Starting phenix.real_space_refine on Fri Mar 6 02:00:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a8v_15241/03_2026/8a8v_15241.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a8v_15241/03_2026/8a8v_15241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a8v_15241/03_2026/8a8v_15241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a8v_15241/03_2026/8a8v_15241.map" model { file = "/net/cci-nas-00/data/ceres_data/8a8v_15241/03_2026/8a8v_15241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a8v_15241/03_2026/8a8v_15241.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 66 5.16 5 C 17044 2.51 5 N 4838 2.21 5 O 5196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27164 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4403 Classifications: {'peptide': 558} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 540} Chain breaks: 4 Chain: "B" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4483 Classifications: {'peptide': 568} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 548} Chain breaks: 3 Chain: "C" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4510 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 553} Chain breaks: 2 Chain: "D" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4530 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 555} Chain breaks: 2 Chain: "E" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4490 Classifications: {'peptide': 569} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 548} Chain breaks: 3 Chain: "F" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4364 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 532} Chain breaks: 5 Chain: "G" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 114 Classifications: {'peptide': 23} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.15, per 1000 atoms: 0.23 Number of scatterers: 27164 At special positions: 0 Unit cell: (123.12, 139.365, 148.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 20 15.00 O 5196 8.00 N 4838 7.00 C 17044 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: 2.19 Conformation dependent library (CDL) restraints added in 999.4 milliseconds 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6310 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 28 sheets defined 59.3% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 177 through 185 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 221 through 236 Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.511A pdb=" N LYS A 243 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 290 through 295 removed outlier: 4.440A pdb=" N GLY A 294 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 Proline residue: A 310 - end of helix Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 351 through 371 removed outlier: 4.663A pdb=" N ASP A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 removed outlier: 4.280A pdb=" N ARG A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 415 removed outlier: 3.960A pdb=" N MET A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 493 Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 502 through 509 removed outlier: 3.555A pdb=" N ARG A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 521 through 537 Processing helix chain 'A' and resid 558 through 572 Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.632A pdb=" N ARG A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 631 through 645 Processing helix chain 'A' and resid 690 through 705 removed outlier: 3.622A pdb=" N LYS A 694 " --> pdb=" O TYR A 690 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 702 " --> pdb=" O ASN A 698 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 4.142A pdb=" N LEU A 710 " --> pdb=" O ARG A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 743 Processing helix chain 'A' and resid 744 through 746 No H-bonds generated for 'chain 'A' and resid 744 through 746' Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 772 through 780 removed outlier: 3.906A pdb=" N GLN A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 791 Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.673A pdb=" N GLU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 204 Processing helix chain 'B' and resid 221 through 236 Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 262 through 280 removed outlier: 4.743A pdb=" N GLU B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 293 removed outlier: 3.572A pdb=" N VAL B 293 " --> pdb=" O HIS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 315 removed outlier: 3.601A pdb=" N ILE B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Proline residue: B 310 - end of helix removed outlier: 3.750A pdb=" N ARG B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 335 through 341 removed outlier: 3.849A pdb=" N ARG B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 371 removed outlier: 4.669A pdb=" N ASP B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 390 Processing helix chain 'B' and resid 396 through 415 Processing helix chain 'B' and resid 480 through 493 Processing helix chain 'B' and resid 500 through 509 Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 521 through 538 removed outlier: 3.599A pdb=" N GLY B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 572 removed outlier: 3.939A pdb=" N SER B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 575 No H-bonds generated for 'chain 'B' and resid 573 through 575' Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing helix chain 'B' and resid 590 through 596 removed outlier: 3.574A pdb=" N LEU B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.705A pdb=" N LYS B 613 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 631 removed outlier: 3.620A pdb=" N LYS B 629 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA B 630 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N HIS B 631 " --> pdb=" O GLU B 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 626 through 631' Processing helix chain 'B' and resid 632 through 644 removed outlier: 3.973A pdb=" N ASN B 636 " --> pdb=" O GLN B 632 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLN B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 705 Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 723 through 743 removed outlier: 3.845A pdb=" N ASP B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 746 No H-bonds generated for 'chain 'B' and resid 744 through 746' Processing helix chain 'B' and resid 752 through 763 Processing helix chain 'B' and resid 770 through 780 Processing helix chain 'B' and resid 781 through 791 Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.765A pdb=" N PHE C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 170 through 174' Processing helix chain 'C' and resid 178 through 184 removed outlier: 4.063A pdb=" N GLU C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 221 through 236 removed outlier: 3.557A pdb=" N VAL C 226 " --> pdb=" O LYS C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.561A pdb=" N LYS C 243 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 280 Processing helix chain 'C' and resid 289 through 292 Processing helix chain 'C' and resid 303 through 314 Proline residue: C 310 - end of helix removed outlier: 3.559A pdb=" N ARG C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 335 through 341 Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 362 through 371 removed outlier: 3.693A pdb=" N TYR C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 389 Processing helix chain 'C' and resid 396 through 415 removed outlier: 3.563A pdb=" N MET C 415 " --> pdb=" O ARG C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 493 removed outlier: 3.531A pdb=" N ILE C 484 " --> pdb=" O ASP C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 509 Processing helix chain 'C' and resid 509 through 516 removed outlier: 3.508A pdb=" N GLU C 513 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 537 Processing helix chain 'C' and resid 558 through 572 removed outlier: 3.923A pdb=" N SER C 563 " --> pdb=" O LYS