Starting phenix.real_space_refine on Thu Sep 18 13:57:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5va1_8650/09_2025/5va1_8650.cif Found real_map, /net/cci-nas-00/data/ceres_data/5va1_8650/09_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_8650/09_2025/5va1_8650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5va1_8650/09_2025/5va1_8650.map" model { file = "/net/cci-nas-00/data/ceres_data/5va1_8650/09_2025/5va1_8650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5va1_8650/09_2025/5va1_8650.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ASP:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 63 Restraints were copied for chains: B, C, D Time building chain proxies: 4.02, per 1000 atoms: 0.23 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: 1.48 Conformation dependent library (CDL) restraints added in 819.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.54 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: 2.96 Time building geometry restraints manager: 2.01 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.940 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.530 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.430 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 863 TYR 0.011 0.001 TYR D 652 PHE 0.011 0.001 PHE D 68 TRP 0.008 0.001 TRP A 585 HIS 0.004 0.001 HIS A 674 Details of bonding type rmsd covalent geometry : bond 0.00764 (18056) covalent geometry : angle 1.02037 (24512) hydrogen bonds : bond 0.30233 ( 940) hydrogen bonds : angle 9.26482 ( 2688) *********************** 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 : 0.709 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: 0.1348 time to fit residues: 146.8960 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 : 0.721 ------------------------------------------------------------------------------- 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 216 optimal weight: 40.0000 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.068473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.051544 restraints weight = 77962.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.053311 restraints weight = 44317.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.054574 restraints weight = 30386.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.055481 restraints weight = 23063.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.056121 restraints weight = 18789.068| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18056 Z= 0.171 Angle : 0.718 10.702 24512 Z= 0.354 Chirality : 0.045 0.173 2792 Planarity : 0.005 0.044 3080 Dihedral : 4.817 29.572 2440 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.05 % Allowed : 14.69 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.16), residues: 2192 helix: -0.15 (0.14), residues: 1216 sheet: -1.69 (0.35), residues: 168 loop : -1.56 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 734 TYR 0.017 0.001 TYR B 545 PHE 0.024 0.002 PHE A 557 TRP 0.010 0.001 TRP C 497 HIS 0.007 0.001 HIS C 831 Details of bonding type rmsd covalent geometry : bond 0.00357 (18056) covalent geometry : angle 0.71849 (24512) hydrogen bonds : bond 0.05123 ( 940) hydrogen bonds : angle 5.17407 ( 2688) *********************** 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 567 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 529 time to evaluate : 0.699 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: 0.9459 (ttp-170) cc_final: 0.8983 (ttt90) REVERT: A 124 MET cc_start: 0.9682 (mmm) cc_final: 0.9052 (tpp) REVERT: A 466 ASP cc_start: 0.9627 (t0) cc_final: 0.9210 (t0) REVERT: A 470 ASN cc_start: 0.9313 (m-40) cc_final: 0.8816 (m-40) REVERT: A 542 TYR cc_start: 0.8857 (m-80) cc_final: 0.8447 (m-80) REVERT: A 651 MET cc_start: 0.9556 (mmp) cc_final: 0.9217 (mmp) REVERT: A 677 MET cc_start: 0.9890 (tpp) cc_final: 0.9421 (tpp) REVERT: A 682 GLU cc_start: 0.9667 (mt-10) cc_final: 0.9452 (pt0) REVERT: A 691 ASN cc_start: 0.9768 (m-40) cc_final: 0.9468 (p0) REVERT: A 705 TRP cc_start: 0.9444 (t60) cc_final: 0.9192 (t60) REVERT: A 712 ASP cc_start: 0.9645 (t0) cc_final: 0.9421 (t0) REVERT: A 723 CYS cc_start: 0.9157 (m) cc_final: 0.8937 (p) REVERT: A 729 CYS cc_start: 0.9305 (m) cc_final: 0.8763 (m) REVERT: A 748 LYS cc_start: 0.9862 (mttt) cc_final: 0.9605 (ttpp) REVERT: A 756 MET cc_start: 0.9120 (mmm) cc_final: 0.8699 (mmm) REVERT: A 821 ASP cc_start: 0.9092 (m-30) cc_final: 0.8879 (p0) REVERT: A 836 ASP cc_start: 0.9247 (OUTLIER) cc_final: 0.8807 (p0) REVERT: A 837 ASP cc_start: 0.9433 (m-30) cc_final: 0.9073 (m-30) REVERT: B 4 ARG cc_start: 0.9439 (ttp-170) cc_final: 0.8968 (ttt90) REVERT: B 462 MET cc_start: 0.9691 (mmp) cc_final: 0.9456 (mmp) REVERT: B 466 ASP cc_start: 0.9670 (t0) cc_final: 0.9384 (t0) REVERT: B 542 TYR cc_start: 0.8865 (m-80) cc_final: 0.8459 (m-80) REVERT: B 651 MET cc_start: 0.9605 (mmp) cc_final: 0.9315 (mmp) REVERT: B 677 MET cc_start: 0.9880 (tpp) cc_final: 0.9319 (tpp) REVERT: B 681 ARG cc_start: 0.9493 (mtt180) cc_final: 0.9273 (ptp-110) REVERT: B 682 GLU cc_start: 0.9677 (mt-10) cc_final: 0.9441 (pt0) REVERT: B 691 ASN cc_start: 0.9749 (m-40) cc_final: 0.9446 (p0) REVERT: B 712 ASP cc_start: 0.9605 (t0) cc_final: 0.9400 (t0) REVERT: B 723 CYS cc_start: 0.9088 (m) cc_final: 0.8819 (p) REVERT: B 729 CYS cc_start: 0.9457 (m) cc_final: 0.8917 (m) REVERT: B 748 LYS cc_start: 0.9872 (mttt) cc_final: 0.9639 (ttpp) REVERT: B 756 MET cc_start: 0.9111 (mmm) cc_final: 0.8670 (mmm) REVERT: B 857 GLU cc_start: 0.9227 (mt-10) cc_final: 0.9010 (mm-30) REVERT: C 4 ARG cc_start: 0.9442 (ttp-170) cc_final: 0.9049 (ttm-80) REVERT: C 31 ILE cc_start: 0.9699 (pt) cc_final: 0.9451 (tp) REVERT: C 462 MET cc_start: 0.9689 (mmp) cc_final: 0.9461 (mmp) REVERT: C 466 ASP cc_start: 0.9646 (t0) cc_final: 0.9218 (t0) REVERT: C 470 ASN cc_start: 0.9317 (m-40) cc_final: 0.8837 (m110) REVERT: C 500 ILE cc_start: 0.9087 (mm) cc_final: 0.8844 (pt) REVERT: C 542 TYR cc_start: 0.8919 (m-80) cc_final: 0.8441 (m-80) REVERT: C 651 MET cc_start: 0.9624 (mmp) cc_final: 0.9258 (mmp) REVERT: C 677 MET cc_start: 0.9880 (tpp) cc_final: 0.9286 (tpp) REVERT: C 681 ARG cc_start: 0.9499 (mtt180) cc_final: 0.9266 (ptp-110) REVERT: C 682 GLU cc_start: 0.9663 (mt-10) cc_final: 0.9409 (pt0) REVERT: C 691 ASN cc_start: 0.9750 (m-40) cc_final: 0.9453 (p0) REVERT: C 697 LEU cc_start: 0.9924 (mt) cc_final: 0.9665 (pp) REVERT: C 712 ASP cc_start: 0.9638 (t0) cc_final: 0.9405 (t0) REVERT: C 729 CYS cc_start: 0.9478 (m) cc_final: 0.8951 (m) REVERT: C 748 LYS cc_start: 0.9860 (mttt) cc_final: 0.9630 (ttpp) REVERT: C 756 MET cc_start: 0.9158 (mmm) cc_final: 0.8774 (mmm) REVERT: C 844 MET cc_start: 0.9137 (mmm) cc_final: 0.8922 (mmm) REVERT: D 4 ARG cc_start: 0.9464 (ttp-170) cc_final: 