Starting phenix.real_space_refine on Sun Jun 15 11:32:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5va1_8650/06_2025/5va1_8650.cif Found real_map, /net/cci-nas-00/data/ceres_data/5va1_8650/06_2025/5va1_8650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5va1_8650/06_2025/5va1_8650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5va1_8650/06_2025/5va1_8650.map" model { file = "/net/cci-nas-00/data/ceres_data/5va1_8650/06_2025/5va1_8650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5va1_8650/06_2025/5va1_8650.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.003 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 108 5.16 5 C 11484 2.51 5 N 3008 2.21 5 O 3028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17628 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4407 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 537} Chain breaks: 5 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Restraints were copied for chains: C, B, D Time building chain proxies: 9.05, per 1000 atoms: 0.51 Number of scatterers: 17628 At special positions: 0 Unit cell: (146.87, 146.77, 121.283, 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 108 16.00 O 3028 8.00 N 3008 7.00 C 11484 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: 3.87 Conformation dependent library (CDL) restraints added in 2.3 seconds 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4200 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 61.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 13 through 26 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.532A pdb=" N CYS A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.567A pdb=" N GLN A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 431 removed outlier: 3.763A pdb=" N TRP A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 450 through 473 removed outlier: 3.564A pdb=" N VAL A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 472 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.566A pdb=" N ILE A 489 " --> pdb=" O HIS A 485 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 505 removed outlier: 3.765A pdb=" N VAL A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.534A pdb=" N ALA A 527 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.851A pdb=" N ALA A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.894A pdb=" N TYR A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 575 removed outlier: 3.605A pdb=" N VAL A 549 " --> pdb=" O TYR A 545 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 550 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 572 " --> pdb=" O TRP A 568 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 593 removed outlier: 3.624A pdb=" N ASN A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 removed outlier: 3.549A pdb=" N ALA A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 667 removed outlier: 3.870A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 688 removed outlier: 3.583A pdb=" N HIS A 674 " --> pdb=" O THR A 670 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 680 " --> pdb=" O GLN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 709 removed outlier: 4.037A pdb=" N ARG A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 removed outlier: 3.714A pdb=" N VAL A 716 " --> pdb=" O ASP A 712 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 Processing helix chain 'A' and resid 733 through 740 removed outlier: 3.924A pdb=" N HIS A 739 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 758 removed outlier: 3.871A pdb=" N LYS A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 813 removed outlier: 4.658A pdb=" N TYR A 812 " --> pdb=" O PRO A 808 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 808 through 813' Processing helix chain 'A' and resid 834 through 845 removed outlier: 3.743A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 841 " --> pdb=" O ASP A 837 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 856 removed outlier: 3.823A pdb=" N ASP A 850 " --> pdb=" O PRO A 846 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 854 " --> pdb=" O ASP A 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 26 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.532A pdb=" N CYS B 49 " --> pdb=" O ASN B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 75 through 89 removed outlier: 3.567A pdb=" N GLN B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 431 removed outlier: 3.763A pdb=" N TRP B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 450 through 473 removed outlier: 3.564A pdb=" N VAL B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 472 " --> pdb=" O LEU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.566A pdb=" N ILE B 489 " --> pdb=" O HIS B 485 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 505 removed outlier: 3.765A pdb=" N VAL B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 504 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 531 removed outlier: 3.534A pdb=" N ALA B 527 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.851A pdb=" N ALA B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.894A pdb=" N TYR B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 575 removed outlier: 3.605A pdb=" N VAL B 549 " --> pdb=" O TYR B 545 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 550 " --> pdb=" O GLY B 546 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 572 " --> pdb=" O TRP B 568 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 593 removed outlier: 3.624A pdb=" N ASN B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 623 removed outlier: 3.549A pdb=" N ALA B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 667 removed outlier: 3.870A pdb=" N PHE B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 688 removed outlier: 3.583A pdb=" N HIS B 674 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 680 " --> pdb=" O GLN B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 709 removed outlier: 4.037A pdb=" N ARG B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 removed outlier: 3.714A pdb=" N VAL B 716 " --> pdb=" O ASP B 712 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 733 Processing helix chain 'B' and resid 733 through 740 removed outlier: 3.924A pdb=" N HIS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 758 removed outlier: 3.871A pdb=" N LYS B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 813 removed outlier: 4.658A pdb=" N TYR B 812 " --> pdb=" O PRO B 808 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 808 through 813' Processing helix chain 'B' and resid 834 through 845 removed outlier: 3.743A pdb=" N GLU B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 841 " --> pdb=" O ASP B 837 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET B 844 " --> pdb=" O GLU B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 856 removed outlier: 3.823A pdb=" N ASP B 850 " --> pdb=" O PRO B 846 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER B 854 " --> pdb=" O ASP B 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.532A pdb=" N CYS C 49 " --> pdb=" O ASN C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 75 through 89 removed outlier: 3.567A pdb=" N GLN C 81 " --> pdb=" O ARG C 77 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 431 removed outlier: 3.763A pdb=" N TRP C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 450 through 473 removed outlier: 3.564A pdb=" N VAL C 455 " --> pdb=" O PRO C 451 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 471 " --> pdb=" O ILE C 467 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG C 472 " --> pdb=" O LEU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 494 removed outlier: 3.566A pdb=" N ILE C 489 " --> pdb=" O HIS C 485 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL C 491 " --> pdb=" O GLY C 487 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 505 removed outlier: 3.765A pdb=" N VAL C 503 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 504 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 531 removed outlier: 3.534A pdb=" N ALA C 527 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 538 removed outlier: 3.851A pdb=" N ALA C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 removed outlier: 3.894A pdb=" N TYR C 542 " --> pdb=" O LYS C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 575 removed outlier: 3.605A pdb=" N VAL C 549 " --> pdb=" O TYR C 545 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 550 " --> pdb=" O GLY C 546 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 572 " --> pdb=" O TRP C 568 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 575 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 593 removed outlier: 3.624A pdb=" N ASN C 588 " --> pdb=" O GLY C 584 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 623 removed outlier: 3.549A pdb=" N ALA C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 667 removed outlier: 3.870A pdb=" N PHE C 656 " --> pdb=" O TYR C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 688 removed outlier: 3.583A pdb=" N HIS C 674 " --> pdb=" O THR C 670 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 680 " --> pdb=" O GLN C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 709 removed outlier: 4.037A pdb=" N ARG C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 removed outlier: 3.714A pdb=" N VAL C 716 " --> pdb=" O ASP C 712 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 717 " --> pdb=" O MET C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 733 Processing helix chain 'C' and resid 733 through 740 removed outlier: 3.924A pdb=" N HIS C 739 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 758 removed outlier: 3.871A pdb=" N LYS C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 813 removed outlier: 4.658A pdb=" N TYR C 812 " --> pdb=" O PRO C 808 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA C 813 " --> pdb=" O LEU C 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 808 through 813' Processing helix chain 'C' and resid 834 through 845 removed outlier: 3.743A pdb=" N GLU C 840 " --> pdb=" O ASP C 836 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 841 " --> pdb=" O ASP C 837 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET C 844 " --> pdb=" O GLU C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 856 removed outlier: 3.823A pdb=" N ASP C 850 " --> pdb=" O PRO C 846 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS C 851 " --> pdb=" O GLU C 847 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER C 854 " --> pdb=" O ASP C 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 45 through 53 removed outlier: 3.532A pdb=" N CYS D 49 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 75 through 89 removed outlier: 3.567A pdb=" N GLN D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 431 removed outlier: 3.763A pdb=" N TRP D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 450 through 473 removed outlier: 3.564A pdb=" N VAL D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D 472 " --> pdb=" O LEU D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 494 removed outlier: 3.566A pdb=" N ILE D 489 " --> pdb=" O HIS D 485 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 490 " --> pdb=" O PRO D 486 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL D 491 " --> pdb=" O GLY D 487 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 505 removed outlier: 3.765A pdb=" N VAL D 503 " --> pdb=" O LEU D 499 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA D 504 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA D 505 " --> pdb=" O ASP D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 531 removed outlier: 3.534A pdb=" N ALA D 527 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 538 removed outlier: 3.851A pdb=" N ALA D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 removed outlier: 3.894A pdb=" N TYR D 542 " --> pdb=" O LYS D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 575 removed outlier: 3.605A pdb=" N VAL D 549 " --> pdb=" O TYR D 545 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 550 " --> pdb=" O GLY D 546 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY D 572 " --> pdb=" O TRP D 568 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 593 removed outlier: 3.624A pdb=" N ASN D 588 " --> pdb=" O GLY D 584 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 623 removed outlier: 3.549A pdb=" N ALA D 614 " --> pdb=" O LYS D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 667 removed outlier: 3.870A pdb=" N PHE D 656 " --> pdb=" O TYR D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 688 removed outlier: 3.583A pdb=" N HIS D 674 " --> pdb=" O THR D 670 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 680 " --> pdb=" O GLN D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 709 removed outlier: 4.037A pdb=" N ARG D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 718 removed outlier: 3.714A pdb=" N VAL D 716 " --> pdb=" O ASP D 712 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU D 717 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 733 Processing helix chain 'D' and resid 733 through 740 removed outlier: 3.924A pdb=" N HIS D 739 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 758 removed outlier: 3.871A pdb=" N LYS D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 813 removed outlier: 4.658A pdb=" N TYR D 812 " --> pdb=" O PRO D 808 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D 813 " --> pdb=" O LEU D 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 808 through 813' Processing helix chain 'D' and resid 834 through 845 removed outlier: 3.743A pdb=" N GLU D 840 " --> pdb=" O ASP D 836 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 841 " --> pdb=" O ASP D 837 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET D 844 " --> pdb=" O GLU D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 856 removed outlier: 3.823A pdb=" N ASP D 850 " --> pdb=" O PRO D 846 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS D 851 " --> pdb=" O GLU D 847 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER D 854 " --> pdb=" O ASP D 850 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.274A pdb=" N ILE A 31 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N CYS A 44 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE A 29 " --> pdb=" O CYS A 44 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS A 28 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 30 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET A 124 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 130 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 112 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG A 92 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 759 through 763 removed outlier: 3.908A pdb=" N LEU A 830 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 803 " --> pdb=" O ILE A 782 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 860 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 806 " --> pdb=" O PHE A 860 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 768 through 770 removed outlier: 7.088A pdb=" N VAL A 822 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.274A pdb=" N ILE B 31 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N CYS B 44 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE B 29 " --> pdb=" O CYS B 44 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS B 28 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 30 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET B 124 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 130 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 112 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG B 92 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 759 through 763 removed outlier: 3.908A pdb=" N LEU B 830 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP B 803 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 860 " --> pdb=" O ILE B 804 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 806 " --> pdb=" O PHE B 860 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 768 through 770 removed outlier: 7.088A pdb=" N VAL B 822 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.274A pdb=" N ILE C 31 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N CYS C 44 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE C 29 " --> pdb=" O CYS C 44 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS C 28 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 30 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET C 124 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 130 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 112 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG C 92 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 759 through 763 removed outlier: 3.908A pdb=" N LEU C 830 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP C 803 " --> pdb=" O ILE C 782 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 860 " --> pdb=" O ILE C 804 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 806 " --> pdb=" O PHE C 860 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 768 through 770 removed outlier: 7.088A pdb=" N VAL C 822 " --> pdb=" O LEU C 769 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.274A pdb=" N ILE D 31 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N CYS D 44 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE D 29 " --> pdb=" O CYS D 44 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS D 28 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 30 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET D 124 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU D 130 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 112 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG D 92 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'D' and resid 759 through 763 removed outlier: 3.908A pdb=" N LEU D 830 " --> pdb=" O THR D 761 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP D 803 " --> pdb=" O ILE D 782 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D 860 " --> pdb=" O ILE D 804 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 806 " --> pdb=" O PHE D 860 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'D' and resid 768 through 770 removed outlier: 7.088A pdb=" N VAL D 822 " --> pdb=" O LEU D 769 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.24 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5512 1.34 - 1.46: 2352 1.46 - 1.58: 10040 1.58 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 18056 Sorted by residual: bond pdb=" N GLY B 603 " pdb=" CA GLY B 603 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.68e+00 bond pdb=" N GLY A 603 " pdb=" CA GLY A 603 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.68e+00 bond pdb=" N GLY D 603 " pdb=" CA GLY D 603 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.68e+00 bond pdb=" N GLY C 603 " pdb=" CA GLY C 603 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.68e+00 bond pdb=" CA PRO B 764 " pdb=" C PRO B 764 " ideal model delta sigma weight residual 1.517 1.540 -0.023 9.30e-03 1.16e+04 6.32e+00 ... (remaining 18051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 19660 1.22 - 2.44: 4172 2.44 - 3.66: 600 3.66 - 4.88: 48 4.88 - 6.10: 32 Bond angle restraints: 24512 Sorted by residual: angle pdb=" N ASN D 691 " pdb=" CA ASN D 691 " pdb=" C ASN D 691 " ideal model delta sigma weight residual 112.75 118.20 -5.45 1.36e+00 5.41e-01 1.60e+01 angle pdb=" N ASN B 691 " pdb=" CA ASN B 691 " pdb=" C ASN B 691 " ideal model delta sigma weight residual 112.75 118.20 -5.45 1.36e+00 5.41e-01 1.60e+01 angle pdb=" N ASN A 691 " pdb=" CA ASN A 691 " pdb=" C ASN A 691 " ideal model