C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 590 Processing helix chain 'C' and resid 591 through 596 removed outlier: 4.315A pdb=" N PHE C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 617 removed outlier: 3.760A pdb=" N GLU C 612 " --> pdb=" O GLY C 608 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 613 " --> pdb=" O GLN C 609 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 630 Processing helix chain 'C' and resid 631 through 645 removed outlier: 4.108A pdb=" N TYR C 635 " --> pdb=" O HIS C 631 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLN C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL C 641 " --> pdb=" O SER C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 705 Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.561A pdb=" N LEU C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 743 Processing helix chain 'C' and resid 744 through 746 No H-bonds generated for 'chain 'C' and resid 744 through 746' Processing helix chain 'C' and resid 752 through 762 Processing helix chain 'C' and resid 773 through 781 removed outlier: 3.552A pdb=" N ILE C 777 " --> pdb=" O LEU C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 791 Processing helix chain 'D' and resid 170 through 174 Processing helix chain 'D' and resid 178 through 184 removed outlier: 3.925A pdb=" N GLU D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 221 through 236 removed outlier: 3.898A pdb=" N VAL D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 263 through 280 Processing helix chain 'D' and resid 289 through 293 removed outlier: 3.909A pdb=" N VAL D 293 " --> pdb=" O HIS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 314 removed outlier: 3.589A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) Proline residue: D 310 - end of helix removed outlier: 3.790A pdb=" N ARG D 314 " --> pdb=" O PRO D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 335 through 342 removed outlier: 3.590A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 371 removed outlier: 4.694A pdb=" N ASP D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARG D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 390 removed outlier: 3.665A pdb=" N MET D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 380 " --> pdb=" O ASP D 376 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 390 " --> pdb=" O ALA D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 415 removed outlier: 3.548A pdb=" N MET D 415 " --> pdb=" O ARG D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 493 Processing helix chain 'D' and resid 500 through 509 Processing helix chain 'D' and resid 509 through 516 Processing helix chain 'D' and resid 521 through 537 Processing helix chain 'D' and resid 558 through 572 removed outlier: 3.657A pdb=" N SER D 563 " --> pdb=" O LYS D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 577 removed outlier: 3.579A pdb=" N ALA D 576 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 585 No H-bonds generated for 'chain 'D' and resid 583 through 585' Processing helix chain 'D' and resid 587 through 590 Processing helix chain 'D' and resid 591 through 596 removed outlier: 3.731A pdb=" N PHE D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 617 Processing helix chain 'D' and resid 632 through 644 removed outlier: 3.784A pdb=" N ASN D 636 " --> pdb=" O GLN D 632 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER D 637 " --> pdb=" O GLU D 633 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 638 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLN D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL D 641 " --> pdb=" O SER D 637 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 705 Processing helix chain 'D' and resid 706 through 711 Processing helix chain 'D' and resid 723 through 744 removed outlier: 3.726A pdb=" N ASP D 732 " --> pdb=" O ILE D 728 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL D 738 " --> pdb=" O MET D 734 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER D 744 " --> pdb=" O GLY D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 763 Processing helix chain 'D' and resid 770 through 781 removed outlier: 3.624A pdb=" N ARG D 774 " --> pdb=" O ALA D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 791 Processing helix chain 'E' and resid 169 through 174 removed outlier: 3.505A pdb=" N PHE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 193 through 204 Processing helix chain 'E' and resid 221 through 236 removed outlier: 3.745A pdb=" N VAL E 226 " --> pdb=" O LYS E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 257 Processing helix chain 'E' and resid 263 through 280 Processing helix chain 'E' and resid 289 through 293 removed outlier: 4.058A pdb=" N VAL E 293 " --> pdb=" O HIS E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 315 removed outlier: 3.581A pdb=" N ILE E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Proline residue: E 310 - end of helix Processing helix chain 'E' and resid 324 through 332 removed outlier: 3.586A pdb=" N ARG E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 332 " --> pdb=" O TYR E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 340 removed outlier: 3.988A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 362 Processing helix chain 'E' and resid 362 through 371 removed outlier: 3.546A pdb=" N TYR E 366 " --> pdb=" O LEU E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 390 removed outlier: 3.547A pdb=" N THR E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 415 removed outlier: 3.961A pdb=" N LEU E 402 " --> pdb=" O LYS E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 493 removed outlier: 3.822A pdb=" N ILE E 484 " --> pdb=" O ASP E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 509 removed outlier: 3.537A pdb=" N ARG E 509 " --> pdb=" O THR E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 516 Processing helix chain 'E' and resid 521 through 537 Processing helix chain 'E' and resid 558 through 572 removed outlier: 3.570A pdb=" N SER E 563 " --> pdb=" O LYS E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 577 removed outlier: 3.660A pdb=" N ALA E 576 " --> pdb=" O ASP E 573 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 577 " --> pdb=" O ASP E 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 573 through 577' Processing helix chain 'E' and resid 591 through 596 removed outlier: 3.637A pdb=" N PHE E 595 " --> pdb=" O ALA E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 617 Processing helix chain 'E' and resid 626 through 630 Processing helix chain 'E' and resid 631 through 645 removed outlier: 4.076A pdb=" N TYR E 635 " --> pdb=" O HIS E 631 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER E 637 " --> pdb=" O GLU E 633 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN E 640 " --> pdb=" O ASN E 636 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL E 641 " --> pdb=" O SER E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 691 through 705 Processing helix chain 'E' and resid 706 through 711 removed outlier: 3.521A pdb=" N LEU E 710 " --> pdb=" O ARG E 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 743 Processing helix chain 'E' and resid 744 through 746 No H-bonds generated for 'chain 'E' and resid 744 through 746' Processing helix chain 'E' and resid 752 through 763 Processing helix chain 'E' and resid 770 through 781 removed outlier: 3.975A pdb=" N ARG E 774 " --> pdb=" O ALA E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 791 removed outlier: 3.696A pdb=" N LEU E 790 " --> pdb=" O SER E 786 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE E 791 " --> pdb=" O GLU E 787 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 174 No H-bonds generated for 'chain 'F' and resid 171 through 174' Processing helix chain 'F' and resid 178 through 185 removed outlier: 4.107A pdb=" N MET F 183 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU F 184 " --> pdb=" O ALA F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 221 through 236 removed outlier: 3.802A pdb=" N VAL