0.5296 (ppp) cc_final: 0.4958 (ppp) REVERT: F 451 ASP cc_start: 0.8256 (m-30) cc_final: 0.7854 (m-30) REVERT: F 486 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8170 (mtmm) REVERT: F 491 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8162 (tm-30) REVERT: F 578 GLU cc_start: 0.8575 (mt-10) cc_final: 0.7936 (mt-10) REVERT: F 607 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8066 (mm-30) REVERT: F 696 LYS cc_start: 0.8004 (tttt) cc_final: 0.7553 (tptm) REVERT: F 741 ARG cc_start: 0.7991 (mtm110) cc_final: 0.7579 (mtm110) REVERT: F 752 ILE cc_start: 0.8807 (tt) cc_final: 0.8351 (tt) REVERT: F 755 TYR cc_start: 0.6858 (m-10) cc_final: 0.6610 (m-10) REVERT: F 756 GLU cc_start: 0.8485 (tp30) cc_final: 0.7733 (pt0) outliers start: 66 outliers final: 60 residues processed: 606 average time/residue: 0.1753 time to fit residues: 172.0336 Evaluate side-chains 652 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 586 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 695 CYS Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 695 CYS Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 763 GLN Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 695 CYS Chi-restraints excluded: chain D residue 763 GLN Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 695 CYS Chi-restraints excluded: chain E residue 763 GLN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 695 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 1 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 283 optimal weight: 0.1980 chunk 172 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 404 HIS ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN C 404 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 404 HIS ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN F 404 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108331 restraints weight = 40176.718| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.98 r_work: 0.3176 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26658 Z= 0.142 Angle : 0.724 9.298 36018 Z= 0.345 Chirality : 0.045 0.201 3984 Planarity : 0.005 0.075 4710 Dihedral : 12.030 179.702 3786 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.56 % Allowed : 19.37 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.08 (0.15), residues: 3258 helix: 1.11 (0.12), residues: 1740 sheet: -1.90 (0.26), residues: 354 loop : -0.81 (0.20), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 625 TYR 0.013 0.001 TYR B 244 PHE 0.027 0.001 PHE B 682 TRP 0.006 0.001 TRP B 454 HIS 0.004 0.001 HIS F 226 Details of bonding type rmsd covalent geometry : bond 0.00332 (26658) covalent geometry : angle 0.72373 (36018) hydrogen bonds : bond 0.03298 ( 1327) hydrogen bonds : angle 4.51007 ( 3801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6656.80 seconds wall clock time: 114 minutes 53.24 seconds (6893.24 seconds total)