Starting phenix.real_space_refine on Thu Jan 15 12:14:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zu0_14964/01_2026/7zu0_14964.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zu0_14964/01_2026/7zu0_14964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zu0_14964/01_2026/7zu0_14964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zu0_14964/01_2026/7zu0_14964.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zu0_14964/01_2026/7zu0_14964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zu0_14964/01_2026/7zu0_14964.map" } resolution = 4.4 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 16336 2.51 5 N 4430 2.21 5 O 4905 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25763 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 6914 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 234} Link IDs: {'PTRANS': 36, 'TRANS': 917} Chain breaks: 6 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 822 Unresolved non-hydrogen angles: 1035 Unresolved non-hydrogen dihedrals: 672 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'ASP:plan': 14, 'PHE:plan': 14, 'ASN:plan1': 16, 'GLU:plan': 29, 'ARG:plan': 9, 'TYR:plan': 4, 'GLN:plan1': 6, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 422 Chain: "B" Number of atoms: 5981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5981 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 713} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 5549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 5549 Classifications: {'peptide': 842} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 404} Link IDs: {'PTRANS': 20, 'TRANS': 821} Chain breaks: 10 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1486 Unresolved non-hydrogen angles: 1906 Unresolved non-hydrogen dihedrals: 1256 Unresolved non-hydrogen chiralities: 139 Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 38, 'PHE:plan': 25, 'TYR:plan': 10, 'ASP:plan': 27, 'GLU:plan': 27, 'GLN:plan1': 11, 'HIS:plan': 12, 'TRP:plan': 11} Unresolved non-hydrogen planarities: 776 Chain: "D" Number of atoms: 4749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4749 Classifications: {'peptide': 597} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 20, 'TRANS': 576} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 1704 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 316} Link IDs: {'PTRANS': 12, 'TRANS': 330} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1166 Unresolved non-hydrogen angles: 1481 Unresolved non-hydrogen dihedrals: 989 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 9, 'ASP:plan': 17, 'GLU:plan': 26, 'ASN:plan1': 24, 'TYR:plan': 16, 'ARG:plan': 16, 'PHE:plan': 16, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 632 Chain: "F" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 5.77, per 1000 atoms: 0.22 Number of scatterers: 25763 At special positions: 0 Unit cell: (138.6, 178.332, 291.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 4905 8.00 N 4430 7.00 C 16336 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: 2.34 Conformation dependent library (CDL) restraints added in 1.2 seconds 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6926 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 27 sheets defined 55.1% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.735A pdb=" N ILE A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.639A pdb=" N HIS A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 397 removed outlier: 3.537A pdb=" N LYS A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 396 " --> pdb=" O TYR A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 408 removed outlier: 3.755A pdb=" N GLN A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 4.095A pdb=" N ILE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 446 removed outlier: 3.641A pdb=" N ASN A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 465 Processing helix chain 'A' and resid 466 through 477 removed outlier: 3.538A pdb=" N ILE A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'A' and resid 533 through 543 removed outlier: 4.158A pdb=" N ILE A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 540 " --> pdb=" O ILE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 557 removed outlier: 3.750A pdb=" N SER A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 578 removed outlier: 5.980A pdb=" N LYS A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LYS A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 591 removed outlier: 4.131A pdb=" N GLU A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 633 Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.998A pdb=" N VAL A 675 " --> pdb=" O PHE A 671 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 709 removed outlier: 3.669A pdb=" N ARG A 694 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP A 703 " --> pdb=" O THR A 699 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 704 " --> pdb=" O THR A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 716 through 736 removed outlier: 3.863A pdb=" N TRP A 720 " --> pdb=" O ARG A 716 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 721 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 726 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 735 " --> pdb=" O SER A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.579A pdb=" N LEU A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 774 removed outlier: 3.713A pdb=" N ALA A 774 " --> pdb=" O ILE A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 796 Processing helix chain 'A' and resid 797 through 809 Processing helix chain 'A' and resid 812 through 824 removed outlier: 3.867A pdb=" N LEU A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 817 " --> pdb=" O PRO A 813 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER A 821 " --> pdb=" O GLN A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 833 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 843 through 851 Processing helix chain 'A' and resid 854 through 865 removed outlier: 4.009A pdb=" N THR A 865 " --> pdb=" O ALA A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 912 removed outlier: 4.432A pdb=" N ASP A 875 " --> pdb=" O GLY A 871 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 881 " --> pdb=" O ILE A 877 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR A 883 " --> pdb=" O ASP A 879 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU A 884 " --> pdb=" O HIS A 880 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP A 885 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 886 " --> pdb=" O LYS A 882 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 887 " --> pdb=" O THR A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 974 removed outlier: 4.452A pdb=" N PHE A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 992 removed outlier: 3.706A pdb=" N LYS A 978 " --> pdb=" O PHE A 974 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS A 979 " --> pdb=" O LYS A 975 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 991 " --> pdb=" O ASN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1001 removed outlier: 3.922A pdb=" N VAL A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1007 Processing helix chain 'A' and resid 1008 through 1019 Processing helix chain 'B' and resid 28 through 33 removed outlier: 4.163A pdb=" N GLU B 32 " --> pdb=" O THR B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 307 through 318 removed outlier: 3.529A