F 226 " --> pdb=" O LYS F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 280 Processing helix chain 'F' and resid 289 through 292 Processing helix chain 'F' and resid 304 through 314 removed outlier: 3.627A pdb=" N LYS F 309 " --> pdb=" O ALA F 305 " (cutoff:3.500A) Proline residue: F 310 - end of helix Processing helix chain 'F' and resid 324 through 331 Processing helix chain 'F' and resid 351 through 371 removed outlier: 4.723A pdb=" N ASP F 364 " --> pdb=" O LYS F 360 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ARG F 365 " --> pdb=" O GLY F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 390 removed outlier: 3.668A pdb=" N ILE F 390 " --> pdb=" O ALA F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 415 removed outlier: 3.851A pdb=" N LEU F 402 " --> pdb=" O LYS F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 493 Processing helix chain 'F' and resid 502 through 509 Processing helix chain 'F' and resid 509 through 516 removed outlier: 3.971A pdb=" N GLU F 513 " --> pdb=" O ARG F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 537 removed outlier: 3.704A pdb=" N ALA F 537 " --> pdb=" O ARG F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 571 Processing helix chain 'F' and resid 587 through 592 Processing helix chain 'F' and resid 610 through 617 removed outlier: 3.531A pdb=" N LYS F 617 " --> pdb=" O LYS F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 630 removed outlier: 3.633A pdb=" N ALA F 630 " --> pdb=" O ILE F 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 627 through 630' Processing helix chain 'F' and resid 631 through 645 Processing helix chain 'F' and resid 688 through 704 Processing helix chain 'F' and resid 706 through 712 removed outlier: 3.838A pdb=" N LEU F 710 " --> pdb=" O ARG F 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 744 removed outlier: 3.720A pdb=" N LEU F 733 " --> pdb=" O ARG F 729 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG F 737 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL F 738 " --> pdb=" O MET F 734 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 763 Processing helix chain 'F' and resid 770 through 781 removed outlier: 3.685A pdb=" N ARG F 774 " --> pdb=" O ALA F 770 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG F 775 " --> pdb=" O ARG F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 792 removed outlier: 3.552A pdb=" N LEU F 790 " --> pdb=" O SER F 786 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 250 removed outlier: 8.108A pdb=" N ILE A 320 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 284 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA A 322 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A 286 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 374 removed outlier: 6.630A pdb=" N SER A 373 " --> pdb=" O VAL A 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 581 removed outlier: 3.625A pdb=" N ILE A 580 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 625 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY A 547 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE A 664 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE A 549 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER A 548 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE A 717 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 550 " --> pdb=" O ILE A 717 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 Processing sheet with id=AA5, first strand: chain 'A' and resid 748 through 751 Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 177 removed outlier: 5.142A pdb=" N ASP B 287 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 373 through 374 removed outlier: 6.281A pdb=" N SER B 373 " --> pdb=" O VAL B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 577 through 581 removed outlier: 6.293A pdb=" N ILE B 578 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASP B 625 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 580 " --> pdb=" O ASP B 625 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 622 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR B 665 " --> pdb=" O VAL B 622 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE B 624 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY B 547 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE B 664 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE B 549 " --> pdb=" O PHE B 664 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B 548 " --> pdb=" O ASP B 715 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE B 717 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE B 550 " --> pdb=" O ILE B 717 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 Processing sheet with id=AB1, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.444A pdb=" N ALA B 748 " --> pdb=" O VAL B 800 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL B 802 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B 750 " --> pdb=" O VAL B 802 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N VAL B 804 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 175 through 177 removed outlier: 5.178A pdb=" N ASP C 287 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 578 through 581 removed outlier: 6.391A pdb=" N VAL C 622 " --> pdb=" O ILE C 663 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR C 665 " --> pdb=" O VAL C 622 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE C 624 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLY C 547 " --> pdb=" O LEU C 662 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE C 664 " --> pdb=" O GLY C 547 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE C 549 " --> pdb=" O PHE C 664 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N SER C 666 " --> pdb=" O PHE C 549 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE C 551 " --> pdb=" O SER C 666 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER C 548 " --> pdb=" O ASP C 715 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE C 717 " --> pdb=" O SER C 548 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE C 550 " --> pdb=" O ILE C 717 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 646 through 648 Processing sheet with id=AB5, first strand: chain 'C' and resid 749 through 751 removed outlier: 7.024A pdb=" N VAL C 750 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N VAL C 804 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 175 through 177 removed outlier: 6.072A pdb=" N GLN D 246 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE D 285 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR D 248 " --> pdb=" O PHE D 285 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP D 287 " --> pdb=" O TYR D 248 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU D 250 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL D 213 " --> pdb=" O VAL D 345 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 373 through 374 removed outlier: 6.658A pdb=" N SER D 373 " --> pdb=" O VAL D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 578 through 581 removed outlier: 6.714A pdb=" N ILE D 578 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASP D 625 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE D 580 " --> pdb=" O ASP D 625 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL D 622 " --> pdb=" O ILE D 663 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR D 665 " --> pdb=" O VAL D 622 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE D 624 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER D 548 " --> pdb=" O ASP D 715 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE D 717 " --> pdb=" O SER D 548 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE D 550 " --> pdb=" O ILE D 717 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 646 through 648 Processing sheet with id=AC1, first strand: chain 'D' and resid 748 through 751 Processing sheet with id=AC2, first strand: chain 'E' and resid 175 through 177 removed outlier: 5.000A pdb=" N ASP E 287 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA E 322 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN E 211 " --> pdb=" O GLN E 343 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL E 345 " --> pdb=" O ASN E 211 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL E 213 " --> pdb=" O VAL E 345 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 373 through 374 removed outlier: 6.700A pdb=" N SER E 373 " --> pdb=" O VAL E 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 578 through 581 removed outlier: 6.098A pdb=" N GLY E 547 " --> pdb=" O LEU E 662 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE E 664 " --> pdb=" O GLY E 547 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE E 549 " --> pdb=" O PHE E 664 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N SER E 666 " --> pdb=" O PHE E 549 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE E 551 " --> pdb=" O SER E 666 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N SER E 548 " --> pdb=" O ASP E 715 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE E 717 " --> pdb=" O SER E 548 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE E 550 " --> pdb=" O ILE E 717 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 646 through 648 Processing sheet with id=AC6, first strand: chain 'E' and resid 749 through 751 Processing sheet with id=AC7, first strand: chain 'F' and resid 175 through 177 removed outlier: 6.020A pdb=" N GLN F 246 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE F 285 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR F 248 " --> pdb=" O PHE F 285 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASP F 287 " --> pdb=" O TYR F 248 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU F 250 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE F 282 " --> pdb=" O GLN F 318 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ILE F 320 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU F 284 " --> pdb=" O ILE F 320 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ALA F 322 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE F 286 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASN F 211 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL F 345 " --> pdb=" O ASN F 211 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL F 213 " --> pdb=" O VAL F 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 578 through 581 removed outlier: 6.962A pdb=" N ILE F 578 " --> pdb=" O LEU F 623 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASP F 625 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE F 580 " --> pdb=" O ASP F 625 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY F 547 " --> pdb=" O LEU F 662 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE F 664 " --> pdb=" O GLY F 547 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE F 549 " --> pdb=" O PHE F 664 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N SER F 666 " --> pdb=" O PHE F 549 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE F 551 " --> pdb=" O SER F 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 646 through 648 Processing sheet with id=AD1, first strand: chain 'F' and resid 748 through 751 removed outlier: 6.153A pdb=" N ALA F 748 " --> pdb=" O VAL F 800 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL F 802 " --> pdb=" O ALA F 748 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL F 750 " --> pdb=" O VAL F 802 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N VAL F 804 " --> pdb=" O VAL F 750 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR F 801 " --> pdb=" O THR F 821 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR F 821 " --> pdb=" O THR F 801 " (cutoff:3.500A) 1320 hydrogen bonds defined for protein. 3885 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: 4.62 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9245 1.34 - 1.46: 4452 1.46 - 1.58: 13693 1.58 - 1.70: 31 1.70 - 1.82: 132 Bond restraints: 27553 Sorted by residual: bond pdb=" N ASP E 732 " pdb=" CA ASP E 732 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.09e+00 bond pdb=" N MET E 734 " pdb=" CA MET E 734 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.30e-02 5.92e+03 3.75e+00 bond pdb=" N LEU E 733 " pdb=" CA LEU E 733 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.64e+00 bond pdb=" CA ARG F 712 " pdb=" C ARG F 712 " ideal model delta sigma weight residual 1.522 1.549 -0.026 1.43e-02 4.89e+03 3.35e+00 bond pdb=" CB PRO C 495 " pdb=" CG PRO C 495 " ideal model delta sigma weight residual 1.492 1.580 -0.088 5.00e-02 4.00e+02 3.13e+00 ... (remaining 27548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 36287 2.26 - 4.52: 716 4.52 - 6.78: 141 6.78 - 9.04: 17 9.04 - 11.30: 8 Bond angle restraints: 37169 Sorted by residual: angle pdb=" CA ARG F 509 " pdb=" CB ARG F 509 " pdb=" CG ARG F 509 " ideal model delta sigma weight residual 114.10 123.52 -9.42 2.00e+00 2.50e-01 2.22e+01 angle pdb=" CA PRO C 495 " pdb=" N PRO C 495 " pdb=" CD PRO C 495 " ideal model delta sigma weight residual 112.00 105.51 6.49 1.40e+00 5.10e-01 2.15e+01 angle pdb=" N VAL C 220 " pdb=" CA VAL C 220 " pdb=" C VAL C 220 " ideal model delta sigma weight residual 113.47 109.15 4.32 1.01e+00 9.80e-01 1.83e+01 angle pdb=" N LYS E 543 " pdb=" CA LYS E 543 " pdb=" C LYS E 543 " ideal model delta sigma weight residual 114.64 108.47 6.17 1.52e+00 4.33e-01 1.65e+01 angle pdb=" CB MET E 183 " pdb=" CG MET E 183 " pdb=" SD MET E 183 " ideal model delta sigma weight residual 112.70 124.00 -11.30 3.00e+00 1.11e-01 1.42e+01 ... (remaining 37164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.02: 16247 32.02 - 64.05: 565 64.05 - 96.07: 36 96.07 - 128.09: 7 128.09 - 160.11: 5 Dihedral angle restraints: 16860 sinusoidal: 7103 harmonic: 9757 Sorted by residual: dihedral pdb=" C5' ADP E 901 " pdb=" O5' ADP E 901 " pdb=" PA ADP E 901 " pdb=" O2A ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 100.12 -160.11 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O2A ADP D 902 " pdb=" O3A ADP D 902 " pdb=" PA ADP D 902 " pdb=" PB ADP D 902 " ideal model delta sinusoidal sigma weight residual -60.00 99.29 -159.29 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 83.19 -143.18 1 2.00e+01 2.50e-03 4.32e+01 ... (remaining 16857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3646 0.066 - 0.133: 563 0.133 - 0.199: 24 0.199 - 0.266: 2 0.266 - 0.332: 4 Chirality restraints: 4239 Sorted by residual: chirality pdb=" CB ILE B 716 " pdb=" CA ILE B 716 " pdb=" CG1 ILE B 716 " pdb=" CG2 ILE B 716 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE B 550 " pdb=" CA ILE B 550 " pdb=" CG1 ILE B 550 " pdb=" CG2 ILE B 550 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB VAL C 767 " pdb=" CA VAL C 767 " pdb=" CG1 VAL C 767 " pdb=" CG2 VAL C 767 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 4236 not shown) Planarity restraints: 4820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 706 " -0.059 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO C 707 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 707 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 707 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 771 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO E 772 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO E 772 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 772 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 811 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO F 812 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 812 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 812 " -0.038 5.00e-02 4.00e+02 ... (remaining 4817 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2768 2.75 - 3.28: 27148 3.28 - 3.82: 45235 3.82 - 4.36: 53876 4.36 - 4.90: 92572 Nonbonded interactions: 221599 Sorted by model distance: nonbonded pdb=" O ILE D 627 " pdb=" OH TYR D 635 " model vdw 2.208 3.040 nonbonded pdb=" NH2 ARG A 775 " pdb=" O LEU F 710 " model vdw 2.212 3.120 nonbonded pdb=" O ILE E 627 " pdb=" OH TYR E 635 " model vdw 2.227 3.040 nonbonded pdb=" NH1 ARG B 262 " pdb=" O UNK G 7 " model vdw 2.241 3.120 nonbonded pdb=" O THR F 560 " pdb=" OG SER F 563 " model vdw 2.242 3.040 ... (remaining 221594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 594 or resid 609 through 668 or resid 691 through 808 or resid 815 through 9 \ 01)) selection = (chain 'B' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 901)) selection = (chain 'C' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 901)) selection = (chain 'D' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 901)) selection = (chain 'E' and (resid 170 through 255 or resid 263 through 293 or resid 303 thro \ ugh 415 or resid 477 through 594 or resid 609 through 668 or resid 691 through 8 \ 08 or resid 815 through 901)) selection = (chain 'F' and (resid 170 through 415 or resid 477 through 668 or resid 691 thro \ ugh 808 or resid 815 through 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 9.