0.8893 (ttt90) REVERT: D 60 MET cc_start: 0.9148 (mmp) cc_final: 0.8937 (mmm) REVERT: D 466 ASP cc_start: 0.9608 (t0) cc_final: 0.9174 (t0) REVERT: D 470 ASN cc_start: 0.9318 (m-40) cc_final: 0.8843 (m110) REVERT: D 500 ILE cc_start: 0.9023 (mm) cc_final: 0.8780 (pt) REVERT: D 542 TYR cc_start: 0.8945 (m-80) cc_final: 0.8517 (m-80) REVERT: D 651 MET cc_start: 0.9558 (mmp) cc_final: 0.9344 (mmp) REVERT: D 677 MET cc_start: 0.9872 (tpp) cc_final: 0.9308 (tpp) REVERT: D 682 GLU cc_start: 0.9661 (mt-10) cc_final: 0.9446 (pt0) REVERT: D 691 ASN cc_start: 0.9755 (m-40) cc_final: 0.9357 (t0) REVERT: D 702 GLN cc_start: 0.9668 (mt0) cc_final: 0.9467 (mp10) REVERT: D 712 ASP cc_start: 0.9641 (t0) cc_final: 0.9401 (t0) REVERT: D 714 ASN cc_start: 0.9660 (m-40) cc_final: 0.9457 (p0) REVERT: D 727 ASP cc_start: 0.9393 (m-30) cc_final: 0.9156 (m-30) REVERT: D 729 CYS cc_start: 0.9391 (m) cc_final: 0.8825 (m) REVERT: D 748 LYS cc_start: 0.9856 (mttt) cc_final: 0.9629 (tttm) REVERT: D 756 MET cc_start: 0.9184 (mmm) cc_final: 0.8779 (mmm) REVERT: D 836 ASP cc_start: 0.9205 (p0) cc_final: 0.8669 (p0) REVERT: D 837 ASP cc_start: 0.9385 (m-30) cc_final: 0.9128 (m-30) outliers start: 38 outliers final: 21 residues processed: 541 average time/residue: 0.1320 time to fit residues: 109.3225 Evaluate side-chains 461 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 439 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 134 optimal weight: 30.0000 chunk 6 optimal weight: 40.0000 chunk 165 optimal weight: 20.0000 chunk 194 optimal weight: 30.0000 chunk 102 optimal weight: 50.0000 chunk 96 optimal weight: 10.0000 chunk 36 optimal weight: 50.0000 chunk 161 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 63 optimal weight: 50.0000 overall best weight: 17.5998 ------------------------------------------------------------------------------- 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 ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN B 592 GLN C 33 ASN D 33 ASN D 61 GLN D 592 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.062794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.047679 restraints weight = 89755.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.049361 restraints weight = 48117.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.050543 restraints weight = 31801.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.051356 restraints weight = 23711.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.051936 restraints weight = 19165.203| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 18056 Z= 0.282 Angle : 0.747 11.453 24512 Z= 0.389 Chirality : 0.045 0.148 2792 Planarity : 0.005 0.045 3080 Dihedral : 4.751 20.747 2428 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.40 % Allowed : 17.33 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.17), residues: 2192 helix: 0.31 (0.14), residues: 1224 sheet: -1.09 (0.37), residues: 160 loop : -1.09 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 734 TYR 0.018 0.002 TYR D 43 PHE 0.025 0.002 PHE A 557 TRP 0.024 0.002 TRP B 705 HIS 0.008 0.002 HIS D 771 Details of bonding type rmsd covalent geometry : bond 0.00552 (18056) covalent geometry : angle 0.74674 (24512) hydrogen bonds : bond 0.04800 ( 940) hydrogen bonds : angle 5.22426 ( 2688) *********************** 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 507 