delta sigma weight residual 112.75 118.20 -5.45 1.36e+00 5.41e-01 1.60e+01 angle pdb=" N ASN C 691 " pdb=" CA ASN C 691 " pdb=" C ASN C 691 " ideal model delta sigma weight residual 112.75 118.20 -5.45 1.36e+00 5.41e-01 1.60e+01 angle pdb=" N ASN B 629 " pdb=" CA ASN B 629 " pdb=" C ASN B 629 " ideal model delta sigma weight residual 111.14 107.14 4.00 1.08e+00 8.57e-01 1.37e+01 ... (remaining 24507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.03: 9312 12.03 - 24.06: 860 24.06 - 36.09: 288 36.09 - 48.12: 96 48.12 - 60.16: 24 Dihedral angle restraints: 10580 sinusoidal: 4072 harmonic: 6508 Sorted by residual: dihedral pdb=" CA GLY C 628 " pdb=" C GLY C 628 " pdb=" N ASN C 629 " pdb=" CA ASN C 629 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA GLY D 628 " pdb=" C GLY D 628 " pdb=" N ASN D 629 " pdb=" CA ASN D 629 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA GLY B 628 " pdb=" C GLY B 628 " pdb=" N ASN B 629 " pdb=" CA ASN B 629 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 10577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1712 0.046 - 0.091: 720 0.091 - 0.137: 216 0.137 - 0.182: 104 0.182 - 0.228: 40 Chirality restraints: 2792 Sorted by residual: chirality pdb=" CA ILE A 804 " pdb=" N ILE A 804 " pdb=" C ILE A 804 " pdb=" CB ILE A 804 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE D 804 " pdb=" N ILE D 804 " pdb=" C ILE D 804 " pdb=" CB ILE D 804 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE B 804 " pdb=" N ILE B 804 " pdb=" C ILE B 804 " pdb=" CB ILE B 804 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 2789 not shown) Planarity restraints: 3080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 450 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO B 451 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 451 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 451 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 450 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO C 451 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 451 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 451 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 450 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO A 451 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " -0.018 5.00e-02 4.00e+02 ... (remaining 3077 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 16 2.35 - 2.99: 7492 2.99 - 3.63: 24892 3.63 - 4.26: 36240 4.26 - 4.90: 63270 Nonbonded interactions: 131910 Sorted by model distance: nonbonded pdb=" CG2 ILE C 42 " pdb=" O VAL D 796 " model vdw 1.715 3.460 nonbonded pdb=" CG2 ILE A 42 " pdb=" O VAL B 796 " model vdw 1.715 3.460 nonbonded pdb=" CG2 ILE B 42 " pdb=" O VAL C 796 " model vdw 1.715 3.460 nonbonded pdb=" O VAL A 796 " pdb=" CG2 ILE D 42 " model vdw 1.715 3.460 nonbonded pdb=" NH1 ARG C 752 " pdb=" NE2 HIS D 771 " model vdw 1.963 3.200 ... (remaining 131905 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.130 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.810 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.008 0.046 18056 Z= 0.539 Angle : 1.020 6.103 24512 Z= 0.703 Chirality : 0.063 0.228 2792 Planarity : 0.004 0.032 3080 Dihedral : 11.845 60.156 6380 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.30 % Allowed : 5.83 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.14), residues: 2192 helix: -2.21 (0.11), residues: 1124 sheet: -2.62 (0.37), residues: 132 loop : -2.27 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 585 HIS 0.004 0.001 HIS A 674 PHE 0.011 0.001 PHE D 68 TYR 0.011 0.001 TYR D 652 ARG 0.002 0.000 ARG A 863 Details of bonding type rmsd hydrogen bonds : bond 0.30233 ( 940) hydrogen bonds : angle 9.26482 ( 2688) covalent geometry : bond 0.00764 (18056) covalent geometry : angle 1.02037 (24512) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 719 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.9090 (ttp-170) cc_final: 0.8504 (ttt180) REVERT: A 130 GLU cc_start: 0.9714 (tp30) cc_final: 0.9514 (pm20) REVERT: A 407 LYS cc_start: 0.9550 (tptm) cc_final: 0.9159 (tptp) REVERT: A 466 ASP cc_start: 0.9632 (t0) cc_final: 0.9354 (t0) REVERT: A 541 ARG cc_start: 0.9271 (ttm170) cc_final: 0.8417 (ttp80) REVERT: A 542 TYR cc_start: 0.9264 (m-80) cc_final: 0.8022 (m-80) REVERT: A 576 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7897 (tp40) REVERT: A 640 PHE cc_start: 0.9684 (t80) cc_final: 0.9364 (t80) REVERT: A 668 SER cc_start: 0.9591 (t) cc_final: 0.9341 (m) REVERT: A 677 MET cc_start: 0.9883 (tpp) cc_final: 0.9645 (tpp) REVERT: A 679 ARG cc_start: 0.9798 (mtt180) cc_final: 0.9588 (mtt180) REVERT: A 681 ARG cc_start: 0.9736 (mtt180) cc_final: 0.9390 (ptp-110) REVERT: A 682 GLU cc_start: 0.9686 (mt-10) cc_final: 0.9442 (pt0) REVERT: A 695 GLN cc_start: 0.9667 (mt0) cc_final: 0.9352 (mp10) REVERT: A 698 GLU cc_start: 0.9691 (mt-10) cc_final: 0.9479 (pt0) REVERT: A 702 GLN cc_start: 0.9699 (mt0) cc_final: 0.9485 (mm-40) REVERT: A 714 ASN cc_start: 0.9774 (m-40) cc_final: 0.9442 (p0) REVERT: A 723 CYS cc_start: 0.9433 (m) cc_final: 0.8706 (p) REVERT: A 729 CYS cc_start: 0.9529 (m) cc_final: 0.8719 (p) REVERT: A 734 ARG cc_start: 0.9735 (ptt180) cc_final: 0.9476 (mtm110) REVERT: A 739 HIS cc_start: 0.9843 (m-70) cc_final: 0.9634 (m90) REVERT: A 748 LYS cc_start: 0.9866 (mttt) cc_final: 0.9568 (tttm) REVERT: A 756 MET cc_start: 0.9134 (mmm) cc_final: 0.8833 (mmm) REVERT: A 782 ILE cc_start: 0.9756 (mt) cc_final: 0.9452 (tp) REVERT: A 821 ASP cc_start: 0.9309 (m-30) cc_final: 0.9026 (p0) REVERT: A 854 SER cc_start: 0.9799 (t) cc_final: 0.9590 (p) REVERT: A 857 GLU cc_start: 0.9416 (mt-10) cc_final: 0.9123 (mm-30) REVERT: B 4 ARG cc_start: 0.9067 (ttp-170) cc_final: 0.8457 (ttt180) REVERT: B 31 ILE cc_start: 0.9799 (mt) cc_final: 0.9578 (pt) REVERT: B 126 ILE cc_start: 0.9785 (mt) cc_final: 0.9584 (tt) REVERT: B 130 GLU cc_start: 0.9723 (tp30) cc_final: 0.9488 (pm20) REVERT: B 407 LYS cc_start: 0.9573 (tptm) cc_final: 0.9205 (tptp) REVERT: B 415 LEU cc_start: 0.9955 (tt) cc_final: 0.9715 (tt) REVERT: B 466 ASP cc_start: 0.9687 (t0) cc_final: 0.9311 (t0) REVERT: B 541 ARG cc_start: 0.9287 (ttm170) cc_final: 0.8508 (ttp80) REVERT: B 542 TYR cc_start: 0.9262 (m-80) cc_final: 0.8157 (m-80) REVERT: B 576 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8156 (tp40) REVERT: B 588 ASN cc_start: 0.9739 (t0) cc_final: 0.9423 (t0) REVERT: B 592 GLN cc_start: 0.9142 (mt0) cc_final: 0.8894 (mt0) REVERT: B 620 SER cc_start: 0.9693 (p) cc_final: 0.9459 (t) REVERT: B 677 MET cc_start: 0.9871 (tpp) cc_final: 0.9630 (tpp) REVERT: B 681 ARG cc_start: 0.9728 (mtt180) cc_final: 0.9373 (ptp-110) REVERT: B 682 GLU cc_start: 0.9707 (mt-10) cc_final: 0.9479 (pt0) REVERT: B 695 GLN cc_start: 0.9625 (mt0) cc_final: 0.9308 (mp10) REVERT: B 698 GLU cc_start: 0.9656 (mt-10) cc_final: 0.9419 (pt0) REVERT: B 702 GLN cc_start: 0.9685 (mt0) cc_final: 0.9442 (mm-40) REVERT: B 705 TRP cc_start: 0.9450 (t60) cc_final: 0.9223 (t60) REVERT: B 714 ASN cc_start: 0.9793 (m-40) cc_final: 0.9508 (p0) REVERT: B 723 CYS cc_start: 0.9405 (m) cc_final: 0.8611 (p) REVERT: B 729 CYS cc_start: 0.9526 (m) cc_final: 0.8746 (p) REVERT: B 734 ARG cc_start: 0.9746 (ptt180) cc_final: 0.9484 (mtm110) REVERT: B 739 HIS cc_start: 0.9837 (m-70) cc_final: 0.9636 (m90) REVERT: B 748 LYS cc_start: 0.9894 (mttt) cc_final: 0.9614 (tttm) REVERT: B 756 MET cc_start: 0.9073 (mmm) cc_final: 0.8771 (mmm) REVERT: B 782 ILE cc_start: 0.9754 (mt) cc_final: 0.9447 (tp) REVERT: B 821 ASP cc_start: 0.9306 (m-30) cc_final: 0.9061 (p0) REVERT: B 854 SER cc_start: 0.9771 (t) cc_final: 0.9541 (p) REVERT: B 857 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9061 (mm-30) REVERT: C 4 ARG cc_start: 0.9049 (ttp-170) cc_final: 0.8496 (ttt180) REVERT: C 130 GLU cc_start: 0.9721 (tp30) cc_final: 0.9509 (pm20) REVERT: C 407 LYS cc_start: 0.9562 (tptm) cc_final: 0.9189 (tptp) REVERT: C 466 ASP cc_start: 0.9655 (t0) cc_final: 0.9405 (t0) REVERT: C 501 ASP cc_start: 0.9460 (m-30) cc_final: 0.9050 (p0) REVERT: C 541 ARG cc_start: 0.9241 (ttm170) cc_final: 0.8504 (ttp80) REVERT: C 542 TYR cc_start: 0.9323 (m-80) cc_final: 0.8065 (m-80) REVERT: C 576 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8003 (tp40) REVERT: C 588 ASN cc_start: 0.9710 (t0) cc_final: 0.9390 (t0) REVERT: C 592 GLN cc_start: 0.9238 (mt0) cc_final: 0.8936 (mt0) REVERT: C 620 SER cc_start: 0.9642 (p) cc_final: 0.9430 (t) REVERT: C 677 MET cc_start: 0.9864 (tpp) cc_final: 0.9536 (tpp) REVERT: C 681 ARG cc_start: 0.9724 (mtt180) cc_final: 0.9366 (ptp-110) REVERT: C 682 GLU cc_start: 0.9696 (mt-10) cc_final: 0.9463 (pt0) REVERT: C 695 GLN cc_start: 0.9631 (mt0) cc_final: 0.9356 (mp10) REVERT: C 697 LEU cc_start: 0.9936 (mt) cc_final: 0.9634 (pp) REVERT: C 698 GLU cc_start: 0.9643 (mt-10) cc_final: 0.9437 (pt0) REVERT: C 699 GLU cc_start: 0.9703 (pt0) cc_final: 0.9498 (pt0) REVERT: C 702 GLN cc_start: 0.9677 (mt0) cc_final: 0.9420 (mm-40) REVERT: C 705 TRP cc_start: 0.9469 (t60) cc_final: 0.9227 (t60) REVERT: C 714 ASN cc_start: 0.9800 (m-40) cc_final: 0.9488 (p0) REVERT: C 723 CYS cc_start: 0.9364 (m) cc_final: 0.8700 (p) REVERT: C 729 CYS cc_start: 0.9544 (m) cc_final: 0.8783 (p) REVERT: C 748 LYS cc_start: 0.9900 (mttt) cc_final: 0.9632 (tttm) REVERT: C 756 MET cc_start: 0.9115 (mmm) cc_final: 0.8835 (mmm) REVERT: C 782 ILE cc_start: 0.9704 (mt) cc_final: 0.9358 (tp) REVERT: C 821 ASP cc_start: 0.9254 (m-30) cc_final: 0.9041 (p0) REVERT: C 854 SER cc_start: 0.9801 (t) cc_final: 0.9560 (p) REVERT: C 857 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9067 (mm-30) REVERT: D 4 ARG cc_start: 0.9089 (ttp-170) cc_final: 0.8535 (ttt180) REVERT: D 31 ILE cc_start: 0.9806 (mt) cc_final: 0.9538 (tp) REVERT: D 124 MET cc_start: 0.9335 (mmt) cc_final: 0.9086 (mmm) REVERT: D 407 LYS cc_start: 0.9529 (tptm) cc_final: 0.9134 (tptp) REVERT: D 415 LEU cc_start: 0.9945 (tt) cc_final: 