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.860 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 : 0.004 0.088 27553 Z= 0.173 Angle : 0.791 11.301 37169 Z= 0.406 Chirality : 0.047 0.332 4239 Planarity : 0.006 0.091 4820 Dihedral : 15.570 160.114 10550 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.11 % Allowed : 0.35 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3346 helix: -0.33 (0.11), residues: 1801 sheet: -0.44 (0.24), residues: 389 loop : -0.11 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 729 TYR 0.040 0.002 TYR F 389 PHE 0.030 0.002 PHE A 265 TRP 0.014 0.001 TRP F 807 HIS 0.005 0.001 HIS D 720 Details of bonding type rmsd covalent geometry : bond 0.00391 (27553) covalent geometry : angle 0.79101 (37169) hydrogen bonds : bond 0.13675 ( 1320) hydrogen bonds : angle 6.71170 ( 3885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 370 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 ARG cc_start: 0.7502 (ptp-110) cc_final: 0.6979 (mtp180) REVERT: A 582 MET cc_start: 0.4675 (ppp) cc_final: 0.4460 (mmt) REVERT: A 779 ARG cc_start: 0.7434 (mmt180) cc_final: 0.7212 (mmm160) REVERT: B 415 MET cc_start: 0.3682 (mmm) cc_final: 0.3198 (mtt) REVERT: B 606 GLU cc_start: 0.7438 (pp20) cc_final: 0.7172 (pt0) REVERT: B 774 ARG cc_start: 0.6169 (mmm-85) cc_final: 0.5876 (mtp85) REVERT: D 331 TYR cc_start: 0.8321 (m-10) cc_final: 0.8090 (m-10) REVERT: D 518 ILE cc_start: 0.8666 (mm) cc_final: 0.8444 (mm) REVERT: D 695 GLN cc_start: 0.7710 (tp40) cc_final: 0.7477 (tp-100) REVERT: E 582 MET cc_start: 0.8037 (mmm) cc_final: 0.7805 (mmt) REVERT: E 589 PHE cc_start: 0.5554 (m-10) cc_final: 0.5033 (m-10) REVERT: E 727 ILE cc_start: 0.7575 (mm) cc_final: 0.7336 (mm) REVERT: E 734 MET cc_start: 0.8235 (mtt) cc_final: 0.7976 (mtt) outliers start: 3 outliers final: 1 residues processed: 372 average time/residue: 0.2022 time to fit residues: 113.9492 Evaluate side-chains 285 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 568 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.0050 chunk 298 optimal weight: 0.9980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 235 HIS ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 667 ASN B 211 ASN B 391 ASN B 490 ASN C 343 GLN C 391 ASN C 640 GLN C 651 GLN E 640 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.180055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143426 restraints weight = 34817.191| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.87 r_work: 0.3657 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27553 Z= 0.117 Angle : 0.594 8.087 37169 Z= 0.285 Chirality : 0.042 0.144 4239 Planarity : 0.005 0.069 4820 Dihedral : 8.659 176.043 3833 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.81 % Allowed : 7.20 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 3346 helix: 0.49 (0.12), residues: 1836 sheet: -0.50 (0.24), residues: 386 loop : 0.08 (0.20), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 329 TYR 0.017 0.001 TYR A 635 PHE 0.021 0.001 PHE C 497 TRP 0.025 0.001 TRP B 807 HIS 0.012 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00263 (27553) covalent geometry : angle 0.59411 (37169) hydrogen bonds : bond 0.03493 ( 1320) hydrogen bonds : angle 5.04387 ( 3885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 314 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 ASN cc_start: 0.6988 (m110) cc_final: 0.6667 (m110) REVERT: A 779 ARG cc_start: 0.7516 (mmt180) cc_final: 0.7307 (mmt-90) REVERT: B 339 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8271 (tt0) REVERT: B 415 MET cc_start: 0.3675 (mmm) cc_final: 0.3121 (mtt) REVERT: B 595 PHE cc_start: 0.6688 (m-80) cc_final: 0.6259 (m-10) REVERT: B 774 ARG cc_start: 0.6480 (mmm-85) cc_final: 0.6174 (mtp85) REVERT: D 695 GLN cc_start: 0.7950 (tp40) cc_final: 0.7420 (tp-100) REVERT: E 201 MET cc_start: 0.7590 (mmt) cc_final: 0.7330 (mmt) REVERT: E 589 PHE cc_start: 0.5979 (m-10) cc_final: 0.5309 (m-10) REVERT: E 732 ASP cc_start: 0.8321 (t0) cc_final: 0.7756 (m-30) outliers start: 23 outliers final: 12 residues processed: 333 average time/residue: 0.2038 time to fit residues: 102.9206 Evaluate side-chains 292 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 280 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 656 ASP Chi-restraints excluded: chain F residue 733 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 202 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 317 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 244 optimal weight: 0.0970 chunk 119 optimal weight: 0.4980 chunk 330 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 667 ASN C 568 ASN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN D 631 HIS ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.176444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137963 restraints weight = 35210.368| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.08 r_work: 0.3602 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27553 Z= 0.158 Angle : 0.610 10.615 37169 Z= 0.291 Chirality : 0.043 0.164 4239 Planarity : 0.004 0.071 4820 Dihedral : 8.279 174.825 3831 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.47 % Allowed : 10.18 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3346 helix: 0.64 (0.12), residues: 1840 sheet: -0.65 (0.24), residues: 386 loop : 0.05 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 329 TYR 0.030 0.002 TYR F 635 PHE 0.020 0.001 PHE C 549 TRP 0.010 0.001 TRP B 807 HIS 0.010 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00377 (27553) covalent geometry : angle 0.60959 (37169) hydrogen bonds : bond 0.03550 ( 1320) hydrogen bonds : angle 4.88036 ( 3885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 303 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ARG cc_start: 0.6635 (tpt170) cc_final: 0.6315 (tpt170) REVERT: A 387 ASP cc_start: 0.7875 (t0) cc_final: 0.7465 (m-30) REVERT: A 391 ASN cc_start: 0.7088 (m110) cc_final: 0.6791 (m110) REVERT: B 171 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8036 (tp) REVERT: B 267 GLU cc_start: 0.8441 (tp30) cc_final: 0.8118 (tt0) REVERT: B 339 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8356 (tt0) REVERT: B 415 MET cc_start: 0.3453 (mmm) cc_final: 0.3032 (mtt) REVERT: B 575 ASP cc_start: 0.7106 (m-30) cc_final: 0.6375 (p0) REVERT: B 667 ASN cc_start: 0.7706 (t0) cc_final: 0.7495 (t0) REVERT: B 774 ARG cc_start: 0.6584 (mmm-85) cc_final: 0.6379 (mtp85) REVERT: C 783 ASP cc_start: 0.7811 (m-30) cc_final: 0.7597 (m-30) REVERT: D 379 MET cc_start: 0.8061 (mtm) cc_final: 0.7770 (mtt) REVERT: D 581 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7115 (p0) REVERT: D 695 GLN cc_start: 0.7938 (tp40) cc_final: 0.7390 (tp-100) REVERT: E 201 MET cc_start: 0.7724 (mmt) cc_final: 0.7492 (mmt) REVERT: E 589 PHE cc_start: 0.6026 (m-10) cc_final: 0.5318 (m-10) REVERT: E 715 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: E 732 ASP cc_start: 0.8416 (t0) cc_final: 0.7791 (m-30) REVERT: F 783 ASP cc_start: 0.6928 (t70) cc_final: 0.6507 (t0) outliers start: 42 outliers final: 20 residues processed: 334 average time/residue: 0.1923 time to fit