pdb=" N LEU B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'B' and resid 327 through 333 removed outlier: 3.767A pdb=" N LYS B 331 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 347 removed outlier: 3.563A pdb=" N LEU B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 347 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 367 removed outlier: 4.221A pdb=" N ALA B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 395 removed outlier: 3.910A pdb=" N ARG B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 394 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 395 " --> pdb=" O CYS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.568A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'B' and resid 435 through 452 Processing helix chain 'B' and resid 457 through 472 removed outlier: 3.643A pdb=" N ASP B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.512A pdb=" N VAL B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 501 removed outlier: 3.702A pdb=" N ARG B 497 " --> pdb=" O PHE B 493 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN B 498 " --> pdb=" O GLN B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 516 Processing helix chain 'B' and resid 518 through 530 removed outlier: 3.561A pdb=" N ILE B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 529 " --> pdb=" O GLU B 525 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 530 " --> pdb=" O CYS B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 546 removed outlier: 4.108A pdb=" N LYS B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.679A pdb=" N THR B 552 " --> pdb=" O ASN B 548 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 569 removed outlier: 3.806A pdb=" N TYR B 567 " --> pdb=" O PRO B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 584 removed outlier: 3.509A pdb=" N LEU B 576 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 581 " --> pdb=" O TYR B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 600 removed outlier: 3.817A pdb=" N HIS B 591 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 621 through 647 removed outlier: 3.518A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B 641 " --> pdb=" O TRP B 637 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 642 " --> pdb=" O ILE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 667 Processing helix chain 'B' and resid 669 through 680 removed outlier: 3.709A pdb=" N LYS B 673 " --> pdb=" O ASP B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 695 removed outlier: 3.590A pdb=" N LEU B 686 " --> pdb=" O SER B 682 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS B 688 " --> pdb=" O LYS B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 707 Processing helix chain 'B' and resid 717 through 725 removed outlier: 3.806A pdb=" N THR B 721 " --> pdb=" O MET B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 739 removed outlier: 3.579A pdb=" N ASN B 737 " --> pdb=" O SER B 733 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 739 " --> pdb=" O TYR B 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 337 through 349 removed outlier: 5.424A pdb=" N ALA C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.514A pdb=" N ILE C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 379 Processing helix chain 'C' and resid 385 through 393 removed outlier: 3.828A pdb=" N ALA C 393 " --> pdb=" O PHE C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 410 Processing helix chain 'C' and resid 414 through 425 removed outlier: 3.557A pdb=" N LEU C 425 " --> pdb=" O THR C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 456 removed outlier: 3.981A pdb=" N LYS C 435 " --> pdb=" O TRP C 431 " (cutoff:3.500A) Proline residue: C 449 - end of helix removed outlier: 3.770A pdb=" N GLU C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 455 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 492 removed outlier: 3.982A pdb=" N LYS C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 503 Processing helix chain 'C' and resid 507 through 519 removed outlier: 3.565A pdb=" N LEU C 511 " --> pdb=" O ARG C 507 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 513 " --> pdb=" O ASN C 509 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 515 " --> pdb=" O LEU C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 532 Processing helix chain 'C' and resid 535 through 544 removed outlier: 4.005A pdb=" N LYS C 539 " --> pdb=" O TYR C 535 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 541 " --> pdb=" O SER C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 561 removed outlier: 3.669A pdb=" N LYS C 552 " --> pdb=" O ASP C 548 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 553 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C 555 " --> pdb=" O TYR C 551 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE C 556 " --> pdb=" O LYS C 552 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASN C 560 " --> pdb=" O ILE C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 572 Processing helix chain 'C' and resid 580 through 598 removed outlier: 3.616A pdb=" N ASN C 590 " --> pdb=" O LYS C 586 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU C 597 " --> pdb=" O ASN C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.783A pdb=" N THR C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 639 removed outlier: 3.614A pdb=" N ASN C 630 " --> pdb=" O PRO C 626 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET C 636 " --> pdb=" O ILE C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 657 removed outlier: 3.939A pdb=" N ILE C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS C 652 " --> pdb=" O ASN C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 671 removed outlier: 3.602A pdb=" N ARG C 668 " --> pdb=" O ASN C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 688 through 699 Processing helix chain 'C' and resid 701 through 710 removed outlier: 4.193A pdb=" N VAL C 707 " --> pdb=" O ASP C 703 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 708 " --> pdb=" O ASP C 704 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 709 " --> pdb=" O CYS C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 735 removed outlier: 3.571A pdb=" N ILE C 728 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA C 729 " --> pdb=" O TRP C 725 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS C 731 " --> pdb=" O LYS C 727 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER C 735 " --> pdb=" O HIS C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 753 removed outlier: 3.620A pdb=" N ARG C 746 " --> pdb=" O LYS C 742 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 762 removed outlier: 3.514A pdb=" N LEU C 762 " --> pdb=" O ILE C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 763 through 765 No H-bonds generated for 'chain 'C' and resid 763 through 765' Processing helix chain 'C' and resid 775 through 817 removed outlier: 3.628A pdb=" N SER C 793 " --> pdb=" O MET C 789 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL C 804 " --> pdb=" O LYS C 800 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 811 " --> pdb=" O ASN C 807 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS C 812 " --> pdb=" O THR C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 858 removed outlier: 3.566A pdb=" N ILE C 853 " --> pdb=" O TRP C 849 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C 854 " --> pdb=" O ASN C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 