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 444 time to evaluate : 0.763 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: 0.9454 (ttp-170) cc_final: 0.8936 (ttt180) REVERT: A 42 ILE cc_start: 0.9772 (pt) cc_final: 0.9411 (mt) REVERT: A 462 MET cc_start: 0.9716 (mmm) cc_final: 0.9472 (mmm) REVERT: A 466 ASP cc_start: 0.9592 (t0) cc_final: 0.9090 (t0) REVERT: A 470 ASN cc_start: 0.9120 (m-40) cc_final: 0.8619 (m110) REVERT: A 542 TYR cc_start: 0.9045 (m-80) cc_final: 0.8516 (m-80) REVERT: A 651 MET cc_start: 0.9631 (mmp) cc_final: 0.9320 (mmp) REVERT: A 677 MET cc_start: 0.9793 (tpp) cc_final: 0.9022 (tpp) REVERT: A 681 ARG cc_start: 0.9215 (mtm110) cc_final: 0.8992 (ptp90) REVERT: A 682 GLU cc_start: 0.9684 (mt-10) cc_final: 0.9484 (pt0) REVERT: A 691 ASN cc_start: 0.9752 (m-40) cc_final: 0.9493 (p0) REVERT: A 705 TRP cc_start: 0.9464 (t60) cc_final: 0.9105 (t60) REVERT: A 729 CYS cc_start: 0.9266 (m) cc_final: 0.8679 (m) REVERT: A 748 LYS cc_start: 0.9850 (mttt) cc_final: 0.9640 (ttpp) REVERT: A 756 MET cc_start: 0.8973 (mmm) cc_final: 0.8517 (mmm) REVERT: B 4 ARG cc_start: 0.9445 (ttp-170) cc_final: 0.8947 (ttt180) REVERT: B 462 MET cc_start: 0.9749 (mmp) cc_final: 0.9506 (mmp) REVERT: B 542 TYR cc_start: 0.8986 (m-80) cc_final: 0.8555 (m-80) REVERT: B 651 MET cc_start: 0.9609 (mmp) cc_final: 0.9359 (mmp) REVERT: B 677 MET cc_start: 0.9707 (tpp) cc_final: 0.9411 (tpp) REVERT: B 691 ASN cc_start: 0.9747 (m-40) cc_final: 0.9450 (p0) REVERT: B 756 MET cc_start: 0.8961 (mmm) cc_final: 0.8683 (mmm) REVERT: B 840 GLU cc_start: 0.9521 (mt-10) cc_final: 0.9297 (mt-10) REVERT: C 4 ARG cc_start: 0.9459 (ttp-170) cc_final: 0.9011 (ttm-80) REVERT: C 124 MET cc_start: 0.9618 (mmm) cc_final: 0.9112 (tpp) REVERT: C 462 MET cc_start: 0.9675 (mmp) cc_final: 0.9417 (mmp) REVERT: C 500 ILE cc_start: 0.9223 (mm) cc_final: 0.9018 (pt) REVERT: C 542 TYR cc_start: 0.9048 (m-80) cc_final: 0.8661 (m-80) REVERT: C 638 LYS cc_start: 0.9819 (mttt) cc_final: 0.9557 (mttm) REVERT: C 651 MET cc_start: 0.9634 (mmp) cc_final: 0.9405 (mmp) REVERT: C 677 MET cc_start: 0.9699 (tpp) cc_final: 0.9395 (tpp) REVERT: C 691 ASN cc_start: 0.9743 (m-40) cc_final: 0.9333 (t0) REVERT: C 756 MET cc_start: 0.8948 (mmm) cc_final: 0.8683 (mmm) REVERT: D 4 ARG cc_start: 0.9445 (ttp-170) cc_final: 0.8910 (ttt180) REVERT: D 466 ASP cc_start: 0.9548 (t0) cc_final: 0.9035 (t0) REVERT: D 470 ASN cc_start: 0.9125 (m-40) cc_final: 0.8614 (m110) REVERT: D 542 TYR cc_start: 0.9053 (m-80) cc_final: 0.8643 (m-80) REVERT: D 651 MET cc_start: 0.9635 (mmp) cc_final: 0.9396 (mmp) REVERT: D 664 GLN cc_start: 0.9755 (mt0) cc_final: 0.9497 (mm-40) REVERT: D 677 MET cc_start: 0.9779 (tpp) cc_final: 0.8953 (tpp) REVERT: D 691 ASN cc_start: 0.9763 (m-40) cc_final: 0.9374 (t0) REVERT: D 697 LEU cc_start: 0.9927 (mt) cc_final: 0.9589 (pp) REVERT: D 702 GLN cc_start: 0.9644 (mt0) cc_final: 0.9385 (mm-40) REVERT: D 714 ASN cc_start: 0.9761 (m-40) cc_final: 0.9553 (p0) REVERT: D 729 CYS cc_start: 0.9325 (m) cc_final: 0.8808 (m) REVERT: D 748 LYS cc_start: 0.9845 (mttt) cc_final: 0.9642 (ttpp) REVERT: D 756 MET cc_start: 0.8976 (mmm) cc_final: 0.8528 (mmm) outliers start: 63 outliers final: 46 residues processed: 475 average time/residue: 0.1243 time to fit residues: 92.9675 Evaluate side-chains 435 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 389 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 