residues: 98.9429 Evaluate side-chains 305 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 282 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 715 ASP Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 244 optimal weight: 0.6980 chunk 202 optimal weight: 0.5980 chunk 215 optimal weight: 0.9990 chunk 333 optimal weight: 0.3980 chunk 292 optimal weight: 6.9990 chunk 254 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 249 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 227 optimal weight: 0.0470 chunk 77 optimal weight: 0.7980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN C 343 GLN C 391 ASN C 568 ASN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN E 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.178835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139253 restraints weight = 34784.538| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.85 r_work: 0.3629 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27553 Z= 0.107 Angle : 0.562 7.297 37169 Z= 0.265 Chirality : 0.041 0.154 4239 Planarity : 0.004 0.072 4820 Dihedral : 7.900 179.701 3831 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.79 % Allowed : 12.11 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3346 helix: 0.83 (0.12), residues: 1862 sheet: -0.59 (0.24), residues: 376 loop : 0.09 (0.20), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 329 TYR 0.032 0.001 TYR F 635 PHE 0.017 0.001 PHE F 657 TRP 0.006 0.001 TRP B 807 HIS 0.010 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00244 (27553) covalent geometry : angle 0.56238 (37169) hydrogen bonds : bond 0.02983 ( 1320) hydrogen bonds : angle 4.65583 ( 3885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 315 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 TYR cc_start: 0.5744 (m-80) cc_final: 0.5538 (m-80) REVERT: B 339 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8341 (tt0) REVERT: B 415 MET cc_start: 0.3353 (mmm) cc_final: 0.2913 (mtt) REVERT: B 575 ASP cc_start: 0.6951 (m-30) cc_final: 0.6314 (p0) REVERT: B 606 GLU cc_start: 0.7763 (pp20) cc_final: 0.7115 (pp20) REVERT: C 783 ASP cc_start: 0.7742 (m-30) cc_final: 0.7534 (m-30) REVERT: D 379 MET cc_start: 0.7943 (mtm) cc_final: 0.7724 (mtt) REVERT: D 581 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6962 (p0) REVERT: D 695 GLN cc_start: 0.7877 (tp40) cc_final: 0.7353 (tp-100) REVERT: E 339 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7958 (tp30) REVERT: E 589 PHE cc_start: 0.6067 (m-10) cc_final: 0.5326 (m-10) REVERT: E 732 ASP cc_start: 0.8326 (t0) cc_final: 0.7735 (m-30) REVERT: F 623 LEU cc_start: 0.7276 (tt) cc_final: 0.6954 (tt) outliers start: 51 outliers final: 26 residues processed: 351 average time/residue: 0.1953 time to fit residues: 105.4781 Evaluate side-chains 315 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 288 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 641 VAL Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 733 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 56 optimal weight: 3.9990 chunk 263 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 326 optimal weight: 0.6980 chunk 312 optimal weight: 3.9990 chunk 262 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 325 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 659 ASN A 667 ASN C 343 GLN C 391 ASN C 568 ASN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN F 586 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.176798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139501 restraints weight = 35062.281| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.05 r_work: 0.3596 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27553 Z= 0.134 Angle : 0.585 7.394 37169 Z= 0.278 Chirality : 0.042 0.177 4239 Planarity : 0.004 0.072 4820 Dihedral : 7.718 177.656 3831 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.93 % Allowed : 13.51 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 3346 helix: 0.91 (0.12), residues: 1850 sheet: -0.69 (0.24), residues: 399 loop : 0.19 (0.20), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 329 TYR 0.037 0.001 TYR F 635 PHE 0.027 0.001 PHE C 497 TRP 0.006 0.001 TRP B 491 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00320 (27553) covalent geometry : angle 0.58520 (37169) hydrogen bonds : bond 0.03149 ( 1320) hydrogen bonds : angle 4.65794 ( 3885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 295 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7836 (t0) cc_final: 0.7460 (m-30) REVERT: B 339 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8360 (tt0) REVERT: B 415 MET cc_start: 0.3393 (mmm) cc_final: 0.3022 (mtt) REVERT: B 595 PHE cc_start: 0.6828 (m-80) cc_final: 0.6409 (m-10) REVERT: B 606 GLU cc_start: 0.7788 (pp20) cc_final: 0.7213 (pp20) REVERT: B 787 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6876 (mt-10) REVERT: C 783 ASP cc_start: 0.7748 (m-30) cc_final: 0.7497 (m-30) REVERT: D 581 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.7039 (p0) REVERT: D 695 GLN cc_start: 0.7936 (tp40) cc_final: 0.7323 (tp-100) REVERT: E 201 MET cc_start: 0.7804 (mmt) cc_final: 0.7565 (mmt) REVERT: E 339 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8028 (tp30) REVERT: E 732 ASP cc_start: 0.8342 (t0) cc_final: 0.7747 (m-30) REVERT: F 585 PHE cc_start: 0.5942 (m-80) cc_final: 0.5640 (m-80) REVERT: F 623 LEU cc_start: 0.7262 (tt) cc_final: 0.6924 (tt) outliers start: 55 outliers final: 35 residues processed: 336 average time/residue: 0.1974 time to fit residues: 101.5769 Evaluate side-chains 314 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 277 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 635 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 733 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 327 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 302 optimal weight: 0.7980 chunk 203 optimal weight: 0.9990 chunk 190 optimal weight: 0.7980 chunk 173 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 245 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN B 667 ASN C 343 GLN C 391 ASN C 568 ASN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN F 720 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.177420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140427 restraints weight = 34911.726| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.01 r_work: 0.3601 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27553 Z= 0.126 Angle : 0.578 7.691 37169 Z= 0.275 Chirality : 0.042 0.174 4239 Planarity : 0.004 0.071 4820 Dihedral : 7.431 179.818 3831 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.11 % Allowed : 13.97 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.15), residues: 3346 helix: 0.96 (0.12), residues: 1851 sheet: -0.76 (0.24), residues: 399 loop : 0.22 (0.21), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 329 TYR 0.039 0.001 TYR F 635 PHE 0.024 0.001 PHE C 497 TRP 0.006 0.001 TRP B 491 HIS 0.004 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00295 (27553) covalent geometry : angle 0.57772 (37169) hydrogen bonds : bond 0.03059 ( 1320) hydrogen bonds : angle 4.61891 ( 3885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 300 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7896 (t0) cc_final: 0.7457 (m-30) REVERT: B 339 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8347 (tt0) REVERT: B 415 MET cc_start: 0.3247 (mmm) cc_final: 0.2896 (mtt) REVERT: B 575 ASP cc_start: 0.6960 (m-30) cc_final: 0.6295 (p0) REVERT: B 595 PHE cc_start: 0.6711 (m-80) cc_final: 0.6334 (m-10) REVERT: B 606 GLU cc_start: 0.7794 (pp20) cc_final: 0.7341 (pp20) REVERT: B 787 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6883 (mt-10) REVERT: C 783 ASP cc_start: 0.7680 (m-30) cc_final: 0.7440 (m-30) REVERT: D 581 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7234 (p0) REVERT: D 695 GLN cc_start: 0.7909 (tp40) cc_final: 0.7322 (tp-100) REVERT: E 201 MET cc_start: 0.7818 (mmt) cc_final: 0.7516 (mmt) REVERT: E 339 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8018 (tp30) REVERT: E 582 MET cc_start: 0.8622 (mmm) cc_final: 0.8317 (mmt) REVERT: E 732 ASP cc_start: 0.8311 (t0) cc_final: 0.7722 (m-30) REVERT: F 585 PHE cc_start: 0.5999 (m-80) cc_final: 0.5705 (m-80) REVERT: F 623 LEU cc_start: 0.7271 (tt) cc_final: 0.6922 (tt) REVERT: F 646 ARG cc_start: 0.7292 (tpp80) cc_final: 0.7066 (tpp80) REVERT: F 747 MET cc_start: 0.7871 (mmt) cc_final: 0.7538 (mmt) outliers start: 60 outliers final: 39 residues processed: 340 average time/residue: 0.1887 time to fit residues: 98.7432 Evaluate side-chains 328 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 287 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 635 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 604 TYR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 720 HIS Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 777 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 31 optimal weight: 0.3980 chunk 90 optimal weight: 0.4980 chunk 119 optimal weight: 0.7980 chunk 320 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 125 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 218 optimal weight: 0.7980 chunk 214 optimal weight: 0.5980 chunk 192 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN B 667 ASN C 343 GLN C 391 ASN C 568 ASN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN F 720 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.179198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.141188 restraints weight = 35074.161| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.06 r_work: 0.3612 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27553 Z= 0.113 Angle : 0.577 8.715 37169 Z= 0.274 Chirality : 0.041 0.145 4239 Planarity : 0.004 0.071 4820 Dihedral : 7.223 178.369 3831 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.11 % Allowed : 14.71 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.15), residues: 3346 helix: 1.03 (0.12), residues: 1856 sheet: -0.75 (0.24), residues: 399 loop : 0.21 (0.21), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 329 TYR 0.040 0.001 TYR F 635 PHE 0.026 0.001 PHE C 497 TRP 0.007 0.001 TRP B 491 HIS 0.007 0.001 HIS F 720 Details of bonding type rmsd covalent geometry : bond 0.00262 (27553) covalent geometry : angle 0.57668 (37169) hydrogen bonds : bond 0.02945 ( 1320) hydrogen bonds : angle 4.56679 ( 3885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 295 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 ASN cc_start: 0.7758 (t0) cc_final: 0.7505 (t0) REVERT: A 534 ARG cc_start: 0.7806 (ptp-110) cc_final: 0.7525 (ptp-110) REVERT: B 171 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8066 (tp) REVERT: B 339 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8346 (tt0) REVERT: B 415 MET cc_start: 0.3201 (mmm) cc_final: 0.2897 (mtt) REVERT: B 606 GLU cc_start: 0.7803 (pp20) cc_final: 0.7403 (pp20) REVERT: B 787 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: C 783 ASP cc_start: 0.7692 (m-30) cc_final: 0.7453 (m-30) REVERT: D 414 ARG cc_start: 0.6782 (tpt170) cc_final: 0.6451 (tpm170) REVERT: D 695 GLN cc_start: 0.7922 (tp40) cc_final: 0.7333 (tp-100) REVERT: E 201 MET cc_start: 0.7793 (mmt) cc_final: 0.7477 (mmt) REVERT: E 339 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8023 (tp30) REVERT: E 732 ASP cc_start: 0.8347 (t0) cc_final: 0.7763 (m-30) REVERT: F 582 MET cc_start: 0.5241 (mmm) cc_final: 0.4743 (mmm) REVERT: F 585 PHE cc_start: 0.6063 (m-80) cc_final: 0.5683 (m-80) REVERT: F 623 LEU cc_start: 0.7240 (tt) cc_final: 0.6877 (tt) REVERT: F 646 ARG cc_start: 0.7339 (tpp80) cc_final: 0.7063 (tpp80) REVERT: F 747 MET cc_start: 0.7951 (mmt) cc_final: 0.7648 (mmt) outliers start: 60 outliers final: 41 residues processed: 340 average time/residue: 0.1884 time to fit residues: 98.4789 Evaluate side-chains 327 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 284 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 635 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 651 GLN Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 604 TYR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 777 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 84 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 324 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 135 optimal weight: 0.9990 chunk 69 optimal weight: 0.0570 chunk 142 optimal weight: 0.0170 chunk 45 optimal weight: 0.9980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN A 667 ASN B 640 GLN C 343 GLN C 391 ASN C 568 ASN C 632 GLN C 636 ASN C 651 GLN D 640 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.178354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141412 restraints weight = 34989.205| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.03 r_work: 0.3621 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 27553 Z= 0.111 Angle : 0.579 8.325 37169 Z= 0.275 Chirality : 0.041 0.158 4239 Planarity : 0.004 0.071 4820 Dihedral : 7.086 179.403 3831 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.18 % Allowed : 15.55 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.15), residues: 3346 helix: 1.07 (0.12), residues: 1858 sheet: -0.75 (0.24), residues: 404 loop : 0.22 (0.21), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 329 TYR 0.039 0.001 TYR F 635 PHE 0.025 0.001 PHE C 497 TRP 0.007 0.001 TRP B 491 HIS 0.004 0.000 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00259 (27553) covalent geometry : angle 0.57925 (37169) hydrogen bonds : bond 0.02914 ( 1320) hydrogen bonds : angle 4.53208 ( 3885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 297 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7606 (t0) cc_final: 0.7355 (m-30) REVERT: A 490 ASN cc_start: 0.7756 (t0) cc_final: 0.7507 (t0) REVERT: A 534 ARG cc_start: 0.7786 (ptp-110) cc_final: 0.7506 (ptp-110) REVERT: A 582 MET cc_start: 0.4841 (ppp) cc_final: 0.3531 (mpp) REVERT: B 171 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8063 (tp) REVERT: B 339 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8350 (tt0) REVERT: B 606 GLU cc_start: 0.7786 (pp20) cc_final: 0.7409 (pp20) REVERT: B 787 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6937 (mt-10) REVERT: C 783 ASP cc_start: 0.7741 (m-30) cc_final: 0.7501 (m-30) REVERT: D 414 ARG cc_start: 0.6733 (tpt170) cc_final: 0.6403 (tpm170) REVERT: D 695 GLN cc_start: 0.7938 (tp40) cc_final: 0.7359 (tp-100) REVERT: E 201 MET cc_start: 0.7787 (mmt) cc_final: 0.7450 (mmt) REVERT: E 339 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7963 (tp30) REVERT: E 510 MET cc_start: 0.7690 (ptm) cc_final: 0.7012 (ttp) REVERT: E 589 PHE cc_start: 0.6190 (m-10) cc_final: 0.5611 (m-80) REVERT: E 732 ASP cc_start: 0.8391 (t0) cc_final: 0.7779 (m-30) REVERT: F 585 PHE cc_start: 0.6052 (m-80) cc_final: 0.5734 (m-80) REVERT: F 623 LEU cc_start: 0.7206 (tt) cc_final: 0.6869 (tt) REVERT: F 646 ARG cc_start: 0.7345 (tpp80) cc_final: 0.7071 (tpp80) REVERT: F 747 MET cc_start: 0.7906 (mmt) cc_final: 0.7650 (mmt) outliers start: 62 outliers final: 42 residues processed: 339 average time/residue: 0.1923 time to fit residues: 100.5747 Evaluate side-chains 335 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 291 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 604 TYR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 777 ILE Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 241 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 144 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 272 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN B 391 ASN C 343 GLN C 391 ASN C 568 ASN C 636 ASN ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.177350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142474 restraints weight = 34814.373| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.75 r_work: 0.3647 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27553 Z= 0.124 Angle : 0.596 10.164 37169 Z= 0.282 Chirality : 0.042 0.155 4239 Planarity : 0.004 0.072 4820 Dihedral : 7.030 178.501 3831 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.04 % Allowed : 15.62 