873 Processing helix chain 'C' and resid 880 through 888 removed outlier: 4.979A pdb=" N ILE C 886 " --> pdb=" O ASP C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 917 removed outlier: 3.573A pdb=" N LYS C 915 " --> pdb=" O THR C 911 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP C 916 " --> pdb=" O GLU C 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 26 removed outlier: 3.920A pdb=" N PHE D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER D 11 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE D 25 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.746A pdb=" N GLN D 53 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 Proline residue: D 79 - end of helix Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.936A pdb=" N GLN D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 157 removed outlier: 3.635A pdb=" N GLU D 156 " --> pdb=" O GLN D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 200 through 224 removed outlier: 3.594A pdb=" N GLU D 205 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 250 removed outlier: 3.713A pdb=" N ARG D 239 " --> pdb=" O ASN D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.784A pdb=" N LYS D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 269 removed outlier: 4.132A pdb=" N ASN D 269 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 284 No H-bonds generated for 'chain 'D' and resid 282 through 284' Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 323 through 330 removed outlier: 3.546A pdb=" N ASN D 327 " --> pdb=" O ASP D 323 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP D 328 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 350 removed outlier: 4.171A pdb=" N GLY D 338 " --> pdb=" O PHE D 334 " (cutoff:3.500A) Proline residue: D 339 - end of helix removed outlier: 3.581A pdb=" N ASN D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS D 343 " --> pdb=" O PRO D 339 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR D 350 " --> pdb=" O LYS D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 398 removed outlier: 3.746A pdb=" N LYS D 382 " --> pdb=" O GLN D 378 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 415 removed outlier: 3.691A pdb=" N LEU D 411 " --> pdb=" O LEU D 407 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU D 412 " --> pdb=" O GLU D 408 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 437 through 451 removed outlier: 3.501A pdb=" N ILE D 441 " --> pdb=" O ASP D 437 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU D 444 " --> pdb=" O LYS D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 472 removed outlier: 3.690A pdb=" N GLU D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 485 removed outlier: 3.829A pdb=" N GLU D 480 " --> pdb=" O CYS D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 removed outlier: 3.581A pdb=" N ILE D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 562 removed outlier: 3.652A pdb=" N ARG D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU D 560 " --> pdb=" O LEU D 556 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR D 561 " --> pdb=" O VAL D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 removed outlier: 3.935A pdb=" N HIS D 568 " --> pdb=" O SER D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 596 Processing helix chain 'D' and resid 608 through 611 Processing helix chain 'D' and resid 612 through 623 removed outlier: 3.514A pdb=" N LYS D 620 " --> pdb=" O ASN D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 667 removed outlier: 3.802A pdb=" N ALA D 655 " --> pdb=" O MET D 651 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 667 " --> pdb=" O ILE D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 688 Processing helix chain 'E' and resid 703 through 719 removed outlier: 3.580A pdb=" N ILE E 712 " --> pdb=" O LYS E 708 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR E 713 " --> pdb=" O SER E 709 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA E 714 " --> pdb=" O SER E 710 " (cutoff:3.500A) Proline residue: E 717 - end of helix Processing helix chain 'E' and resid 721 through 730 removed outlier: 3.519A pdb=" N ALA E 727 " --> pdb=" O LYS E 723 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 740 Processing helix chain 'E' and resid 741 through 749 Processing helix chain 'E' and resid 750 through 752 No H-bonds generated for 'chain 'E' and resid 750 through 752' Processing helix chain 'E' and resid 754 through 759 Processing helix chain 'E' and resid 760 through 768 Processing helix chain 'E' and resid 772 through 786 removed outlier: 3.702A pdb=" N THR E 776 " --> pdb=" O ASN E 772 " (cutoff:3.500A) Processing helix chain 'E' and resid 789 through 803 Processing helix chain 'E' and resid 807 through 824 removed outlier: 4.474A pdb=" N TYR E 824 " --> pdb=" O GLU E 820 " (cutoff:3.500A) Processing helix chain 'E' and resid 827 through 846 removed outlier: 4.151A pdb=" N ILE E 839 " --> pdb=" O MET E 835 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TRP E 840 " --> pdb=" O ARG E 836 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU E 841 " --> pdb=" O VAL E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 847 through 857 Processing helix chain 'E' and resid 862 through 876 Processing helix chain 'E' and resid 876 through 899 Proline residue: E 882 - end of helix Proline residue: E 886 - end of helix removed outlier: 3.951A pdb=" N LYS E 896 " --> pdb=" O GLU E 892 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 897 " --> pdb=" O LYS E 893 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS E 898 " --> pdb=" O THR E 894 " (cutoff:3.500A) Processing helix chain 'E' and resid 901 through 911 Processing helix chain 'E' and resid 916 through 921 Processing helix chain 'E' and resid 922 through 924 No H-bonds generated for 'chain 'E' and resid 922 through 924' Processing helix chain 'E' and resid 929 through 973 removed outlier: 4.474A pdb=" N PHE E 933 " --> pdb=" O ASP E 929 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER E 935 " --> pdb=" O GLN E 931 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N MET E 936 " --> pdb=" O SER E 932 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU E 956 " --> pdb=" O THR E 952 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG E 957 " --> pdb=" O ILE E 953 " (cutoff:3.500A) Processing helix chain 'E' and resid 1013 through 1049 removed outlier: 3.574A pdb=" N PHE E1019 " --> pdb=" O SER E1015 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET E1022 " --> pdb=" O GLU E1018 " (cutoff:3.500A) Processing helix chain 'F' and resid 868 through 878 removed outlier: 3.632A pdb=" N ASN F 875 " --> pdb=" O ASP F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 883 through 893 removed outlier: 3.621A pdb=" N PHE F 887 " --> pdb=" O GLU F 883 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET F 888 " --> pdb=" O LEU F 884 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR F 891 " --> pdb=" O PHE F 887 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 893 " --> pdb=" O ILE F 889 " (cutoff:3.500A) Processing helix chain 'F' and resid 899 through 904 Processing helix chain 'F' and resid 911 through 920 removed outlier: 3.607A pdb=" N LYS F 915 " --> pdb=" O GLU F 911 " (cutoff:3.500A) Processing helix chain 'F' and resid 928 through 958 removed outlier: 3.626A pdb=" N VAL F 937 " --> pdb=" O ILE F 933 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN F 938 " --> pdb=" O LYS F 934 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU F 939 " --> pdb=" O HIS F 935 " (cutoff:3.500A) Processing helix chain 'F' and resid 958 through 970 removed outlier: 3.526A pdb=" N ILE F 968 " --> pdb=" O GLU F 964 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER F 970 " --> pdb=" O LEU F 966 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 3.583A pdb=" N THR A 348 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 41 removed outlier: 3.984A pdb=" N VAL A 40 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE A 68 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 136 removed outlier: 3.613A pdb=" N VAL A 145 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.772A pdb=" N ALA A 193 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 228 through 230 removed outlier: 3.701A pdb=" N ILE A 244 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 256 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 266 through 270 removed outlier: 6.694A pdb=" N HIS A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 315 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 323 through 328 removed outlier: 3.709A pdb=" N ASP A 323 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE A 325 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 9 through 10 Processing sheet with id=AB2, first strand: chain 'B' and resid 19 through 21 removed outlier: 3.561A pdb=" N PHE B 289 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 287 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN B 271 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.656A pdb=" N VAL B 52 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY B 61 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN B 54 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU B 59 " --> pdb=" O ASN B 54 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 72 through 74 removed outlier: 3.992A pdb=" N LYS B 74 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 85 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B 90 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 115 through 118 removed outlier: 6.824A pdb=" N LEU B 124 " --> pdb=" O TRP B 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 254 removed outlier: 4.028A pdb=" N ILE B 251 " --> pdb=" O PHE B 263 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 261 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 3 through 9 removed outlier: 3.955A pdb=" N SER C 330 " --> pdb=" O MET C 9 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE C 322 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE C 323 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N CYS C 313 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLU C 325 " --> pdb=" O PHE C 311 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AB9, first strand: chain 'C' and resid 113 through 114 removed outlier: 3.668A pdb=" N SER C 137 " --> pdb=" O ASN C 126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 153 through 155 removed outlier: 3.696A pdb=" N ASP C 161 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP C 185 " --> pdb=" O TRP C 169 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AC3, first strand: chain 'C' and resid 269 through 274 removed outlier: 3.611A pdb=" N ASP C 281 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER C 282 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY C 288 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 846 through 848 Processing sheet with id=AC5, first strand: chain 'D' and resid 57 through 62 removed outlier: 5.949A pdb=" N GLU D 30 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS D 59 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE D 114 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE D 85 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N CYS D 116 " --> pdb=" O PHE D 85 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE D 87 " --> pdb=" O CYS D 116 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N TRP D 118 " --> pdb=" O ILE D 87 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR D 164 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR D 115 " --> pdb=" O TYR D 164 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 172 through 175 removed outlier: 6.993A pdb=" N GLN D 173 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N LEU D 180 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASP D 175 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU D 179 " --> pdb=" O ALA D 677 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 232 through 233 Processing sheet with id=AC8, first strand: chain 'D' and resid 275 through 280 removed outlier: 5.931A pdb=" N ASP D 275 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL D 644 " --> pdb=" O ASP D 275 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE D 277 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU D 646 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU D 279 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 1002 through 1004 1275 hydrogen bonds defined for protein. 3705 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: 4.90 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4879 1.33 - 1.45: 5997 1.45 - 1.57: 15114 1.57 - 1.69: 0 1.69 - 1.81: 141 Bond restraints: 26131 Sorted by residual: bond pdb=" C ILE E1038 " pdb=" O ILE E1038 " ideal model delta sigma weight residual 1.237 1.317 -0.080 1.12e-02 7.97e+03 5.12e+01 bond pdb=" C MET E1031 " pdb=" O MET E1031 " ideal model delta sigma weight residual 1.237 1.295 -0.059 1.17e-02 7.31e+03 2.51e+01 bond pdb=" C SER E1035 " pdb=" O SER E1035 " ideal model delta sigma weight residual 1.237 1.288 -0.051 1.17e-02 7.31e+03 1.89e+01 bond pdb=" C ASN E1034 " pdb=" O ASN E1034 " ideal model delta sigma weight residual 1.237 1.286 -0.050 1.19e-02 7.06e+03 1.74e+01 bond pdb=" C SER E1027 " pdb=" O SER E1027 " ideal model delta sigma weight residual 1.237 1.284 -0.047 1.17e-02 7.31e+03 1.64e+01 ... (remaining 26126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 34765 2.03 - 4.05: 629 4.05 - 6.08: 73 6.08 - 8.11: 50 8.11 - 10.13: 12 Bond angle restraints: 35529 Sorted by residual: angle pdb=" N PRO A 918 " pdb=" CA PRO A 918 " pdb=" CB PRO A 918 " ideal model delta sigma weight residual 102.79 109.90 -7.11 6.60e-01 2.30e+00 1.16e+02 angle pdb=" N LEU E1030 " pdb=" CA LEU E1030 " pdb=" C LEU E1030 " ideal model delta sigma weight residual 111.36 101.28 10.08 1.09e+00 8.42e-01 8.54e+01 angle pdb=" N PRO C 271 " pdb=" CA PRO C 271 " pdb=" CB PRO C 271 " ideal model delta sigma weight residual 103.36 110.43 -7.07 8.30e-01 1.45e+00 7.26e+01 angle pdb=" N PRO A 854 " pdb=" CA PRO A 854 " pdb=" CB PRO A 854 " ideal model delta sigma weight residual 103.35 110.57 -7.22 8.70e-01 1.32e+00 6.89e+01 angle pdb=" N LEU E1025 " pdb=" CA LEU E1025 " pdb=" C LEU E1025 " ideal model delta sigma weight residual 112.89 102.76 10.13 1.24e+00 6.50e-01 6.68e+01 ... (remaining 35524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14475 17.94 - 35.87: 1131 35.87 - 53.81: 168 53.81 - 71.74: 21 71.74 - 89.68: 17 Dihedral angle restraints: 15812 sinusoidal: 5239 harmonic: 10573 Sorted by residual: dihedral pdb=" CA VAL D 607 " pdb=" C VAL D 607 " pdb=" N PRO D 608 " pdb=" CA PRO D 608 " ideal model delta harmonic sigma weight residual 180.00 -155.44 -24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA LYS B 209 " pdb=" C LYS B 209 " pdb=" N ASP B 210 " pdb=" CA ASP B 210 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PHE A 505 " pdb=" C PHE A 505 " pdb=" N ASP A 506 " pdb=" CA ASP A 506 " ideal model delta harmonic sigma weight residual 180.00 158.86 21.14 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 15809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3657 0.059 - 0.118: 535 0.118 - 0.177: 36 0.177 - 0.236: 28 0.236 - 0.295: 14 Chirality restraints: 4270 Sorted by residual: chirality pdb=" CG LEU B 167 " pdb=" CB LEU B 167 " pdb=" CD1 LEU B 167 " pdb=" CD2 LEU B 167 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA ILE E1038 " pdb=" N ILE E1038 " pdb=" C ILE E1038 " pdb=" CB ILE E1038 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA PRO C 328 " pdb=" N PRO C 328 " pdb=" C PRO C 328 " pdb=" CB PRO C 328 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 4267 not shown) Planarity restraints: 4601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E1033 " 0.015 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C TYR E1033 " -0.055 2.00e-02 2.50e+03 pdb=" O TYR E1033 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN E1034 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E1023 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C GLN E1023 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN E1023 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR E1024 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E1029 " -0.013 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C LEU E1029 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU E1029 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU E1030 " -0.017 2.00e-02 2.50e+03 ... (remaining 4598 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 458 2.67 - 3.23: 26797 3.23 - 3.78: 38594 3.78 - 4.34: 51758 4.34 - 4.90: 80900 Nonbonded interactions: 198507 Sorted by model distance: nonbonded pdb=" O LYS B 88 " pdb=" OG1 THR B 114 " model vdw 2.109 3.040 nonbonded pdb=" O ALA A 527 " pdb=" OG SER A 531 " model vdw 2.145 3.040 nonbonded pdb=" O LEU D 51 " pdb=" OG1 THR D 55 " model vdw 2.178 3.040 nonbonded pdb=" NE1 TRP C 591 " pdb=" O PRO C 605 " model vdw 2.189 3.120 nonbonded pdb=" OG1 THR B 283 " pdb=" O LYS B 286 " model vdw 2.192 3.040 ... (remaining 198502 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 26.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.360 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 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 0.080 26131 Z= 0.222 Angle : 0.693 10.133 35529 Z= 0.461 Chirality : 0.047 0.295 4270 Planarity : 0.003 0.057 4601 Dihedral : 13.396 89.680 8886 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.55 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.15), residues: 3519 helix: 0.65 (0.13), residues: 1623 sheet: -1.72 (0.32), residues: 267 loop : -2.03 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 18 TYR 0.014 0.001 TYR B 577 PHE 0.025 0.001 PHE B 700 TRP 0.019 0.001 TRP B 637 HIS 0.005 0.001 HIS C 848 Details of bonding type rmsd covalent geometry : bond 0.00368 (26131) covalent geometry : angle 0.69335 (35529) hydrogen bonds : bond 0.29107 ( 1275) hydrogen bonds : angle 8.40261 ( 3705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.052 Fit side-chains REVERT: A 102 ARG cc_start: 0.7574 (mtt180) cc_final: 0.7291 (mtp85) REVERT: A 433 MET cc_start: 0.8295 (mpp) cc_final: 0.7544 (mpp) REVERT: A 752 MET cc_start: 0.7776 (mmm) cc_final: 0.7521 (mmm) REVERT: B 167 LEU cc_start: 0.7844 (mt) cc_final: 0.7635 (mt) REVERT: B 224 MET cc_start: 0.6200 (tmm) cc_final: 0.5884 (tmm) REVERT: B 544 LYS cc_start: 0.8762 (tttt) cc_final: 0.8457 (mmtt) REVERT: C 514 PHE cc_start: 0.8799 (p90) cc_final: 0.8059 (p90) REVERT: D 112 HIS cc_start: 0.6234 (m-70) cc_final: 0.6026 (m90) REVERT: F 894 ASP cc_start: 0.8687 (p0) cc_final: 0.8414 (p0) REVERT: F 925 GLN cc_start: 0.8291 (tp-100) cc_final: 0.8042 (tp-100) REVERT: F 927 ASP cc_start: 0.8826 (m-30) cc_final: 0.8425 (m-30) REVERT: F 956 ASP cc_start: 0.7937 (m-30) cc_final: 0.7637 (m-30) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1642 time to fit residues: 63.3449 Evaluate side-chains 191 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN A 710 GLN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 578 ASN C 592 GLN C 625 ASN C 858 ASN D 224 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.099625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.086678 restraints weight = 100158.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.086083 restraints weight = 172811.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.085848 restraints weight = 148867.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.085825 restraints weight = 112216.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.085897 restraints weight = 109050.563| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26131 Z= 0.156 Angle : 0.573 8.704 35529 Z= 0.315 Chirality : 0.042 0.176 4270 Planarity : 0.004 0.057 4601 Dihedral : 4.460 24.261 3738 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.70 % Favored : 92.13 % Rotamer: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3519 helix: 0.86 (0.12), residues: 1763 sheet: -1.64 (0.34), residues: 245 loop : -2.19 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 492 TYR 0.021 0.001 TYR A 499 PHE 0.019 0.001 PHE B 700 TRP 0.012 0.001 TRP B 26 HIS 0.007 0.001 HIS C 848 Details of bonding type rmsd covalent geometry : bond 0.00311 (26131) covalent geometry : angle 0.57320 (35529) hydrogen bonds : bond 0.05721 ( 1275) hydrogen bonds : angle 5.78785 ( 3705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 238 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 ASN cc_start: 0.7921 (p0) cc_final: 0.7105 (t0) REVERT: A 433 MET cc_start: 0.8635 (mpp) cc_final: 0.7779 (mpp) REVERT: B 224 MET cc_start: 0.6642 (tmm) cc_final: 0.6267 (tmm) REVERT: B 544 LYS cc_start: 0.8762 (tttt) cc_final: 0.8434 (mptt) REVERT: B 637 TRP cc_start: 0.7018 (t-100) cc_final: 0.6514 (t-100) REVERT: B 641 GLU cc_start: 0.8077 (mp0) cc_final: 0.7478 (mp0) REVERT: B 706 PHE cc_start: 0.7422 (t80) cc_final: 0.7184 (t80) REVERT: C 650 ILE cc_start: 0.9293 (mt) cc_final: 0.8959 (pt) REVERT: C 743 GLN cc_start: 0.8573 (tp-100) cc_final: 0.8272 (tp-100) REVERT: C 789 MET cc_start: 0.8346 (mmm) cc_final: 0.7781 (tpp) REVERT: D 651 MET cc_start: 0.8191 (mtp) cc_final: 0.7861 (mmm) REVERT: F 894 ASP cc_start: 0.8696 (p0) cc_final: 0.8450 (p0) REVERT: F 927 ASP cc_start: 0.8901 (m-30) cc_final: 0.8615 (m-30) outliers start: 2 outliers final: 0 residues processed: 240 average time/residue: 0.1617 time to fit residues: 64.0504 Evaluate side-chains 194 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 1.9990 chunk 337 optimal weight: 0.7980 chunk 240 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 194 optimal weight: 30.0000 chunk 5 optimal weight: 0.3980 chunk 134 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 292 optimal weight: 5.9990 chunk 210 optimal weight: 0.8980 chunk 265 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 695 GLN A 710 GLN C 578 ASN C 625 ASN C 848 HIS D 112 HIS D 217 GLN ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.098432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.085330 restraints weight = 101344.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.084737 restraints weight = 166994.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.084635 restraints weight = 138265.