ILE 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 591 ASP Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 822 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 550 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 591 ASP 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 413 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 591 ASP Chi-restraints excluded: chain C residue 622 LEU 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 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 591 ASP Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 693 LEU 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 184 optimal weight: 0.0010 chunk 46 optimal weight: 30.0000 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 50.0000 chunk 37 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 overall best weight: 4.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 33 ASN B 592 GLN ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 470 ASN ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.060165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.044694 restraints weight = 85895.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.046489 restraints weight = 45713.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.047743 restraints weight = 30112.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.048651 restraints weight = 22225.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.049292 restraints weight = 17756.157| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18056 Z= 0.127 Angle : 0.684 12.593 24512 Z= 0.336 Chirality : 0.044 0.159 2792 Planarity : 0.004 0.048 3080 Dihedral : 4.365 17.832 2428 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.59 % Allowed : 19.60 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.17), residues: 2192 helix: 0.57 (0.15), residues: 1204 sheet: -1.21 (0.35), residues: 168 loop : -1.09 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 679 TYR 0.014 0.001 TYR B 616 PHE 0.026 0.002 PHE D 640 TRP 0.010 0.001 TRP D 705 HIS 0.006 0.001 HIS C 703 Details of bonding type rmsd covalent geometry : bond 0.00275 (18056) covalent geometry : angle 0.68396 (24512) hydrogen bonds : bond 0.04084 ( 940) hydrogen bonds : angle 4.73725 ( 2688) *********************** 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 488 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 440 time to evaluate : 0.626 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: 0.9468 (ttp-170) cc_final: 0.8899 (ttt90) REVERT: A 31 ILE cc_start: 0.9713 (pt) cc_final: 0.9499 (tp) REVERT: A 60 MET cc_start: 0.9246 (mmp) cc_final: 0.8983 (mmm) REVERT: A 542 TYR cc_start: 0.8981 (m-80) cc_final: 0.8488 (m-80) REVERT: A 651 MET cc_start: 0.9616 (mmp) cc_final: 0.9395 (mmp) REVERT: A 677 MET cc_start: 0.9758 (tpp) cc_final: 0.9404 (tpp) REVERT: A 682 GLU cc_start: 0.9670 (mt-10) cc_final: 0.9459 (pt0) REVERT: A 691 ASN cc_start: 0.9748 (m-40) cc_final: 0.9319 (t0) REVERT: A 705 TRP cc_start: 0.9297 (t60) cc_final: 0.9093 (t60) REVERT: A 729 CYS cc_start: 0.9187 (m) cc_final: 0.8601 (m) REVERT: A 748 LYS cc_start: 0.9855 (mttt) cc_final: 0.9619 (ttpp) REVERT: A 756 MET cc_start: 0.8870 (mmm) cc_final: 0.8420 (mmm) REVERT: B 4 ARG cc_start: 0.9453 (ttp-170) cc_final: 0.8920 (ttm-80) REVERT: B 462 MET cc_start: 0.9731 (mmp) cc_final: 0.9336 (mmp) REVERT: B 542 TYR cc_start: 0.9007 (m-80) cc_final: 0.8595 (m-80) REVERT: B 651 MET cc_start: 0.9547 (mmp) cc_final: 0.9321 (mmp) REVERT: B 677 MET cc_start: 0.9702 (tpp) cc_final: 0.9280 (tpp) REVERT: B 691 ASN cc_start: 0.9739 (m-40) cc_final: 0.9300 (t0) REVERT: B 729 CYS cc_start: 0.9162 (m) cc_final: 0.8572 (m) REVERT: B 756 MET cc_start: 0.8850 (mmm) cc_final: 0.8428 (mmm) REVERT: B 840 GLU cc_start: 0.9496 (mt-10) cc_final: 0.9266 (mt-10) REVERT: C 4 ARG cc_start: 0.9447 (ttp-170) cc_final: 0.9055 (ttm-80) REVERT: C 60 MET cc_start: 0.9248 (mmp) cc_final: 0.8997 (mmm) REVERT: C 500 ILE cc_start: 0.9129 (mm) cc_final: 0.8923 (pt) REVERT: C 542 TYR cc_start: 0.9041 (m-80) cc_final: 0.8651 (m-80) REVERT: C 677 MET cc_start: 0.9686 (tpp) cc_final: 0.9250 (tpp) REVERT: C 691 ASN cc_start: 0.9729 (m-40) cc_final: 0.9303 (t0) REVERT: C 697 LEU cc_start: 0.9838 (mt) cc_final: 0.9554 (pp) REVERT: C 756 MET cc_start: 0.8878 (mmm) cc_final: 0.8633 (mmm) REVERT: D 4 ARG cc_start: 0.9440 (ttp-170) cc_final: 0.8915 (ttt180) REVERT: D 466 ASP cc_start: 0.9487 (t0) cc_final: 0.9284 (t0) REVERT: D 542 TYR cc_start: 0.9035 (m-80) cc_final: 0.8784 (m-80) REVERT: D 638 LYS cc_start: 0.9725 (mttt) cc_final: 0.9467 (mttm) REVERT: D 651 MET cc_start: 0.9598 (mmp) cc_final: 0.9370 (mmp) REVERT: D 677 MET cc_start: 0.9796 (tpp) cc_final: 0.8820 (tpp) REVERT: D 681 ARG cc_start: 0.9559 (ptp90) cc_final: 0.8983 (ptp90) REVERT: D 691 ASN cc_start: 0.9751 (m-40) cc_final: 0.9369 (t0) REVERT: D 714 ASN cc_start: 0.9790 (m-40) cc_final: 0.9499 (p0) REVERT: D 729 CYS cc_start: 0.9075 (m) cc_final: 0.8195 (m) REVERT: D 748 LYS cc_start: 0.9848 (mttt) cc_final: 0.9618 (ttpp) REVERT: D 756 MET cc_start: 0.8801 (mmm) cc_final: 0.8372 (mmm) REVERT: D 781 PHE cc_start: 0.9585 (m-10) cc_final: 0.9322 (m-10) outliers start: 48 outliers final: 30 residues processed: 473 average time/residue: 0.1251 time to fit residues: 92.5401 Evaluate side-chains 428 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 398 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 550 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 676 GLN 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 483 VAL 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 676 GLN 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 461 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 622 LEU 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 211 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 123 optimal weight: 50.0000 chunk 195 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 147 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.059405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.044347 restraints weight = 86818.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.046108 restraints weight = 45899.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.047355 restraints weight = 30094.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.048240 restraints weight = 22132.