0.9683 (tt) REVERT: D 466 ASP cc_start: 0.9603 (t0) cc_final: 0.9338 (t0) REVERT: D 501 ASP cc_start: 0.9415 (m-30) cc_final: 0.9078 (p0) REVERT: D 541 ARG cc_start: 0.9214 (ttm170) cc_final: 0.8411 (ttp80) REVERT: D 542 TYR cc_start: 0.9328 (m-80) cc_final: 0.8195 (m-80) REVERT: D 576 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7764 (tp40) REVERT: D 655 ILE cc_start: 0.9616 (tt) cc_final: 0.9415 (tp) REVERT: D 677 MET cc_start: 0.9876 (tpp) cc_final: 0.9558 (tpp) REVERT: D 679 ARG cc_start: 0.9807 (mtt180) cc_final: 0.9597 (mtt180) REVERT: D 681 ARG cc_start: 0.9731 (mtt180) cc_final: 0.9395 (ptp-110) REVERT: D 682 GLU cc_start: 0.9681 (mt-10) cc_final: 0.9448 (pt0) REVERT: D 695 GLN cc_start: 0.9674 (mt0) cc_final: 0.9376 (mp10) REVERT: D 698 GLU cc_start: 0.9673 (mt-10) cc_final: 0.9417 (pt0) REVERT: D 702 GLN cc_start: 0.9683 (mt0) cc_final: 0.9453 (mm-40) REVERT: D 714 ASN cc_start: 0.9779 (m-40) cc_final: 0.9392 (p0) REVERT: D 723 CYS cc_start: 0.9371 (m) cc_final: 0.8786 (p) REVERT: D 729 CYS cc_start: 0.9538 (m) cc_final: 0.8752 (p) REVERT: D 748 LYS cc_start: 0.9875 (mttt) cc_final: 0.9582 (tttm) REVERT: D 756 MET cc_start: 0.9156 (mmm) cc_final: 0.8869 (mmm) REVERT: D 782 ILE cc_start: 0.9711 (mt) cc_final: 0.9356 (tp) REVERT: D 821 ASP cc_start: 0.9255 (m-30) cc_final: 0.9012 (p0) REVERT: D 837 ASP cc_start: 0.9537 (m-30) cc_final: 0.9322 (m-30) REVERT: D 857 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9122 (mm-30) outliers start: 24 outliers final: 0 residues processed: 735 average time/residue: 0.2995 time to fit residues: 323.1043 Evaluate side-chains 542 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 538 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain B residue 576 GLN Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain D residue 576 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 30.0000 chunk 169 optimal weight: 8.9990 chunk 94 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 chunk 114 optimal weight: 30.0000 chunk 90 optimal weight: 6.9990 chunk 175 optimal weight: 50.0000 chunk 67 optimal weight: 50.0000 chunk 106 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 203 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 70 HIS A 576 GLN A 802 ASN B 61 GLN B 70 HIS B 576 GLN B 592 GLN B 802 ASN C 61 GLN C 70 HIS C 576 GLN C 592 GLN C 802 ASN D 70 HIS D 576 GLN D 802 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.051550 restraints weight = 77934.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.053327 restraints weight = 44397.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.054593 restraints weight = 30543.867| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18056 Z= 0.170 Angle : 0.720 10.602 24512 Z= 0.354 Chirality : 0.045 0.180 2792 Planarity : 0.005 0.042 3080 Dihedral : 4.793 29.897 2440 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.00 % Allowed : 14.85 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2192 helix: -0.15 (0.14), residues: 1216 sheet: -1.64 (0.35), residues: 168 loop : -1.59 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 497 HIS 0.007 0.001 HIS C 831 PHE 0.023 0.002 PHE A 557 TYR 0.018 0.001 TYR B 545 ARG 0.006 0.001 ARG C 734 Details of bonding type rmsd hydrogen bonds : bond 0.05229 ( 940) hydrogen bonds : angle 5.19091 ( 2688) covalent geometry : bond 0.00356 (18056) covalent geometry : angle 0.71996 (24512) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 524 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.9455 (ttp-170) cc_final: 0.8967 (ttt90) REVERT: A 124 MET cc_start: 0.9693 (mmm) cc_final: 0.9066 (tpp) REVERT: A 466 ASP cc_start: 0.9642 (t0) cc_final: 0.9270 (t0) REVERT: A 470 ASN cc_start: 0.9319 (m-40) cc_final: 0.8867 (m-40) REVERT: A 542 TYR cc_start: 0.8851 (m-80) cc_final: 0.8431 (m-80) REVERT: A 651 MET cc_start: 0.9559 (mmp) cc_final: 0.9221 (mmp) REVERT: A 677 MET cc_start: 0.9893 (tpp) cc_final: 0.9476 (tpp) REVERT: A 681 ARG cc_start: 0.9515 (mtt180) cc_final: 0.9308 (ptp-110) REVERT: A 682 GLU cc_start: 0.9678 (mt-10) cc_final: 0.9453 (pt0) REVERT: A 691 ASN cc_start: 0.9778 (m-40) cc_final: 0.9484 (p0) REVERT: A 712 ASP cc_start: 0.9647 (t0) cc_final: 0.9441 (t0) REVERT: A 723 CYS cc_start: 0.9145 (m) cc_final: 0.8924 (p) REVERT: A 729 CYS cc_start: 0.9337 (m) cc_final: 0.8811 (m) REVERT: A 748 LYS cc_start: 0.9863 (mttt) cc_final: 0.9604 (ttpp) REVERT: A 756 MET cc_start: 0.9132 (mmm) cc_final: 0.8718 (mmm) REVERT: A 821 ASP cc_start: 0.9139 (m-30) cc_final: 0.8923 (p0) REVERT: A 836 ASP cc_start: 0.9252 (OUTLIER) cc_final: 0.8819 (p0) REVERT: A 837 ASP cc_start: 0.9463 (m-30) cc_final: 0.9113 (m-30) REVERT: B 4 ARG cc_start: 0.9437 (ttp-170) cc_final: 0.8957 (ttt90) REVERT: B 462 MET cc_start: 0.9698 (mmp) cc_final: 0.9463 (mmp) REVERT: B 466 ASP cc_start: 0.9684 (t0) cc_final: 0.9400 (t0) REVERT: B 542 TYR cc_start: 0.8859 (m-80) cc_final: 0.8442 (m-80) REVERT: B 651 MET cc_start: 0.9602 (mmp) cc_final: 0.9303 (mmp) REVERT: B 677 MET cc_start: 0.9882 (tpp) cc_final: 0.9335 (tpp) REVERT: B 681 ARG cc_start: 0.9503 (mtt180) cc_final: 0.9283 (ptp-110) REVERT: B 682 GLU cc_start: 0.9691 (mt-10) cc_final: 0.9441 (pt0) REVERT: B 691 ASN cc_start: 0.9760 (m-40) cc_final: 0.9452 (p0) REVERT: B 723 CYS cc_start: 0.9077 (m) cc_final: 0.8808 (p) REVERT: B 729 CYS cc_start: 0.9487 (m) cc_final: 0.8963 (m) REVERT: B 748 LYS cc_start: 0.9873 (mttt) cc_final: 0.9634 (ttpp) REVERT: B 756 MET cc_start: 0.9120 (mmm) cc_final: 0.8692 (mmm) REVERT: B 857 GLU cc_start: 0.9249 (mt-10) cc_final: 0.9030 (mm-30) REVERT: C 4 ARG cc_start: 0.9442 (ttp-170) cc_final: 0.9049 (ttm-80) REVERT: C 31 ILE cc_start: 0.9708 (pt) cc_final: 0.9460 (tp) REVERT: C 462 MET cc_start: 0.9697 (mmp) cc_final: 0.9481 (mmp) REVERT: C 466 ASP cc_start: 0.9665 (t0) cc_final: 0.9234 (t0) REVERT: C 470 ASN cc_start: 0.9320 (m-40) cc_final: 0.8839 (m110) REVERT: C 500 ILE cc_start: 0.9087 (mm) cc_final: 0.8833 (pt) REVERT: C 542 TYR cc_start: 0.8925 (m-80) cc_final: 0.8520 (m-80) REVERT: C 651 MET cc_start: 0.9622 (mmp) cc_final: 0.9350 (mmp) REVERT: C 677 MET cc_start: 0.9884 (tpp) cc_final: 0.9303 (tpp) REVERT: C 681 ARG cc_start: 0.9509 (mtt180) cc_final: 0.9279 (ptp-110) REVERT: C 682 GLU cc_start: 0.9679 (mt-10) cc_final: 0.9425 (pt0) REVERT: C 691 ASN cc_start: 0.9763 (m-40) cc_final: 0.9459 (p0) REVERT: C 697 LEU cc_start: 0.9927 (mt) cc_final: 0.9666 (pp) REVERT: C 712 ASP cc_start: 0.9646 (t0) cc_final: 0.9419 (t0) REVERT: C 729 CYS cc_start: 0.9509 (m) cc_final: 0.9003 (m) REVERT: C 748 LYS cc_start: 0.9863 (mttt) cc_final: 0.9631 (ttpp) REVERT: C 756 MET cc_start: 0.9163 (mmm) cc_final: 0.8780 (mmm) REVERT: C 844 MET cc_start: 0.9175 (mmm) cc_final: 0.8945 (mmm) REVERT: D 4 ARG cc_start: 0.9460 (ttp-170) cc_final: 0.8890 (ttt90) REVERT: D 60 MET cc_start: 0.9157 (mmp) cc_final: 0.8957 (mmm) REVERT: D 466 ASP cc_start: 0.9622 (t0) cc_final: 0.9192 (t0) REVERT: D 470 ASN cc_start: 0.9322 (m-40) cc_final: 0.8851 (m110) REVERT: D 500 ILE cc_start: 0.9017 (mm) cc_final: 0.8776 (pt) REVERT: D 542 TYR cc_start: 0.8944 (m-80) cc_final: 0.8505 (m-80) REVERT: D 651 MET cc_start: 0.9560 (mmp) cc_final: 0.9348 (mmp) REVERT: D 677 MET cc_start: 0.9880 (tpp) cc_final: 0.9376 (tpp) REVERT: D 681 ARG cc_start: 0.9506 (mtt180) cc_final: 0.9277 (ptp-110) REVERT: D 682 GLU cc_start: 0.9677 (mt-10) cc_final: 0.9447 (pt0) REVERT: D 691 ASN cc_start: 0.9768 (m-40) cc_final: 0.9372 (t0) REVERT: D 712 ASP cc_start: 0.9648 (t0) cc_final: 0.9424 (t0) REVERT: D 729 CYS cc_start: 0.9414 (m) cc_final: 0.8863 (m) REVERT: D 748 LYS cc_start: 0.9858 (mttt) cc_final: 0.9632 (tttm) REVERT: D 756 MET cc_start: 0.9189 (mmm) cc_final: 0.8790 (mmm) REVERT: D 836 ASP cc_start: 0.9226 (p0) cc_final: 0.8821 (p0) REVERT: D 837 ASP cc_start: 0.9424 (m-30) cc_final: 0.9196 (m-30) outliers start: 37 outliers final: 22 residues processed: 535 average time/residue: 0.2878 time to fit residues: 233.4172 Evaluate side-chains 461 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 438 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 779 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 138 optimal weight: 30.0000 chunk 67 optimal weight: 40.0000 chunk 3 optimal weight: 8.9990 chunk 189 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.061936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.046112 restraints weight = 84961.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.047943 restraints weight = 45848.