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.084699 restraints weight = 105371.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.084632 restraints weight = 109177.794| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26131 Z= 0.173 Angle : 0.565 8.610 35529 Z= 0.306 Chirality : 0.042 0.180 4270 Planarity : 0.004 0.062 4601 Dihedral : 4.442 22.623 3738 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.16 % Favored : 91.67 % Rotamer: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.14), residues: 3519 helix: 1.01 (0.13), residues: 1752 sheet: -1.68 (0.34), residues: 244 loop : -2.17 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 969 TYR 0.019 0.001 TYR A 499 PHE 0.020 0.002 PHE A 666 TRP 0.014 0.001 TRP B 26 HIS 0.006 0.001 HIS C 848 Details of bonding type rmsd covalent geometry : bond 0.00382 (26131) covalent geometry : angle 0.56526 (35529) hydrogen bonds : bond 0.04821 ( 1275) hydrogen bonds : angle 5.34868 ( 3705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 235 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 544 LYS cc_start: 0.8783 (tttt) cc_final: 0.8439 (mmtt) REVERT: B 637 TRP cc_start: 0.7065 (t-100) cc_final: 0.6591 (t-100) REVERT: B 641 GLU cc_start: 0.8159 (mp0) cc_final: 0.7702 (mp0) REVERT: B 706 PHE cc_start: 0.7426 (t80) cc_final: 0.7162 (t80) REVERT: C 514 PHE cc_start: 0.8412 (p90) cc_final: 0.8156 (p90) REVERT: C 650 ILE cc_start: 0.9397 (mt) cc_final: 0.8870 (mt) REVERT: C 743 GLN cc_start: 0.8554 (tp-100) cc_final: 0.8279 (tp-100) REVERT: D 112 HIS cc_start: 0.6176 (m-70) cc_final: 0.5930 (m90) REVERT: D 205 GLU cc_start: 0.8401 (tt0) cc_final: 0.8189 (tt0) REVERT: F 894 ASP cc_start: 0.8715 (p0) cc_final: 0.8493 (p0) REVERT: F 927 ASP cc_start: 0.8892 (m-30) cc_final: 0.8615 (m-30) outliers start: 2 outliers final: 0 residues processed: 237 average time/residue: 0.1565 time to fit residues: 61.4245 Evaluate side-chains 193 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 173 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 168 optimal weight: 30.0000 chunk 107 optimal weight: 0.3980 chunk 176 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 331 optimal weight: 9.9990 chunk 230 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 278 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN B 157 HIS B 226 HIS C 648 ASN ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.100252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.086616 restraints weight = 98170.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.085578 restraints weight = 157101.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.085143 restraints weight = 159358.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.084745 restraints weight = 133251.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.084904 restraints weight = 119158.131| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26131 Z= 0.127 Angle : 0.532 8.716 35529 Z= 0.286 Chirality : 0.041 0.189 4270 Planarity : 0.003 0.059 4601 Dihedral : 4.345 24.185 3738 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.62 % Favored : 92.21 % Rotamer: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 3519 helix: 1.20 (0.13), residues: 1756 sheet: -1.64 (0.34), residues: 243 loop : -2.18 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 969 TYR 0.018 0.001 TYR A 499 PHE 0.036 0.001 PHE D 258 TRP 0.014 0.001 TRP B 26 HIS 0.011 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00276 (26131) covalent geometry : angle 0.53209 (35529) hydrogen bonds : bond 0.04117 ( 1275) hydrogen bonds : angle 5.02693 ( 3705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 224 MET cc_start: 0.6479 (tmm) cc_final: 0.6139 (tmm) REVERT: B 544 LYS cc_start: 0.8758 (tttt) cc_final: 0.8397 (mmtt) REVERT: B 706 PHE cc_start: 0.7379 (t80) cc_final: 0.7131 (t80) REVERT: C 514 PHE cc_start: 0.8629 (p90) cc_final: 0.8398 (p90) REVERT: C 650 ILE cc_start: 0.9402 (mt) cc_final: 0.9122 (pt) REVERT: C 654 MET cc_start: 0.8611 (mpp) cc_final: 0.8338 (mpp) REVERT: C 743 GLN cc_start: 0.8744 (tp-100) cc_final: 0.8313 (tp40) REVERT: C 789 MET cc_start: 0.8402 (mmm) cc_final: 0.7988 (tpp) REVERT: D 112 HIS cc_start: 0.6253 (m-70) cc_final: 0.5792 (m-70) REVERT: F 910 SER cc_start: 0.8538 (t) cc_final: 0.8300 (p) REVERT: F 927 ASP cc_start: 0.8940 (m-30) cc_final: 0.8634 (m-30) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.1562 time to fit residues: 62.7934 Evaluate side-chains 195 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 239 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 284 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 255 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 290 optimal weight: 0.0570 chunk 246 optimal weight: 5.9990 chunk 245 optimal weight: 0.6980 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 157 HIS B 226 HIS C 648 ASN C 657 ASN C 860 ASN ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.099516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.086430 restraints weight = 99649.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.085919 restraints weight = 173178.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.085415 restraints weight = 136054.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.085237 restraints weight = 117545.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.085209 restraints weight = 112071.034| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26131 Z= 0.133 Angle : 0.539 8.667 35529 Z= 0.287 Chirality : 0.042 0.172 4270 Planarity : 0.003 0.060 4601 Dihedral : 4.275 23.566 3738 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.81 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.15), residues: 3519 helix: 1.27 (0.13), residues: 1760 sheet: -1.70 (0.32), residues: 255 loop : -2.23 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 3 TYR 0.030 0.001 TYR C 499 PHE 0.057 0.001 PHE A 673 TRP 0.027 0.001 TRP B 637 HIS 0.007 0.001 HIS C 848 Details of bonding type rmsd covalent geometry : bond 0.00293 (26131) covalent geometry : angle 0.53891 (35529) hydrogen bonds : bond 0.03926 ( 1275) hydrogen bonds : angle 4.90250 ( 3705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: B 224 MET cc_start: 0.6749 (tmm) cc_final: 0.6363 (tmm) REVERT: B 544 LYS cc_start: 0.8771 (tttt) cc_final: 0.8455 (mmtm) REVERT: B 677 LYS cc_start: 0.8592 (ptmm) cc_final: 0.8161 (pttt) REVERT: B 693 THR cc_start: 0.7991 (m) cc_final: 0.7681 (p) REVERT: B 706 PHE cc_start: 0.7341 (t80) cc_final: 0.7044 (t80) REVERT: C 570 MET cc_start: 0.8594 (mmm) cc_final: 0.8333 (mmt) REVERT: C 650 ILE cc_start: 0.9203 (mt) cc_final: 0.8999 (pt) REVERT: C 743 GLN cc_start: 0.8499 (tp-100) cc_final: 0.8112 (tp40) REVERT: D 112 HIS cc_start: 0.6015 (m-70) cc_final: 0.5670 (m-70) REVERT: D 205 GLU cc_start: 0.8365 (tt0) cc_final: 0.8048 (tt0) REVERT: F 894 ASP cc_start: 0.8651 (p0) cc_final: 0.8441 (p0) REVERT: F 927 ASP cc_start: 0.8888 (m-30) cc_final: 0.8626 (m-30) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1645 time to fit residues: 63.1203 Evaluate side-chains 186 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 281 optimal weight: 7.9990 chunk 169 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 344 optimal weight: 8.9990 chunk 235 optimal weight: 5.9990 chunk 173 optimal weight: 0.1980 chunk 102 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN A 710 GLN B 69 HIS B 226 HIS C 731 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.097965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.084720 restraints weight = 102789.