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048881 restraints weight = 17634.554| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18056 Z= 0.143 Angle : 0.685 11.094 24512 Z= 0.339 Chirality : 0.044 0.177 2792 Planarity : 0.004 0.032 3080 Dihedral : 4.294 18.474 2428 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.65 % Allowed : 20.36 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.18), residues: 2192 helix: 0.57 (0.15), residues: 1208 sheet: -0.84 (0.37), residues: 168 loop : -0.92 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 681 TYR 0.015 0.001 TYR D 616 PHE 0.019 0.002 PHE A 557 TRP 0.013 0.001 TRP C 410 HIS 0.006 0.001 HIS B 831 Details of bonding type rmsd covalent geometry : bond 0.00309 (18056) covalent geometry : angle 0.68498 (24512) hydrogen bonds : bond 0.03955 ( 940) hydrogen bonds : angle 4.75696 ( 2688) *********************** 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 473 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 424 time to evaluate : 0.601 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: A 4 ARG cc_start: 0.9473 (ttp-170) cc_final: 0.8897 (ttm-80) REVERT: A 60 MET cc_start: 0.9145 (mmp) cc_final: 0.8942 (mmm) REVERT: A 124 MET cc_start: 0.9712 (mmm) cc_final: 0.9194 (tpp) REVERT: A 538 LYS cc_start: 0.9667 (mmtt) cc_final: 0.9223 (mppt) REVERT: A 542 TYR cc_start: 0.9036 (m-80) cc_final: 0.8499 (m-80) REVERT: A 651 MET cc_start: 0.9597 (mmp) cc_final: 0.9371 (mmp) REVERT: A 677 MET cc_start: 0.9820 (tpp) cc_final: 0.9545 (tpp) REVERT: A 691 ASN cc_start: 0.9749 (m-40) cc_final: 0.9315 (t0) REVERT: A 699 GLU cc_start: 0.9558 (pt0) cc_final: 0.9346 (pp20) REVERT: A 705 TRP cc_start: 0.9299 (t60) cc_final: 0.9040 (t60) REVERT: A 729 CYS cc_start: 0.9077 (m) cc_final: 0.8470 (m) REVERT: A 748 LYS cc_start: 0.9854 (mttt) cc_final: 0.9621 (ttpp) REVERT: A 756 MET cc_start: 0.8828 (mmm) cc_final: 0.8381 (mmm) REVERT: A 780 TYR cc_start: 0.9578 (m-80) cc_final: 0.9271 (m-10) REVERT: B 4 ARG cc_start: 0.9476 (ttp-170) cc_final: 0.8880 (ttm-80) REVERT: B 542 TYR cc_start: 0.9043 (m-80) cc_final: 0.8640 (m-80) REVERT: B 677 MET cc_start: 0.9683 (tpp) cc_final: 0.9342 (tpp) REVERT: B 691 ASN cc_start: 0.9735 (m-40) cc_final: 0.9279 (t0) REVERT: B 729 CYS cc_start: 0.9209 (m) cc_final: 0.8627 (m) REVERT: B 756 MET cc_start: 0.8819 (mmm) cc_final: 0.8402 (mmm) REVERT: B 840 GLU cc_start: 0.9485 (mt-10) cc_final: 0.9278 (mt-10) REVERT: C 4 ARG cc_start: 0.9405 (ttp-170) cc_final: 0.9061 (ttm-80) REVERT: C 31 ILE cc_start: 0.9730 (pt) cc_final: 0.9479 (tp) REVERT: C 60 MET cc_start: 0.9287 (mmp) cc_final: 0.8988 (mmm) REVERT: C 462 MET cc_start: 0.9650 (tpt) cc_final: 0.9374 (tpt) REVERT: C 542 TYR cc_start: 0.9131 (m-80) cc_final: 0.8731 (m-80) REVERT: C 574 MET cc_start: 0.8515 (ppp) cc_final: 0.8285 (mmt) REVERT: C 651 MET cc_start: 0.9608 (mmp) cc_final: 0.9282 (mmp) REVERT: C 677 MET cc_start: 0.9659 (tpp) cc_final: 0.9294 (tpp) REVERT: C 681 ARG cc_start: 0.9356 (mtt180) cc_final: 0.9147 (mmm160) REVERT: C 691 ASN cc_start: 0.9731 (m-40) cc_final: 0.9306 (t0) REVERT: C 756 MET cc_start: 0.8872 (mmm) cc_final: 0.8647 (mmm) REVERT: D 4 ARG cc_start: 0.9431 (ttp-170) cc_final: 0.8923 (ttt180) REVERT: D 60 MET cc_start: 0.9308 (mmp) cc_final: 0.9045 (mmm) REVERT: D 466 ASP cc_start: 0.9550 (t0) cc_final: 0.9342 (t0) REVERT: D 542 TYR cc_start: 0.9116 (m-80) cc_final: 0.8805 (m-80) REVERT: D 574 MET cc_start: 0.8469 (ppp) cc_final: 0.8236 (mmt) REVERT: D 638 LYS cc_start: 0.9739 (mttt) cc_final: 0.9263 (mmtm) REVERT: D 651 MET cc_start: 0.9552 (mmp) cc_final: 0.9348 (mmp) REVERT: D 677 MET cc_start: 0.9722 (tpp) cc_final: 0.9311 (tpp) REVERT: D 691 ASN cc_start: 0.9747 (m-40) cc_final: 0.9373 (t0) REVERT: D 705 TRP