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.049221 restraints weight = 30385.031| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18056 Z= 0.136 Angle : 0.677 12.713 24512 Z= 0.331 Chirality : 0.044 0.167 2792 Planarity : 0.004 0.037 3080 Dihedral : 4.294 20.999 2428 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.32 % Allowed : 16.85 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2192 helix: 0.31 (0.15), residues: 1232 sheet: -1.38 (0.34), residues: 184 loop : -1.41 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 705 HIS 0.005 0.001 HIS D 771 PHE 0.026 0.002 PHE A 640 TYR 0.014 0.001 TYR B 616 ARG 0.008 0.001 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 940) hydrogen bonds : angle 4.85416 ( 2688) covalent geometry : bond 0.00288 (18056) covalent geometry : angle 0.67749 (24512) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 471 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.9407 (ttp-170) cc_final: 0.8978 (ttm-80) REVERT: A 462 MET cc_start: 0.9872 (mmm) cc_final: 0.9570 (mmm) REVERT: A 466 ASP cc_start: 0.9666 (t0) cc_final: 0.9196 (t0) REVERT: A 470 ASN cc_start: 0.9315 (m-40) cc_final: 0.8821 (m-40) REVERT: A 542 TYR cc_start: 0.8913 (m-80) cc_final: 0.8343 (m-80) REVERT: A 651 MET cc_start: 0.9622 (mmp) cc_final: 0.9312 (mmp) REVERT: A 677 MET cc_start: 0.9886 (tpp) cc_final: 0.9376 (tpp) REVERT: A 681 ARG cc_start: 0.9512 (mtt180) cc_final: 0.9263 (ttm110) REVERT: A 682 GLU cc_start: 0.9688 (mt-10) cc_final: 0.9486 (pt0) REVERT: A 691 ASN cc_start: 0.9764 (m-40) cc_final: 0.9363 (t0) REVERT: A 729 CYS cc_start: 0.9186 (m) cc_final: 0.8549 (m) REVERT: A 748 LYS cc_start: 0.9859 (mttt) cc_final: 0.9602 (ttpp) REVERT: A 756 MET cc_start: 0.8963 (mmm) cc_final: 0.8504 (mmm) REVERT: A 857 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8574 (mm-30) REVERT: B 4 ARG cc_start: 0.9393 (ttp-170) cc_final: 0.8944 (ttm-80) REVERT: B 462 MET cc_start: 0.9722 (mmp) cc_final: 0.9452 (mmp) REVERT: B 542 TYR cc_start: 0.8871 (m-80) cc_final: 0.8343 (m-80) REVERT: B 651 MET cc_start: 0.9616 (mmp) cc_final: 0.9345 (mmp) REVERT: B 677 MET cc_start: 0.9789 (tpp) cc_final: 0.9520 (tpp) REVERT: B 682 GLU cc_start: 0.9681 (mt-10) cc_final: 0.9481 (pt0) REVERT: B 691 ASN cc_start: 0.9746 (m-40) cc_final: 0.9412 (p0) REVERT: B 748 LYS cc_start: 0.9867 (mttt) cc_final: 0.9632 (ttpp) REVERT: B 756 MET cc_start: 0.8923 (mmm) cc_final: 0.8680 (mmm) REVERT: C 4 ARG cc_start: 0.9417 (ttp-170) cc_final: 0.8890 (ttt90) REVERT: C 31 ILE cc_start: 0.9710 (pt) cc_final: 0.9470 (tp) REVERT: C 42 ILE cc_start: 0.9838 (pt) cc_final: 0.9565 (mt) REVERT: C 462 MET cc_start: 0.9657 (mmp) cc_final: 0.9347 (mmp) REVERT: C 542 TYR cc_start: 0.8945 (m-80) cc_final: 0.8424 (m-80) REVERT: C 651 MET cc_start: 0.9636 (mmp) cc_final: 0.9391 (mmp) REVERT: C 677 MET cc_start: 0.9680 (tpp) cc_final: 0.9446 (tpp) REVERT: C 680 VAL cc_start: 0.9934 (t) cc_final: 0.9616 (m) REVERT: C 691 ASN cc_start: 0.9743 (m-40) cc_final: 0.9308 (t0) REVERT: C 748 LYS cc_start: 0.9855 (mttt) cc_final: 0.9623 (ttpp) REVERT: C 756 MET cc_start: 0.8946 (mmm) cc_final: 0.8693 (mmm) REVERT: C 857 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8448 (mm-30) REVERT: D 4 ARG cc_start: 0.9453 (ttp-170) cc_final: 0.8911 (ttt90) REVERT: D 542 TYR cc_start: 0.8967 (m-80) cc_final: 0.8451 (m-80) REVERT: D 651 MET cc_start: 0.9639 (mmp) cc_final: 0.9378 (mmp) REVERT: D 677 MET cc_start: 0.9651 (tpp) cc_final: 0.9390 (tpp) REVERT: D 680 VAL cc_start: 0.9933 (t) cc_final: 0.9647 (m) REVERT: D 691 ASN cc_start: 0.9759 (m-40) cc_final: 0.9362 (t0) REVERT: D 729 CYS cc_start: 0.9257 (m) cc_final: 0.8699 (m) REVERT: D 748 LYS cc_start: 0.9854 (mttt) cc_final: 0.9609 (ttpp) REVERT: D 756 MET cc_start: 0.9004 (mmm) cc_final: 0.8581 (mmm) REVERT: D 857 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8499 (mm-30) outliers start: 43 outliers final: 29 residues processed: 492 average time/residue: 0.2557 time to fit residues: 195.4475 Evaluate side-chains 456 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 427 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 167 optimal weight: 6.9990 chunk 187 optimal weight: 40.0000 chunk 36 optimal weight: 50.0000 chunk 133 optimal weight: 0.0980 chunk 31 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 217 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 592 GLN B 33 ASN B 470 ASN C 33 ASN C 470 ASN D 470 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.061411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.045777 restraints weight = 85239.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.047609 restraints weight = 45818.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.048885 restraints weight = 30158.390| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18056 Z= 0.137 Angle : 0.666 12.229 24512 Z= 0.330 Chirality : 0.044 0.165 2792 Planarity : 0.004 0.038 3080 Dihedral : 4.186 20.377 2428 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.29 % Allowed : 17.98 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2192 helix: 0.45 (0.15), residues: 1200 sheet: -0.99 (0.36), residues: 168 loop : -1.17 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 585 HIS 0.006 0.001 HIS B 831 PHE 0.020 0.002 PHE A 557 TYR 0.013 0.001 TYR D 616 ARG 0.009 0.000 ARG B 681 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 940) hydrogen bonds : angle 4.72263 ( 2688) covalent geometry : bond 0.00290 (18056) covalent geometry : angle 0.66642 (24512) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 463 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.9430 (ttp-170) cc_final: 0.8959 (ttm-80) REVERT: A 124 MET cc_start: 0.9725 (mmm) cc_final: 0.9149 (tpp) REVERT: A 542 TYR cc_start: 0.9022 (m-80) cc_final: 0.8402 (m-80) REVERT: A 651 MET cc_start: 0.9637 (mmp) cc_final: 0.9335 (mmm) REVERT: A 677 MET cc_start: 0.9877 (tpp) cc_final: 0.9412 (tpp) REVERT: A 681 ARG cc_start: 0.9493 (mtt180) cc_final: 0.9230 (ttm110) REVERT: A 682 GLU cc_start: 0.9690 (mt-10) cc_final: 0.9488 (pt0) REVERT: A 691 ASN cc_start: 0.9756 (m-40) cc_final: 0.9353 (t0) REVERT: A 695 GLN cc_start: 0.9792 (mt0) cc_final: 0.9427 (pt0) REVERT: A 729 CYS cc_start: 0.9088 (m) cc_final: 0.8446 (m) REVERT: A 748 LYS cc_start: 0.9854 (mttt) cc_final: 0.9606 (ttpp) REVERT: A 756 MET cc_start: 0.8901 (mmm) cc_final: 0.8451 (mmm) REVERT: A 857 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8213 (mm-30) REVERT: B 4 ARG cc_start: 0.9413 (ttp-170) cc_final: 0.8881 (ttt90) REVERT: B 60 MET cc_start: 0.9410 (mmp) cc_final: 0.9132 (mmm) REVERT: B 462 MET cc_start: 0.9730 (mmp) cc_final: 0.9332 (mmp) REVERT: B 542 TYR cc_start: 0.8956 (m-80) cc_final: 0.8527 (m-80) REVERT: B 651 MET cc_start: 0.9581 (mmp) cc_final: 0.9372 (mmp) REVERT: B 677 MET cc_start: 0.9750 (tpp) cc_final: 0.9388 (tpp) REVERT: B 681 ARG cc_start: 0.9655 (ttm110) cc_final: 0.9229 (mtm110) REVERT: B 682 GLU cc_start: 0.9668 (mt-10) cc_final: 0.9451 (mt-10) REVERT: B 691 ASN cc_start: 0.9736 (m-40) cc_final: 0.9291 (t0) REVERT: B 729 CYS cc_start: 0.9230 (m) cc_final: 0.8632 (m) REVERT: B 748 LYS cc_start: 0.9860 (mttt) cc_final: 0.9635 (ttpp) REVERT: B 756 MET cc_start: 0.8860 (mmm) cc_final: 0.8447 (mmm) REVERT: B 840 GLU cc_start: 0.9482 (mt-10) cc_final: 0.9242 (mt-10) REVERT: B 857 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8513 (mm-30) REVERT: C 4 ARG cc_start: 0.9440 (ttp-170) cc_final: 0.8977 (ttm-80) REVERT: C 31 ILE cc_start: 0.9729 (pt) cc_final: 0.9453 (tp) REVERT: C 42 ILE cc_start: 0.9861 (pt) cc_final: 0.9586 (mp) REVERT: C 60 MET cc_start: 0.9395 (mmp) cc_final: 0.9089 (mmm) REVERT: C 542 TYR cc_start: 0.9011 (m-80) cc_final: 0.8534 (m-80) REVERT: C 677 MET cc_start: 0.9727 (tpp) cc_final: 0.9400 (tpp) REVERT: C 691 ASN cc_start: 0.9731 (m-40) cc_final: 0.9303 (t0) REVERT: C 748 LYS cc_start: 0.9850 (mttt) cc_final: 0.9621 (ttpp) REVERT: C 756 MET cc_start: 0.8902 (mmm) cc_final: 0.8648 (mmm) REVERT: C 856 LEU cc_start: 0.9587 (tt) cc_final: 0.9381 (pp) REVERT: C 857 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8167 (mm-30) REVERT: D 4 ARG cc_start: 0.9452 (ttp-170) cc_final: 0.8921 (ttt180) REVERT: D 542 TYR cc_start: 0.9017 (m-80) cc_final: 0.8563 (m-80) REVERT: D 677 MET cc_start: 0.9677 (tpp) cc_final: 0.9251 (tpt) REVERT: D 681 ARG cc_start: 0.9269 (mmm160) cc_final: 0.9016 (mmm160) REVERT: D 691 ASN cc_start: 0.9756 (m-40) cc_final: 0.9387 (t0) REVERT: D 729 CYS cc_start: 0.9177 (m) cc_final: 0.8534 (m) REVERT: D 748 LYS cc_start: 0.9848 (mttt) cc_final: 0.9609 (ttpp) REVERT: D 756 MET cc_start: 0.8918 (mmm) cc_final: 0.8504 (mmm) REVERT: D 856 LEU cc_start: 0.9629 (tt) cc_final: 0.9412 (pp) REVERT: D 857 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8237 (mm-30) outliers start: 61 outliers final: 43 residues processed: 489 average time/residue: 0.2628 time to fit residues: 197.2374 Evaluate side-chains 451 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 408 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 30.0000 chunk 131 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 30.0000 chunk 115 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 116 optimal weight: 30.0000 chunk 163 optimal weight: 50.0000 chunk 25 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 470 ASN C 470 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.045268 restraints weight = 87120.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.047071 restraints weight = 46721.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.048342 restraints weight = 30815.398| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18056 Z= 0.136 Angle : 0.688 11.106 24512 Z= 0.339 Chirality : 0.044 0.237 2792 Planarity : 0.004 0.048 3080 Dihedral : 4.145 16.926 2428 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.29 % Allowed : 19.49 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2192 helix: 0.36 (0.15), residues: 1208 sheet: -0.63 (0.37), residues: 168 loop : -0.97 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 705 HIS 0.006 0.001 HIS B 831 PHE 0.019 0.002 PHE A 557 TYR 0.014 0.001 TYR D 707 ARG 0.012 0.000 ARG C 681 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 940) hydrogen bonds : angle 4.69681 ( 2688) covalent geometry : bond 0.00293 (18056) covalent geometry : angle 0.68839 (24512) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 441 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.9464 (ttp-170) cc_final: 0.8858 (ttt90) REVERT: A 124 MET cc_start: 0.9696 (mmm) cc_final: 0.9122 (tpp) REVERT: A 462 MET cc_start: 0.9887 (mmm) cc_final: 0.9686 (tpp) REVERT: A 542 TYR cc_start: 0.9064 (m-80) cc_final: 0.8443 (m-80) REVERT: A 651 MET cc_start: 0.9629 (mmp) cc_final: 0.9378 (mmm) REVERT: A 677 MET cc_start: 0.9845 (tpp) cc_final: 0.9262 (tpp) REVERT: A 681 ARG cc_start: 0.9474 (mtt180) cc_final: 0.9238 (ttm110) REVERT: A 691 ASN cc_start: 0.9745 (m-40) cc_final: 0.9348 (t0) REVERT: A 695 GLN cc_start: 0.9708 (mt0) cc_final: 0.9483 (pt0) REVERT: A 729 CYS cc_start: 0.9098 (m) cc_final: 0.8579 (m) REVERT: A 748 LYS cc_start: 0.9852 (mttt) cc_final: 0.9610 (ttpp) REVERT: B 4 ARG cc_start: 0.9444 (ttp-170) cc_final: 0.8913 (ttm-80) REVERT: B 8 VAL cc_start: 0.9544 (m) cc_final: 0.9097 (p) REVERT: B 60 MET cc_start: 0.9443 (mmp) cc_final: 0.9126 (mmm) REVERT: B 542 TYR