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.083956 restraints weight = 174003.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.083604 restraints weight = 150504.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.083420 restraints weight = 121840.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.083524 restraints weight = 112352.308| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26131 Z= 0.201 Angle : 0.593 8.620 35529 Z= 0.318 Chirality : 0.043 0.178 4270 Planarity : 0.004 0.058 4601 Dihedral : 4.465 23.263 3738 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.75 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3519 helix: 1.19 (0.13), residues: 1775 sheet: -1.77 (0.32), residues: 257 loop : -2.26 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 969 TYR 0.017 0.002 TYR A 499 PHE 0.037 0.002 PHE A 673 TRP 0.023 0.002 TRP B 637 HIS 0.009 0.001 HIS C 848 Details of bonding type rmsd covalent geometry : bond 0.00448 (26131) covalent geometry : angle 0.59292 (35529) hydrogen bonds : bond 0.04072 ( 1275) hydrogen bonds : angle 4.98736 ( 3705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 337 LEU cc_start: 0.8569 (mm) cc_final: 0.8203 (mt) REVERT: B 123 MET cc_start: 0.8755 (tmm) cc_final: 0.8470 (tmm) REVERT: B 544 LYS cc_start: 0.8809 (tttt) cc_final: 0.8461 (mmtt) REVERT: B 641 GLU cc_start: 0.8072 (mp0) cc_final: 0.7621 (mp0) REVERT: B 696 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8655 (tp30) REVERT: B 706 PHE cc_start: 0.7586 (t80) cc_final: 0.7336 (t80) REVERT: C 514 PHE cc_start: 0.8500 (p90) cc_final: 0.8188 (p90) REVERT: C 570 MET cc_start: 0.8567 (mmm) cc_final: 0.8326 (mmt) REVERT: C 650 ILE cc_start: 0.9396 (mt) cc_final: 0.9066 (mt) REVERT: C 743 GLN cc_start: 0.8568 (tp-100) cc_final: 0.8263 (tp-100) REVERT: C 789 MET cc_start: 0.8396 (mmm) cc_final: 0.7995 (tpp) REVERT: D 112 HIS cc_start: 0.5918 (m-70) cc_final: 0.5561 (m-70) REVERT: D 205 GLU cc_start: 0.8330 (tt0) cc_final: 0.7957 (tt0) REVERT: F 927 ASP cc_start: 0.8941 (m-30) cc_final: 0.8645 (m-30) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1570 time to fit residues: 59.4231 Evaluate side-chains 184 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 208 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 308 optimal weight: 0.7980 chunk 309 optimal weight: 0.7980 chunk 289 optimal weight: 0.6980 chunk 339 optimal weight: 0.0070 chunk 203 optimal weight: 5.9990 chunk 319 optimal weight: 20.0000 chunk 346 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A 374 GLN A 710 GLN B 226 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.099876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.086787 restraints weight = 99195.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.086107 restraints weight = 175995.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.085918 restraints weight = 148557.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.085967 restraints weight = 112466.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.086003 restraints weight = 108231.608| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26131 Z= 0.115 Angle : 0.543 8.954 35529 Z= 0.286 Chirality : 0.041 0.260 4270 Planarity : 0.003 0.062 4601 Dihedral : 4.289 23.528 3738 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.36 % Favored : 92.47 % Rotamer: Outliers : 0.04 % Allowed : 1.50 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 3519 helix: 1.40 (0.13), residues: 1758 sheet: -1.60 (0.33), residues: 252 loop : -2.25 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 969 TYR 0.020 0.001 TYR C 499 PHE 0.034 0.001 PHE A 673 TRP 0.015 0.001 TRP B 637 HIS 0.007 0.001 HIS B 604 Details of bonding type rmsd covalent geometry : bond 0.00250 (26131) covalent geometry : angle 0.54314 (35529) hydrogen bonds : bond 0.03664 ( 1275) hydrogen bonds : angle 4.71136 ( 3705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 337 LEU cc_start: 0.8431 (mm) cc_final: 0.8151 (mt) REVERT: A 492 MET cc_start: 0.3417 (tpt) cc_final: 0.3108 (tpt) REVERT: A 752 MET cc_start: 0.8308 (mmm) cc_final: 0.7846 (mmm) REVERT: B 224 MET cc_start: 0.7004 (tmm) cc_final: 0.6517 (tmm) REVERT: B 544 LYS cc_start: 0.8823 (tttt) cc_final: 0.8472 (mmtm) REVERT: B 612 ASP cc_start: 0.8858 (t70) cc_final: 0.8540 (t0) REVERT: B 641 GLU cc_start: 0.8215 (mp0) cc_final: 0.7644 (mp0) REVERT: B 677 LYS cc_start: 0.8529 (ptmm) cc_final: 0.8130 (pttt) REVERT: B 693 THR cc_start: 0.8049 (m) cc_final: 0.7702 (p) REVERT: B 696 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8616 (tp30) REVERT: B 706 PHE cc_start: 0.7537 (t80) cc_final: 0.7199 (t80) REVERT: C 514 PHE cc_start: 0.8269 (p90) cc_final: 0.7922 (p90) REVERT: C 570 MET cc_start: 0.8378 (mmm) cc_final: 0.7976 (mmt) REVERT: C 789 MET cc_start: 0.8257 (mmm) cc_final: 0.7877 (tpp) REVERT: D 205 GLU cc_start: 0.8378 (tt0) cc_final: 0.8026 (tt0) REVERT: D 398 GLU cc_start: 0.8268 (tp30) cc_final: 0.8027 (tp30) REVERT: F 927 ASP cc_start: 0.8848 (m-30) cc_final: 0.8565 (m-30) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.1572 time to fit residues: 62.0470 Evaluate side-chains 189 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 213 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 179 optimal weight: 30.0000 chunk 158 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 chunk 336 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 51 GLN B 226 HIS B 601 GLN C 743 GLN D 112 HIS D 173 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.096065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.082477 restraints weight = 104420.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.081718 restraints weight = 159024.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.081728 restraints weight = 157343.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.081469 restraints weight = 125662.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.081753 restraints weight = 109665.372| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 26131 Z= 0.286 Angle : 0.679 8.713 35529 Z= 0.365 Chirality : 0.045 0.255 4270 Planarity : 0.004 0.083 4601 Dihedral : 4.741 23.969 3738 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.78 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.15), residues: 3519 helix: 0.98 (0.13), residues: 1768 sheet: -1.84 (0.31), residues: 284 loop : -2.32 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 969 TYR 0.019 0.002 TYR B 364 PHE 0.038 0.002 PHE A 673 TRP 0.020 0.002 TRP B 637 HIS 0.010 0.002 HIS C 848 Details of bonding type rmsd covalent geometry : bond 0.00634 (26131) covalent geometry : angle 0.67866 (35529) hydrogen bonds : bond 0.04353 ( 1275) hydrogen bonds : angle 5.18025 ( 3705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.045 Fit side-chains REVERT: A 337 LEU cc_start: 0.8684 (mm) cc_final: 0.8055 (mt) REVERT: A 418 ILE cc_start: 0.9242 (mp) cc_final: 0.8927 (mm) REVERT: A 752 MET cc_start: 0.8649 (mmm) cc_final: 0.8206 (mmm) REVERT: B 544 LYS cc_start: 0.8857 (tttt) cc_final: 0.8538 (mmtm) REVERT: B 641 GLU cc_start: 0.8102 (mp0) cc_final: 0.7597 (mp0) REVERT: B 693 THR cc_start: 0.8185 (m) cc_final: 0.7926 (m) REVERT: B 696 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8709 (tp30) REVERT: C 514 PHE cc_start: 0.8788 (p90) cc_final: 0.8408 (p90) REVERT: C 570 MET cc_start: 0.8607 (mmm) cc_final: 0.8327 (mmt) REVERT: C 779 ILE cc_start: 0.9023 (tp) cc_final: 0.8377 (tp) REVERT: C 789 MET cc_start: 0.8456 (mmm) cc_final: 0.8043 (tpp) REVERT: D 112 HIS cc_start: 0.5997 (m-70) cc_final: 0.5717 (m90) REVERT: D 205 GLU cc_start: 0.8317 (tt0) cc_final: 0.7919 (tt0) REVERT: F 894 ASP cc_start: 0.8634 (p0) cc_final: 0.8431 (p0) REVERT: F 927 ASP cc_start: 0.8974 (m-30) cc_final: 0.8497 (m-30) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1529 time to fit residues: 56.2788 Evaluate side-chains 182 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 343 optimal weight: 7.9990 chunk 332 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 323 optimal weight: 30.0000 chunk 177 optimal weight: 30.0000 chunk 222 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN B 226 HIS D 421 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.098280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.084835 restraints weight = 101548.