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.15), residues: 3346 helix: 1.03 (0.12), residues: 1861 sheet: -0.75 (0.24), residues: 405 loop : 0.19 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 329 TYR 0.039 0.001 TYR F 635 PHE 0.047 0.001 PHE E 791 TRP 0.007 0.001 TRP B 491 HIS 0.005 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00294 (27553) covalent geometry : angle 0.59606 (37169) hydrogen bonds : bond 0.03028 ( 1320) hydrogen bonds : angle 4.55266 ( 3885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 295 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7553 (t0) cc_final: 0.7280 (m-30) REVERT: A 534 ARG cc_start: 0.7763 (ptp-110) cc_final: 0.7440 (ptp-110) REVERT: A 582 MET cc_start: 0.4807 (ppp) cc_final: 0.3514 (mpp) REVERT: B 171 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8007 (tp) REVERT: B 339 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8256 (tt0) REVERT: B 606 GLU cc_start: 0.7711 (pp20) cc_final: 0.7384 (pp20) REVERT: B 646 ARG cc_start: 0.8343 (ptm-80) cc_final: 0.8096 (ptm-80) REVERT: B 787 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: C 783 ASP cc_start: 0.7673 (m-30) cc_final: 0.7445 (m-30) REVERT: D 695 GLN cc_start: 0.7898 (tp40) cc_final: 0.7304 (tp-100) REVERT: E 201 MET cc_start: 0.7759 (mmt) cc_final: 0.7423 (mmt) REVERT: E 339 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7911 (tp30) REVERT: E 581 ASP cc_start: 0.6899 (p0) cc_final: 0.6414 (p0) REVERT: E 589 PHE cc_start: 0.6142 (m-10) cc_final: 0.5600 (m-80) REVERT: E 732 ASP cc_start: 0.8230 (t0) cc_final: 0.7683 (m-30) REVERT: F 509 ARG cc_start: 0.5438 (OUTLIER) cc_final: 0.5136 (pmt-80) REVERT: F 582 MET cc_start: 0.5110 (mmm) cc_final: 0.4721 (mmm) REVERT: F 585 PHE cc_start: 0.6042 (m-80) cc_final: 0.5564 (m-80) REVERT: F 623 LEU cc_start: 0.7200 (tt) cc_final: 0.6817 (tt) REVERT: F 624 PHE cc_start: 0.7673 (m-80) cc_final: 0.7372 (m-80) REVERT: F 646 ARG cc_start: 0.7370 (tpp80) cc_final: 0.7110 (tpp80) REVERT: F 747 MET cc_start: 0.7931 (mmt) cc_final: 0.7666 (mmt) outliers start: 58 outliers final: 42 residues processed: 337 average time/residue: 0.1963 time to fit residues: 100.9623 Evaluate side-chains 328 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 283 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 804 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 604 TYR Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 509 ARG Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 777 ILE Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 154 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 325 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN C 343 GLN C 391 ASN C 568 ASN C 651 GLN ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.174274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.137150 restraints weight = 35102.329| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.19 r_work: 0.3538 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27553 Z= 0.176 Angle : 0.649 11.193 37169 Z= 0.310 Chirality : 0.044 0.173 4239 Planarity : 0.004 0.071 4820 Dihedral : 7.270 177.305 3831 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.79 % Allowed : 15.65 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 3346 helix: 0.84 (0.12), residues: 1865 sheet: -0.92 (0.24), residues: 402 loop : 0.09 (0.21), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 329 TYR 0.038 0.002 TYR F 635 PHE 0.037 0.002 PHE E 791 TRP 0.008 0.001 TRP B 491 HIS 0.006 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00427 (27553) covalent geometry : angle 0.64937 (37169) hydrogen bonds : bond 0.03558 ( 1320) hydrogen bonds : angle 4.74533 ( 3885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6692 Ramachandran restraints generated. 3346 Oldfield, 0 Emsley, 3346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 292 time to evaluate : 1.127 Fit side-chains REVERT: A 387 ASP cc_start: 0.7792 (t0) cc_final: 0.7381 (m-30) REVERT: A 534 ARG cc_start: 0.7745 (ptp-110) cc_final: 0.7386 (ptp-110) REVERT: A 582 MET cc_start: 0.4925 (ppp) cc_final: 0.3392 (mpp) REVERT: A 635 TYR cc_start: 0.5796 (m-80) cc_final: 0.5522 (m-80) REVERT: B 171 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8021 (tp) REVERT: B 267 GLU cc_start: 0.8509 (tp30) cc_final: 0.8166 (tt0) REVERT: B 339 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8403 (tt0) REVERT: B 606 GLU cc_start: 0.7802 (pp20) cc_final: 0.7427 (pp20) REVERT: B 787 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6910 (mt-10) REVERT: C 267 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8279 (tt0) REVERT: C 783 ASP cc_start: 0.7811 (m-30) cc_final: 0.7485 (m-30) REVERT: D 695 GLN cc_start: 0.8039 (tp40) cc_final: 0.7362 (tp-100) REVERT: E 201 MET cc_start: 0.7957 (mmt) cc_final: 0.7727 (mmt) REVERT: E 339 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8071 (tp30) REVERT: E 581 ASP cc_start: 0.7228 (p0) cc_final: 0.6638 (p0) REVERT: E 732 ASP cc_start: 0.8460 (t0) cc_final: 0.7836 (m-30) REVERT: F 509 ARG cc_start: 0.5427 (OUTLIER) cc_final: 0.5104 (pmt-80) REVERT: F 582 MET cc_start: 0.5149 (mmm) cc_final: 0.4820 (mmm) REVERT: F 585 PHE cc_start: 0.6093 (m-80) cc_final: 0.5574 (m-80) REVERT: F 623 LEU cc_start: 0.7237 (tt) cc_final: 0.6964 (mt) REVERT: F 624 PHE cc_start: 0.7716 (m-80) cc_final: 0.7178 (m-80) REVERT: F 646 ARG cc_start: 0.7403 (tpp80) cc_final: 0.7149 (tpp80) outliers start: 51 outliers final: 38 residues processed: 329 average time/residue: 0.1967 time to fit residues: 99.3985 Evaluate side-chains 316 residues out of total 2849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 787 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 726 GLU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 595 PHE Chi-restraints excluded: chain D residue 691 GLU Chi-restraints excluded: chain D residue 726 GLU Chi-restraints excluded: chain D residue 727 ILE Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain E residue 387 ASP Chi-restraints excluded: chain E residue 604 TYR Chi-restraints excluded: chain E residue 641 VAL Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 659 ASN Chi-restraints excluded: chain E residue 750 VAL Chi-restraints excluded: chain E residue 799 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 509 ARG Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 706 ARG Chi-restraints excluded: chain F residue 711 ASN Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 777 ILE Chi-restraints excluded: chain F residue 819 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 234 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 137 optimal weight: 0.2980 chunk 334 optimal weight: 20.0000 chunk 209 optimal weight: 1.9990 chunk 218 optimal weight: 0.1980 chunk 223 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 337 optimal weight: 6.9990 chunk 293 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN B 391 ASN C 343 GLN C 391 ASN C 568 ASN ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.177579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.140812 restraints weight = 34681.602| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.06 r_work: 0.3608 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27553 Z= 0.117 Angle : 0.604 10.575 37169 Z= 0.286 Chirality : 0.042 0.147 4239 Planarity : 0.004 0.070 4820 Dihedral : 7.002 177.984 3831 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.61 % Allowed : 16.11 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.15), residues: 3346 helix: 1.01 (0.12), residues: 1882 sheet: -0.90 (0.24), residues: 408 loop : 0.13 (0.21), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 329 TYR 0.039 0.001 TYR F 635 PHE 0.036 0.001 PHE E 791 TRP 0.006 0.001 TRP B 491 HIS 0.004 0.000 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00274 (27553) covalent geometry : angle 0.60426 (37169) hydrogen bonds : bond 0.02981 ( 1320) hydrogen bonds : angle 4.58011 ( 3885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6982.58 seconds wall clock time: 119 minutes 53.40 seconds (7193.40 seconds total)