cc_start: 0.9019 (m-80) cc_final: 0.8545 (m-80) REVERT: B 682 GLU cc_start: 0.9668 (mt-10) cc_final: 0.9435 (mt-10) REVERT: B 691 ASN cc_start: 0.9730 (m-40) cc_final: 0.9268 (t0) REVERT: B 713 MET cc_start: 0.8906 (mmm) cc_final: 0.8608 (mmm) REVERT: B 729 CYS cc_start: 0.9262 (m) cc_final: 0.8681 (m) REVERT: B 748 LYS cc_start: 0.9855 (mttt) cc_final: 0.9629 (ttpp) REVERT: B 756 MET cc_start: 0.8835 (mmm) cc_final: 0.8399 (mmm) REVERT: B 840 GLU cc_start: 0.9478 (mt-10) cc_final: 0.9236 (mt-10) REVERT: B 857 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8177 (mm-30) REVERT: C 4 ARG cc_start: 0.9459 (ttp-170) cc_final: 0.8957 (ttm-80) REVERT: C 31 ILE cc_start: 0.9738 (pt) cc_final: 0.9460 (tp) REVERT: C 42 ILE cc_start: 0.9857 (pt) cc_final: 0.9570 (mp) REVERT: C 60 MET cc_start: 0.9423 (mmp) cc_final: 0.9070 (mmm) REVERT: C 542 TYR cc_start: 0.9069 (m-80) cc_final: 0.8651 (m-80) REVERT: C 638 LYS cc_start: 0.9832 (mttt) cc_final: 0.9556 (mttm) REVERT: C 677 MET cc_start: 0.9748 (tpp) cc_final: 0.9478 (tpp) REVERT: C 691 ASN cc_start: 0.9719 (m-40) cc_final: 0.9284 (t0) REVERT: C 748 LYS cc_start: 0.9845 (mttt) cc_final: 0.9618 (ttpp) REVERT: C 756 MET cc_start: 0.8876 (mmm) cc_final: 0.8629 (mmm) REVERT: C 856 LEU cc_start: 0.9599 (tt) cc_final: 0.9371 (pp) REVERT: C 857 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8201 (mm-30) REVERT: D 4 ARG cc_start: 0.9447 (ttp-170) cc_final: 0.8919 (ttt90) REVERT: D 60 MET cc_start: 0.9393 (mmp) cc_final: 0.9146 (mmm) REVERT: D 542 TYR cc_start: 0.9090 (m-80) cc_final: 0.8678 (m-80) REVERT: D 623 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9316 (t) REVERT: D 638 LYS cc_start: 0.9736 (mttt) cc_final: 0.9488 (mttm) REVERT: D 677 MET cc_start: 0.9646 (tpp) cc_final: 0.9375 (tpt) REVERT: D 691 ASN cc_start: 0.9739 (m-40) cc_final: 0.9352 (t0) REVERT: D 729 CYS cc_start: 0.9159 (m) cc_final: 0.8293 (m) REVERT: D 748 LYS cc_start: 0.9846 (mttt) cc_final: 0.9577 (ttpp) REVERT: D 756 MET cc_start: 0.8880 (mmm) cc_final: 0.8467 (mmm) REVERT: D 857 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8293 (mm-30) outliers start: 61 outliers final: 46 residues processed: 468 average time/residue: 0.2674 time to fit residues: 192.1079 Evaluate side-chains 457 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 410 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 179 optimal weight: 40.0000 chunk 102 optimal weight: 50.0000 chunk 25 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 220 optimal weight: 40.0000 chunk 64 optimal weight: 8.9990 chunk 115 optimal weight: 0.4980 chunk 175 optimal weight: 40.0000 chunk 183 optimal weight: 7.9990 chunk 76 optimal weight: 40.0000 chunk 152 optimal weight: 5.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 592 GLN B 702 GLN D 470 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.045081 restraints weight = 86272.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.046895 restraints weight = 46645.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.048179 restraints weight = 30724.443| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18056 Z= 0.128 Angle : 0.709 11.330 24512 Z= 0.343 Chirality : 0.045 0.271 2792 Planarity : 0.004 0.048 3080 Dihedral : 4.151 16.127 2428 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.86 % Allowed : 20.84 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2192 helix: 0.35 (0.15), residues: 1212 sheet: -0.31 (0.38), residues: 168 loop : -0.74 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 410 HIS 0.005 0.001 HIS B 831 PHE 0.018 0.001 PHE A 557 TYR 0.016 0.001 TYR D 707 ARG 0.012 0.000 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 940) hydrogen bonds : angle 4.68103 ( 2688) covalent geometry : bond 0.00280 (18056) covalent geometry : angle 0.70914 (24512) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 439 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.9463 (ttp-170) cc_final: 0.8834 (ttm-80) REVERT: A 462 MET cc_start: 0.9885 (mmm) cc_final: 0.9469 (tpp) REVERT: A 542 TYR cc_start: 0.9075 (m-80) cc_final: 0.8454 (m-80) REVERT: A 638 LYS cc_start: 0.9741 (mttt) cc_final: 0.9306 (mmtm) REVERT: A 651 MET cc_start: 0.9645 (mmp) cc_final: 0.9394 (mmm) REVERT: A 677 MET cc_start: 0.9838 (tpp) cc_final: 0.9255 (tpp) REVERT: A 681 ARG cc_start: 0.9466 (mtt180) cc_final: 0.9197 (ttm110) REVERT: A 691 ASN cc_start: 0.9748 (m-40) cc_final: 0.9326 (t0) REVERT: A 695 GLN cc_start: 0.9782 (mt0) cc_final: 0.9423 (pt0) REVERT: A 729 CYS cc_start: 0.9240 (m) cc_final: 0.8708 (m) REVERT: A 748 LYS cc_start: 0.9848 (mttt) cc_final: 0.9606 (ttpp) REVERT: A 756 MET cc_start: 0.9410 (tpp) cc_final: 0.9023 (mmm) REVERT: A 768 THR cc_start: 0.8628 (p) cc_final: 0.8104 (t) REVERT: B 4 ARG cc_start: 0.9444 (ttp-170) cc_final: 0.8860 (ttm-80) REVERT: B 60 MET cc_start: 0.9427 (mmp) cc_final: 0.9177 (mmm) REVERT: B 542 TYR cc_start: 0.9053 (m-80) cc_final: 0.8601 (m-80) REVERT: B 592 GLN cc_start: 0.8757 (mt0) cc_final: 0.8437 (mt0) REVERT: B 638 LYS cc_start: 0.9719 (mttt) cc_final: 0.9292 (mmtm) REVERT: B 677 MET cc_start: 0.9761 (tpp) cc_final: 0.9503 (mmm) REVERT: B 682 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9423 (mt-10) REVERT: B 691 ASN cc_start: 0.9715 (m-40) cc_final: 0.9252 (t0) REVERT: B 729 CYS cc_start: 0.9248 (m) cc_final: 0.8653 (m) REVERT: B 748 LYS cc_start: 0.9856 (mttt) cc_final: 0.9623 (ttpp) REVERT: B 756 MET cc_start: 0.8824 (mmm) cc_final: 0.8400 (mmm) REVERT: B 840 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9247 (mt-10) REVERT: C 4 ARG cc_start: 0.9477 (ttp-170) cc_final: 0.9000 (ttm-80) REVERT: C 31 ILE cc_start: 0.9741 (pt) cc_final: 0.9462 (tp) REVERT: C 42 ILE cc_start: 0.9833 (pt) cc_final: 0.9565 (mp) REVERT: C 60 MET cc_start: 0.9395 (mmp) cc_final: 0.9105 (mmm) REVERT: C 462 MET cc_start: 0.9672 (tpt) cc_final: 0.9429 (tpt) REVERT: C 542 TYR cc_start: 0.9110 (m-80) cc_final: 0.8679 (m-80) REVERT: C 638 LYS cc_start: 0.9828 (mttt) cc_final: 0.9431 (mttm) REVERT: C 651 MET cc_start: 0.9610 (mmp) cc_final: 0.9320 (mmp) REVERT: C 677 MET cc_start: 0.9743 (tpp) cc_final: 0.9386 (tpp) REVERT: C 680 VAL cc_start: 0.9867 (t) cc_final: 0.9665 (m) REVERT: C 681 ARG cc_start: 0.9485 (mmm-85) cc_final: 0.8762 (mmm160) REVERT: C 691 ASN cc_start: 0.9704 (m-40) cc_final: 0.9256 (t0) REVERT: C 748 LYS cc_start: 0.9843 (mttt) cc_final: 0.9590 (ttpp) REVERT: C 756 MET cc_start: 0.8890 (mmm) cc_final: 0.8665 (mmm) REVERT: D 4 ARG cc_start: 0.9455 (ttp-170) cc_final: 0.8923 (ttt90) REVERT: D 60 MET cc_start: 0.9419 (mmp) cc_final: 0.9105 (mmm) REVERT: D 542 TYR cc_start: 0.9086 (m-80) cc_final: 0.8680 (m-80) REVERT: D 638 LYS cc_start: 0.9759 (mttt) cc_final: 0.9537 (mttm) REVERT: D 677 MET cc_start: 0.9667 (tpp) cc_final: 0.9420 (tpt) REVERT: D 681 ARG cc_start: 0.9330 (mmm160) cc_final: 0.8899 (mmm160) REVERT: D 691 ASN cc_start: 0.9726 (m-40) cc_final: 0.9349 (t0) REVERT: D 729 CYS cc_start: 0.9023 (m) cc_final: 0.8534 (m) REVERT: D 741 LYS cc_start: 0.9375 (pttp) cc_final: 0.9160 (pttm) REVERT: D 748 LYS cc_start: 0.9844 (mttt) cc_final: 0.9570 (ttpp) REVERT: D 857 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8310 (mm-30) outliers start: 53 outliers final: 44 residues processed: 457 average time/residue: 0.2984 time to fit residues: 209.5583 Evaluate side-chains 449 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 405 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 758 PHE Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 31 optimal weight: 9.9990 chunk 195 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 67 optimal weight: 50.0000 chunk 168 optimal weight: 0.0070 chunk 0 optimal weight: 60.0000 chunk 29 optimal weight: 7.9990 chunk 112 optimal weight: 60.0000 chunk 133 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN C 592 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.060442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.045072 restraints weight = 85644.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.046884 restraints weight = 46414.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.048179 restraints weight = 30665.339| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18056 Z= 0.129 Angle : 0.720 11.577 24512 Z= 0.348 Chirality : 0.045 0.247 2792 Planarity : 0.004 0.060 3080 Dihedral : 4.140 18.172 2428 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.81 % Allowed : 22.79 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2192 helix: 0.37 (0.15), residues: 1212 sheet: -0.13 (0.38), residues: 168 loop : -0.65 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 585 HIS 0.005 0.001 HIS B 831 PHE 0.020 0.001 PHE D 640 TYR 0.017 0.001 TYR D 707 ARG 0.009 0.000 ARG B 681 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 940) hydrogen bonds : angle 4.69069 ( 2688) covalent geometry : bond 0.00284 (18056) covalent geometry : angle 0.71985 (24512) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 433 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.9455 (ttp-170) cc_final: 0.9048 (ptm160) REVERT: A 124 MET cc_start: 0.9694 (mmm) cc_final: 0.9171 (tpp) REVERT: A 462 MET cc_start: 0.9874 (mmm) cc_final: 0.9486 (tpp) REVERT: A 542 TYR cc_start: 0.9098 (m-80) cc_final: 0.8490 (m-80) REVERT: A 551 PHE cc_start: 0.9650 (t80) cc_final: 0.9400 (t80) REVERT: A 638 LYS cc_start: 0.9741 (mttt) cc_final: 0.9343 (mmtm) REVERT: A 651 MET cc_start: 0.9652 (mmp) cc_final: 0.9410 (mmm) REVERT: A 677 MET cc_start: 0.9838 (tpp) cc_final: 0.9345 (tpp) REVERT: A 681 ARG cc_start: 0.9451 (mtt180) cc_final: 0.9195 (ttm110) REVERT: A 691 ASN cc_start: 0.9749 (m-40) cc_final: 0.9324 (t0) REVERT: A 729 CYS cc_start: 0.9279 (m) cc_final: 0.8691 (m) REVERT: A 748 LYS cc_start: 0.9849 (mttt) cc_final: 0.9572 (ttpp) REVERT: A 756 MET cc_start: 0.9458 (tpp) cc_final: 0.9058 (mmm) REVERT: A 768 THR cc_start: 0.8680 (p) cc_final: 0.8174 (t) REVERT: B 4 ARG cc_start: 0.9457 (ttp-170) cc_final: 0.8867 (ttm-80) REVERT: B 60 MET cc_start: 0.9405 (mmp) cc_final: 0.9145 (mmm) REVERT: B 542 TYR cc_start: 0.9076 (m-80) cc_final: 0.8629 (m-80) REVERT: B 638 LYS cc_start: 0.9730 (mttt) cc_final: 0.9315 (mmtm) REVERT: B 677 MET cc_start: 0.9712 (tpp) cc_final: 0.9448 (mmm) REVERT: B 691 ASN cc_start: 0.9723 (m-40) cc_final: 0.9257 (t0) REVERT: B 729 CYS cc_start: 0.9251 (m) cc_final: 0.8650 (m) REVERT: B 748 LYS cc_start: 0.9855 (mttt) cc_final: 0.9621 (ttpp) REVERT: B 756 MET cc_start: 0.8831 (mmm) cc_final: 0.8412 (mmm) REVERT: B 840 GLU cc_start: 0.9487 (mt-10) cc_final: 0.9241 (mt-10) REVERT: C 4 ARG cc_start: 0.9492 (ttp-170) cc_final: 0.8976 (ttm-80) REVERT: C 31 ILE cc_start: 0.9753 (pt) cc_final: 0.9499 (tp) REVERT: C 60 MET cc_start: 0.9362 (mmp) cc_final: 0.9061 (mmm) REVERT: C 462 MET cc_start: 0.9669 (tpt) cc_final: 0.9407 (tpt) REVERT: C 542 TYR cc_start: 0.9119 (m-80) cc_final: 0.8704 (m-80) REVERT: C 638 LYS cc_start: 0.9763 (mttt) cc_final: 0.9554 (mttm) REVERT: C 651 MET cc_start: 0.9654 (mmp) cc_final: 0.9378 (mmp) REVERT: C 677 MET cc_start: 0.9745 (tpp) cc_final: 0.9456 (tpp) REVERT: C 681 ARG cc_start: 0.9530 (mmm-85) cc_final: 0.8840 (mmm160) REVERT: C 691 ASN cc_start: 0.9701 (m-40) cc_final: 0.9242 (t0) REVERT: C 748 LYS cc_start: 0.9845 (mttt) cc_final: 0.9593 (ttpp) REVERT: C 756 MET cc_start: 0.8909 (mmm) cc_final: 0.8658 (mmm) REVERT: C 758 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: D 4 ARG cc_start: 0.9466 (ttp-170) cc_final: 0.8928 (ttt90) REVERT: D 60 MET cc_start: 0.9407 (mmp) cc_final: 0.9050 (mmm) REVERT: D 542 TYR cc_start: 0.9080 (m-80) cc_final: 0.8745 (m-80) REVERT: D 638 LYS cc_start: 0.9770 (mttt) cc_final: 0.9331 (mmtm) REVERT: D 681 ARG cc_start: 0.9357 (mmm160) cc_final: 0.8860 (mmm160) REVERT: D 691 ASN cc_start: 0.9722 (m-40) cc_final: 0.9332 (t0) REVERT: D 729 CYS cc_start: 0.9249 (m) cc_final: 0.8587 (m) REVERT: D 748 LYS cc_start: 0.9842 (mttt) cc_final: 0.9572 (ttpp) REVERT: D 756 MET cc_start: 0.9441 (tpp) cc_final: 0.9101 (mmm) outliers start: 52 outliers final: 40 residues processed: 451 average time/residue: 0.2816 time to fit residues: 195.0422 Evaluate side-chains 440 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 399 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 693 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 18 optimal weight: 30.0000 chunk 45 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 67 optimal weight: 50.0000 chunk 64 optimal weight: 7.9990 chunk 118 optimal weight: 30.0000 chunk 194 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 50.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 703 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.059769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.044535 restraints weight = 87174.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.046342 restraints weight = 46940.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.047610 restraints weight = 30730.467| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.6406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18056 Z= 0.144 Angle : 0.758 11.729 24512 Z= 0.365 Chirality : 0.046 0.337 2792 Planarity : 0.004 0.115 3080 Dihedral : 4.204 20.395 2428 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.01 % Favored : 97.90 % Rotamer: Outliers : 2.75 % Allowed : 24.41 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.18), residues: 2192 helix: 0.34 (0.15), residues: 1216 sheet: 0.07 (0.38), residues: 188 loop : -0.48 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 585 HIS 0.007 0.001 HIS B 703 PHE 0.018 0.001 PHE A 551 TYR 0.022 0.001 TYR C 707 ARG 0.007 0.000 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 940) hydrogen bonds : angle 4.74720 ( 2688) covalent geometry : bond 0.00317 (18056) covalent geometry : angle 0.75838 (24512) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 417 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.9462 (ttp-170) cc_final: 0.9061 (ptm160) REVERT: A 124 MET cc_start: 0.9712 (mmm) cc_final: 0.9169 (tpp) REVERT: A 542 TYR cc_start: 0.9063 (m-80) cc_final: 0.8586 (m-80) REVERT: A 574 MET cc_start: 0.8469 (ppp) cc_final: 0.8262 (mmt) REVERT: A 638 LYS cc_start: 0.9750 (mttt) cc_final: 0.9376 (mmtm) REVERT: A 651 MET cc_start: 0.9655 (mmp) cc_final: 0.9423 (mmm) REVERT: A 668 SER cc_start: 0.9511 (t) cc_final: 0.9275 (p) REVERT: A 677 MET cc_start: 0.9832 (tpp) cc_final: 0.9331 (tpp) REVERT: A 681 ARG cc_start: 0.9451 (mtt180) cc_final: 0.9187 (ttm110) REVERT: A 691 ASN cc_start: 0.9750 (m-40) cc_final: 0.9336 (t0) REVERT: A 729 CYS cc_start: 0.9310 (m) cc_final: 0.8746 (m) REVERT: A 748 LYS cc_start: 0.9850 (mttt) cc_final: 0.9613 (ttpp) REVERT: A 756 MET cc_start: 0.9477 (tpp) cc_final: 0.9074 (mmm) REVERT: A 768 THR cc_start: 0.8659 (p) cc_final: 0.8152 (t) REVERT: B 4 ARG cc_start: 0.9443 (ttp-170) cc_final: 0.8801 (ttm-80) REVERT: B 60 MET cc_start: 0.9355 (mmp) cc_final: 0.9102 (mmm) REVERT: B 542 TYR cc_start: 0.9085 (m-80) cc_final: 0.8632 (m-80) REVERT: B 574 MET cc_start: 0.8612 (ppp) cc_final: 0.8368 (mmt) REVERT: B 638 LYS cc_start: 0.9740 (mttt) cc_final: 0.9345 (mmtm) REVERT: B 677 MET cc_start: 0.9747 (tpp) cc_final: 0.9380 (mmm) REVERT: B 691 ASN cc_start: 0.9733 (m-40) cc_final: 0.9262 (t0) REVERT: B 748 LYS cc_start: 0.9854 (mttt) cc_final: 0.9604 (ttpp) REVERT: B 756 MET cc_start: 0.8843 (mmm) cc_final: 0.8584 (mmm) REVERT: B 799 LEU cc_start: 0.9617 (mm) cc_final: 0.9361 (mm) REVERT: B 840 GLU cc_start: 0.9484 (mt-10) cc_final: 0.9250 (mt-10) REVERT: C 4 ARG cc_start: 0.9485 (ttp-170) cc_final: 0.8808 (ttm-80) REVERT: C 31 ILE cc_start: 0.9812 (pt) cc_final: 0.9552 (tp) REVERT: C 60 MET cc_start: 0.9370 (mmp) cc_final: 0.9058 (mmm) REVERT: C 542 TYR cc_start: 0.9148 (m-80) cc_final: 0.8742 (m-80) REVERT: C 574 MET cc_start: 0.8666 (ppp) cc_final: 0.8422 (mmt) REVERT: C 638 LYS cc_start: 0.9778 (mttt) cc_final: 0.9378 (mmtm) REVERT: C 651 MET cc_start: 0.9651 (mmp) cc_final: 0.9435 (mmp) REVERT: C 677 MET cc_start: 0.9752 (tpp) cc_final: 0.9453 (tpp) REVERT: C 681 ARG cc_start: 0.9558 (mmm-85) cc_final: 0.8851 (mmm160) REVERT: C 691 ASN cc_start: 0.9703 (m-40) cc_final: 0.9241 (t0) REVERT: C 748 LYS cc_start: 0.9848 (mttt) cc_final: 0.9600 (ttpp) REVERT: C 756 MET cc_start: 0.8935 (mmm) cc_final: 0.8673 (mmm) REVERT: C 758 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8769 (m-80) REVERT: C 768 THR cc_start: 0.8658 (p) cc_final: 0.8146 (t) REVERT: D 4 ARG cc_start: 0.9455 (ttp-170) cc_final: 0.8911 (ttt90) REVERT: D 60 MET cc_start: 0.9349 (mmp) cc_final: 0.9010 (mmm) REVERT: D 538 LYS cc_start: 0.9673 (mmtt) cc_final: 0.9276 (mppt) REVERT: D 542 TYR cc_start: 0.9109 (m-80) cc_final: 0.8778 (m-80) REVERT: D 638 LYS cc_start: 0.9780 (mttt) cc_final: 0.9403 (mmtm) REVERT: D 651 MET cc_start: 0.9608 (mmp) cc_final: 0.9323 (mmm) REVERT: D 677 MET cc_start: 0.9514 (tpt) cc_final: 0.9240 (tpp) REVERT: D 691 ASN cc_start: 0.9733 (m-40) cc_final: 0.9337 (t0) REVERT: D 729 CYS cc_start: 0.9276 (m) cc_final: 0.8639 (m) REVERT: D 748 LYS cc_start: 0.9846 (mttt) cc_final: 0.9583 (ttpp) REVERT: D 756 MET cc_start: 0.9443 (tpp) cc_final: 0.9123 (mmm) outliers start: 51 outliers final: 43 residues processed: 434 average time/residue: 0.3074 time to fit residues: 208.0340 Evaluate side-chains 438 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 394 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 839 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 115 optimal weight: 7.9990 chunk 148 optimal weight: 50.0000 chunk 171 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 173 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 215 optimal weight: 50.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 ASN B 629 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.059660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.044402 restraints weight = 86564.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.046202 restraints weight = 46834.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.047472 restraints weight = 30910.207| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18056 Z= 0.138 Angle : 0.774 11.736 24512 Z= 0.370 Chirality : 0.047 0.364 2792 Planarity : 0.004 0.043 3080 Dihedral : 4.220 21.098 2428 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.87 % Favored : 98.08 % Rotamer: Outliers : 2.59 % Allowed : 24.84 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.18), residues: 2192 helix: 0.37 (0.15), residues: 1216 sheet: 0.22 (0.39), residues: 188 loop : -0.46 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 585 HIS 0.007 0.001 HIS A 762 PHE 0.021 0.001 PHE C 640 TYR 0.016 0.001 TYR D 616 ARG 0.013 0.000 ARG B 784 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 940) hydrogen bonds : angle 4.72560 ( 2688) covalent geometry : bond 0.00305 (18056) covalent geometry : angle 0.77366 (24512) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 409 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.9461 (ttp-170) cc_final: 0.8818 (ttm-80) REVERT: A 124 MET cc_start: 0.9714 (mmm) cc_final: 0.9177 (tpp) REVERT: A 541 ARG cc_start: 0.9188 (tpp80) cc_final: 0.8545 (ttp80) REVERT: A 542 TYR cc_start: 0.9013 (m-80) cc_final: 0.8567 (m-80) REVERT: A 551 PHE cc_start: 0.9635 (t80) cc_final: 0.9381 (t80) REVERT: A 638 LYS cc_start: 0.9747 (mttt) cc_final: 0.9394 (mmtm) REVERT: A 651 MET cc_start: 0.9658 (mmp) cc_final: 0.9434 (mmm) REVERT: A 668 SER cc_start: 0.9489 (t) cc_final: 0.9248 (p) REVERT: A 677 MET cc_start: 0.9831 (tpp) cc_final: 0.9326 (tpp) REVERT: A 681 ARG cc_start: 0.9444 (mtt180) cc_final: 0.9183 (ttm110) REVERT: A 691 ASN cc_start: 0.9752 (m-40) cc_final: 0.9328 (t0) REVERT: A 729 CYS cc_start: 0.9290 (m) cc_final: 0.8717 (m) REVERT: A 748 LYS cc_start: 0.9852 (mttt) cc_final: 0.9590 (ttpp) REVERT: A 756 MET cc_start: 0.9481 (tpp) cc_final: 