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.083958 restraints weight = 168332.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.083762 restraints weight = 158264.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.083438 restraints weight = 125568.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.083615 restraints weight = 113963.572| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26131 Z= 0.178 Angle : 0.592 8.884 35529 Z= 0.315 Chirality : 0.043 0.235 4270 Planarity : 0.003 0.059 4601 Dihedral : 4.609 24.131 3738 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.93 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 3519 helix: 1.17 (0.13), residues: 1771 sheet: -1.84 (0.32), residues: 257 loop : -2.28 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 969 TYR 0.016 0.001 TYR A 499 PHE 0.036 0.002 PHE A 673 TRP 0.019 0.001 TRP B 637 HIS 0.009 0.001 HIS C 848 Details of bonding type rmsd covalent geometry : bond 0.00397 (26131) covalent geometry : angle 0.59162 (35529) hydrogen bonds : bond 0.03870 ( 1275) hydrogen bonds : angle 4.90266 ( 3705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 418 ILE cc_start: 0.9220 (mp) cc_final: 0.8914 (mm) REVERT: B 123 MET cc_start: 0.8659 (tmm) cc_final: 0.8417 (tmm) REVERT: B 375 ASP cc_start: 0.8206 (p0) cc_final: 0.7946 (t0) REVERT: B 544 LYS cc_start: 0.8843 (tttt) cc_final: 0.8528 (mmtt) REVERT: B 641 GLU cc_start: 0.8058 (mp0) cc_final: 0.7500 (mp0) REVERT: B 696 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8710 (tp30) REVERT: C 570 MET cc_start: 0.8681 (mmm) cc_final: 0.8316 (mmt) REVERT: C 789 MET cc_start: 0.8422 (mmm) cc_final: 0.8081 (tpp) REVERT: D 205 GLU cc_start: 0.8374 (tt0) cc_final: 0.7965 (tt0) REVERT: D 408 GLU cc_start: 0.7777 (pp20) cc_final: 0.7569 (pp20) REVERT: F 927 ASP cc_start: 0.8930 (m-30) cc_final: 0.8588 (m-30) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1502 time to fit residues: 55.5315 Evaluate side-chains 183 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 318 optimal weight: 20.0000 chunk 232 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 291 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 315 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 51 GLN B 226 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.097767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.084250 restraints weight = 101496.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.083515 restraints weight = 181430.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.083029 restraints weight = 165631.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.082788 restraints weight = 128606.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.082914 restraints weight = 121091.318| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26131 Z= 0.197 Angle : 0.603 8.865 35529 Z= 0.322 Chirality : 0.043 0.274 4270 Planarity : 0.004 0.058 4601 Dihedral : 4.627 24.011 3738 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.24 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.15), residues: 3519 helix: 1.16 (0.13), residues: 1767 sheet: -1.83 (0.32), residues: 263 loop : -2.29 (0.16), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 969 TYR 0.037 0.002 TYR B 150 PHE 0.034 0.002 PHE A 673 TRP 0.017 0.001 TRP B 637 HIS 0.009 0.001 HIS C 848 Details of bonding type rmsd covalent geometry : bond 0.00441 (26131) covalent geometry : angle 0.60343 (35529) hydrogen bonds : bond 0.03920 ( 1275) hydrogen bonds : angle 4.92851 ( 3705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7038 Ramachandran restraints generated. 3519 Oldfield, 0 Emsley, 3519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.093 Fit side-chains REVERT: A 418 ILE cc_start: 0.9247 (mp) cc_final: 0.8928 (mm) REVERT: A 492 MET cc_start: 0.3485 (tpt) cc_final: 0.3105 (tpt) REVERT: B 375 ASP cc_start: 0.8246 (p0) cc_final: 0.7975 (t0) REVERT: B 544 LYS cc_start: 0.8841 (tttt) cc_final: 0.8510 (mmtp) REVERT: B 641 GLU cc_start: 0.8045 (mp0) cc_final: 0.7482 (mp0) REVERT: B 677 LYS cc_start: 0.8515 (ptmm) cc_final: 0.8056 (pttt) REVERT: B 684 LYS cc_start: 0.7425 (mmmm) cc_final: 0.7129 (mmmt) REVERT: B 693 THR cc_start: 0.8027 (m) cc_final: 0.7427 (p) REVERT: B 696 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8718 (tp30) REVERT: C 514 PHE cc_start: 0.8525 (p90) cc_final: 0.8119 (p90) REVERT: C 570 MET cc_start: 0.8638 (mmm) cc_final: 0.8278 (mmt) REVERT: C 789 MET cc_start: 0.8411 (mmm) cc_final: 0.7991 (tpp) REVERT: D 205 GLU cc_start: 0.8374 (tt0) cc_final: 0.7951 (tt0) REVERT: F 894 ASP cc_start: 0.8632 (p0) cc_final: 0.8415 (p0) REVERT: F 927 ASP cc_start: 0.8974 (m-30) cc_final: 0.8448 (m-30) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1515 time to fit residues: 55.4495 Evaluate side-chains 183 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 289 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 267 optimal weight: 0.9980 chunk 251 optimal weight: 0.0070 chunk 324 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 261 optimal weight: 0.7980 chunk 179 optimal weight: 30.0000 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN B 69 HIS B 226 HIS D 173 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.099805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.086780 restraints weight = 98559.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.085983 restraints weight = 162799.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.084951 restraints weight = 126744.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.084886 restraints weight = 118213.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.085132 restraints weight = 100159.104| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26131 Z= 0.115 Angle : 0.557 9.777 35529 Z= 0.291 Chirality : 0.042 0.205 4270 Planarity : 0.003 0.062 4601 Dihedral : 4.374 24.675 3738 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.39 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 3519 helix: 1.41 (0.13), residues: 1772 sheet: -1.77 (0.32), residues: 254 loop : -2.26 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 581 TYR 0.030 0.001 TYR B 639 PHE 0.028 0.001 PHE A 673 TRP 0.015 0.001 TRP B 637 HIS 0.009 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00253 (26131) covalent geometry : angle 0.55655 (35529) hydrogen bonds : bond 0.03499 ( 1275) hydrogen bonds : angle 4.61513 ( 3705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4244.42 seconds wall clock time: 74 minutes 25.91 seconds (4465.91 seconds total)