0.9091 (mmm) REVERT: A 768 THR cc_start: 0.8677 (p) cc_final: 0.8166 (t) REVERT: B 4 ARG cc_start: 0.9437 (ttp-170) cc_final: 0.8809 (ttm-80) REVERT: B 60 MET cc_start: 0.9308 (mmp) cc_final: 0.9052 (mmm) REVERT: B 542 TYR cc_start: 0.9073 (m-80) cc_final: 0.8639 (m-80) REVERT: B 574 MET cc_start: 0.8616 (ppp) cc_final: 0.8345 (mmt) REVERT: B 638 LYS cc_start: 0.9720 (mttt) cc_final: 0.9357 (mmtm) REVERT: B 677 MET cc_start: 0.9758 (tpp) cc_final: 0.9424 (mmm) REVERT: B 691 ASN cc_start: 0.9736 (m-40) cc_final: 0.9268 (t0) REVERT: B 729 CYS cc_start: 0.9266 (m) cc_final: 0.8664 (m) REVERT: B 748 LYS cc_start: 0.9853 (mttt) cc_final: 0.9602 (ttpp) REVERT: B 756 MET cc_start: 0.8830 (mmm) cc_final: 0.8402 (mmm) REVERT: B 768 THR cc_start: 0.8665 (p) cc_final: 0.8153 (t) REVERT: B 799 LEU cc_start: 0.9626 (mm) cc_final: 0.9374 (mm) REVERT: B 840 GLU cc_start: 0.9482 (mt-10) cc_final: 0.9255 (mt-10) REVERT: C 4 ARG cc_start: 0.9488 (ttp-170) cc_final: 0.8957 (ttm-80) REVERT: C 31 ILE cc_start: 0.9817 (pt) cc_final: 0.9563 (tp) REVERT: C 60 MET cc_start: 0.9313 (mmp) cc_final: 0.9003 (mmm) REVERT: C 542 TYR cc_start: 0.9126 (m-80) cc_final: 0.8736 (m-80) REVERT: C 574 MET cc_start: 0.8686 (ppp) cc_final: 0.8385 (mmt) REVERT: C 638 LYS cc_start: 0.9787 (mttt) cc_final: 0.9442 (mmtm) REVERT: C 677 MET cc_start: 0.9750 (tpp) cc_final: 0.9435 (tpp) REVERT: C 681 ARG cc_start: 0.9571 (mmm-85) cc_final: 0.8842 (mmm160) REVERT: C 691 ASN cc_start: 0.9703 (m-40) cc_final: 0.9251 (t0) REVERT: C 748 LYS cc_start: 0.9846 (mttt) cc_final: 0.9594 (ttpp) REVERT: C 756 MET cc_start: 0.8962 (mmm) cc_final: 0.8708 (mmm) REVERT: C 758 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8468 (m-80) REVERT: C 768 THR cc_start: 0.8606 (p) cc_final: 0.8089 (t) REVERT: D 4 ARG cc_start: 0.9446 (ttp-170) cc_final: 0.8905 (ttt90) REVERT: D 60 MET cc_start: 0.9313 (mmp) cc_final: 0.8973 (mmm) REVERT: D 538 LYS cc_start: 0.9664 (mmtt) cc_final: 0.9251 (mppt) REVERT: D 542 TYR cc_start: 0.9100 (m-80) cc_final: 0.8735 (m-80) REVERT: D 638 LYS cc_start: 0.9779 (mttt) cc_final: 0.9431 (mmtm) REVERT: D 651 MET cc_start: 0.9624 (mmp) cc_final: 0.9312 (mmm) REVERT: D 668 SER cc_start: 0.9486 (t) cc_final: 0.9249 (p) REVERT: D 681 ARG cc_start: 0.9312 (mmm160) cc_final: 0.8820 (mmm160) REVERT: D 691 ASN cc_start: 0.9738 (m-40) cc_final: 0.9336 (t0) REVERT: D 729 CYS cc_start: 0.9289 (m) cc_final: 0.8578 (m) REVERT: D 733 ASN cc_start: 0.9155 (m-40) cc_final: 0.8721 (t0) REVERT: D 748 LYS cc_start: 0.9846 (mttt) cc_final: 0.9587 (ttpp) REVERT: D 756 MET cc_start: 0.9466 (tpp) cc_final: 0.9142 (mmm) outliers start: 48 outliers final: 40 residues processed: 429 average time/residue: 0.2661 time to fit residues: 177.0754 Evaluate side-chains 436 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 395 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 693 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 126 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 49 optimal weight: 40.0000 chunk 135 optimal weight: 8.9990 chunk 5 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.062286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.047150 restraints weight = 86566.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.048905 restraints weight = 46752.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.050151 restraints weight = 30849.336| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18056 Z= 0.151 Angle : 0.796 12.302 24512 Z= 0.381 Chirality : 0.047 0.358 2792 Planarity : 0.004 0.032 3080 Dihedral : 4.292 20.784 2428 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.95 % Rotamer: Outliers : 2.43 % Allowed : 25.05 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2192 helix: 0.34 (0.15), residues: 1224 sheet: 0.21 (0.39), residues: 188 loop : -0.50 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 705 HIS 0.006 0.001 HIS A 762 PHE 0.018 0.001 PHE A 557 TYR 0.016 0.001 TYR D 616 ARG 0.010 0.000 ARG B 784 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 940) hydrogen bonds : angle 4.78948 ( 2688) covalent geometry : bond 0.00330 (18056) covalent geometry : angle 0.79620 (24512) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4384 Ramachandran restraints generated. 2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 401 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.9476 (ttp-170) cc_final: 0.8703 (ttt180) REVERT: A 124 MET cc_start: 0.9676 (mmm) cc_final: 0.9161 (tpp) REVERT: A 538 LYS cc_start: 0.9660 (mmtt) cc_final: 0.9185 (mppt) REVERT: A 541 ARG cc_start: 0.9185 (tpp80) cc_final: 0.8543 (ttp80) REVERT: A 542 TYR cc_start: 0.9012 (m-80) cc_final: 0.8515 (m-80) REVERT: A 551 PHE cc_start: 0.9626 (t80) cc_final: 0.9374 (t80) REVERT: A 574 MET cc_start: 0.8522 (ppp) cc_final: 0.8287 (mmt) REVERT: A 638 LYS cc_start: 0.9735 (mttt) cc_final: 0.9381 (mmtm) REVERT: A 651 MET cc_start: 0.9674 (mmp) cc_final: 0.9445 (mmm) REVERT: A 668 SER cc_start: 0.9488 (t) cc_final: 0.9253 (p) REVERT: A 677 MET cc_start: 0.9834 (tpp) cc_final: 0.9327 (tpp) REVERT: A 681 ARG cc_start: 0.9443 (mtt180) cc_final: 0.9175 (ttm110) REVERT: A 691 ASN cc_start: 0.9765 (m-40) cc_final: 0.9334 (t0) REVERT: A 729 CYS cc_start: 0.9373 (m) cc_final: 0.8891 (m) REVERT: A 748 LYS cc_start: 0.9856 (mttt) cc_final: 0.9624 (ttpp) REVERT: A 756 MET cc_start: 0.9515 (tpp) cc_final: 0.9111 (mmm) REVERT: A 768 THR cc_start: 0.8698 (p) cc_final: 0.8187 (t) REVERT: B 4 ARG cc_start: 0.9448 (ttp-170) cc_final: 0.8997 (ptm160) REVERT: B 60 MET cc_start: 0.9258 (mmp) cc_final: 0.9011 (mmm) REVERT: B 542 TYR cc_start: 0.9069 (m-80) cc_final: 0.8628 (m-80) REVERT: B 574 MET cc_start: 0.8653 (ppp) cc_final: 0.8364 (mmt) REVERT: B 638 LYS cc_start: 0.9728 (mttt) cc_final: 0.9368 (mmtm) REVERT: B 677 MET cc_start: 0.9676 (tpp) cc_final: 0.9433 (mmm) REVERT: B 691 ASN cc_start: 0.9745 (m-40) cc_final: 0.9275 (t0) REVERT: B 695 GLN cc_start: 0.9663 (mt0) cc_final: 0.9315 (pt0) REVERT: B 729 CYS cc_start: 0.9292 (m) cc_final: 0.8696 (m) REVERT: B 748 LYS cc_start: 0.9855 (mttt) cc_final: 0.9614 (ttpp) REVERT: B 756 MET cc_start: 0.8847 (mmm) cc_final: 0.8404 (mmm) REVERT: B 768 THR cc_start: 0.8712 (p) cc_final: 0.8204 (t) REVERT: B 799 LEU cc_start: 0.9647 (mm) cc_final: 0.9405 (mm) REVERT: B 840 GLU cc_start: 0.9494 (mt-10) cc_final: 0.9277 (mt-10) REVERT: C 4 ARG cc_start: 0.9461 (ttp-170) cc_final: 0.8745 (ttm-80) REVERT: C 60 MET cc_start: 0.9284 (mmp) cc_final: 0.8975 (mmm) REVERT: C 124 MET cc_start: 0.9646 (mmm) cc_final: 0.9207 (tpp) REVERT: C 542 TYR cc_start: 0.9112 (m-80) cc_final: 0.8733 (m-80) REVERT: C 574 MET cc_start: 0.8720 (ppp) cc_final: 0.8393 (mmt) REVERT: C 638 LYS cc_start: 0.9796 (mttt) cc_final: 0.9407 (mmtm) REVERT: C 677 MET cc_start: 0.9746 (tpp) cc_final: 0.9228 (tpp) REVERT: C 681 ARG cc_start: 0.9580 (mmm-85) cc_final: 0.9338 (mpp80) REVERT: C 691 ASN cc_start: 0.9713 (m-40) cc_final: 0.9254 (t0) REVERT: C 748 LYS cc_start: 0.9847 (mttt) cc_final: 0.9597 (ttpp) REVERT: C 756 MET cc_start: 0.9019 (mmm) cc_final: 0.8798 (mmm) REVERT: C 758 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8792 (m-80) REVERT: C 768 THR cc_start: 0.8683 (p) cc_final: 0.8429 (p) REVERT: D 4 ARG cc_start: 0.9436 (ttp-170) cc_final: 0.8896 (ttt90) REVERT: D 60 MET cc_start: 0.9291 (mmp) cc_final: 0.8929 (mmm) REVERT: D 538 LYS cc_start: 0.9659 (mmtt) cc_final: 0.9243 (mppt) REVERT: D 542 TYR cc_start: 0.9098 (m-80) cc_final: 0.8759 (m-80) REVERT: D 638 LYS cc_start: 0.9779 (mttt) cc_final: 0.9429 (mmtm) REVERT: D 651 MET cc_start: 0.9645 (mmp) cc_final: 0.9339 (mmm) REVERT: D 668 SER cc_start: 0.9489 (t) cc_final: 0.9260 (p) REVERT: D 681 ARG cc_start: 0.9332 (mmm160) cc_final: 0.8796 (mmm160) REVERT: D 691 ASN cc_start: 0.9738 (m-40) cc_final: 0.9344 (t0) REVERT: D 729 CYS cc_start: 0.9296 (m) cc_final: 0.8608 (m) REVERT: D 733 ASN cc_start: 0.9152 (m-40) cc_final: 0.8735 (t0) REVERT: D 748 LYS cc_start: 0.9850 (mttt) cc_final: 0.9598 (ttpp) REVERT: D 756 MET cc_start: 0.9480 (tpp) cc_final: 0.9139 (mmm) outliers start: 45 outliers final: 40 residues processed: 420 average time/residue: 0.2610 time to fit residues: 170.5624 Evaluate side-chains 433 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 392 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 693 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 1 optimal weight: 7.9990 chunk 220 optimal weight: 20.0000 chunk 159 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 100 optimal weight: 20.0000 chunk 52 optimal weight: 50.0000 chunk 127 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN B 702 GLN D 702 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.060785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.045589 restraints weight = 85810.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.047339 restraints weight = 46203.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.048558 restraints weight = 30653.317| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.6839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18056 Z= 0.143 Angle : 0.804 13.209 24512 Z= 0.384 Chirality : 0.048 0.437 2792 Planarity : 0.004 0.083 3080 Dihedral : 4.311 22.607 2428 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.21 % Allowed : 25.38 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.18), residues: 2192 helix: 0.33 (0.15), residues: 1224 sheet: 0.62 (0.36), residues: 224 loop : -0.62 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 705 HIS 0.006 0.001 HIS C 762 PHE 0.021 0.001 PHE B 551 TYR 0.016 0.001 TYR D 616 ARG 0.010 0.000 ARG B 784 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 940) hydrogen bonds : angle 4.82215 ( 2688) covalent geometry : bond 0.00314 (18056) covalent geometry : angle 0.80435 (24512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10720.75 seconds wall clock time: 186 minutes 14.15 seconds (11174.15 seconds total)