cc_start: 0.9267 (t60) cc_final: 0.8896 (t60) REVERT: D 729 CYS cc_start: 0.9136 (m) cc_final: 0.8320 (m) REVERT: D 748 LYS cc_start: 0.9844 (mttt) cc_final: 0.9618 (ttpp) REVERT: D 756 MET cc_start: 0.8792 (mmm) cc_final: 0.8351 (mmm) REVERT: D 768 THR cc_start: 0.8705 (p) cc_final: 0.8447 (p) outliers start: 49 outliers final: 37 residues processed: 447 average time/residue: 0.1245 time to fit residues: 87.2268 Evaluate side-chains 437 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 400 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 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 822 VAL 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 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 676 GLN 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 468 LEU Chi-restraints excluded: chain C residue 483 VAL 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 676 GLN Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain D residue 413 LEU 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 550 LEU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 722 GLU 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 137 optimal weight: 20.0000 chunk 220 optimal weight: 40.0000 chunk 73 optimal weight: 6.9990 chunk 117 optimal weight: 30.0000 chunk 138 optimal weight: 9.9990 chunk 11 optimal weight: 50.0000 chunk 8 optimal weight: 50.0000 chunk 92 optimal weight: 20.0000 chunk 56 optimal weight: 70.0000 chunk 109 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 overall best weight: 11.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN B 33 ASN ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 470 ASN ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.065365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.050293 restraints weight = 86533.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.051959 restraints weight = 46466.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.053138 restraints weight = 30915.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.053985 restraints weight = 23152.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.054571 restraints weight = 18696.065| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18056 Z= 0.195 Angle : 0.715 9.008 24512 Z= 0.358 Chirality : 0.045 0.184 2792 Planarity : 0.004 0.031 3080 Dihedral : 4.407 17.940 2428 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.51 % Favored : 97.40 % Rotamer: Outliers : 3.08 % Allowed : 21.65 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.18), residues: 2192 helix: 0.56 (0.15), residues: 1208 sheet: 0.09 (0.37), residues: 204 loop : -0.80 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 784 TYR 0.016 0.002 TYR D 616 PHE 0.019 0.002 PHE A 557 TRP 0.013 0.001 TRP B 410 HIS 0.006 0.001 HIS B 831 Details of bonding type rmsd covalent geometry : bond 0.00399 (18056) covalent geometry : angle 0.71469 (24512) hydrogen bonds : bond 0.03976 ( 940) hydrogen bonds : angle 4.92753 ( 2688) *********************** 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 477 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 420 time to evaluate : 0.528 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: A 4 ARG cc_start: 0.9475 (ttp-170) cc_final: 0.8918 (ttm-80) REVERT: A 124 MET cc_start: 0.9633 (mmm) cc_final: 0.9152 (tpp) REVERT: A 538 LYS cc_start: 0.9666 (mmtt) cc_final: 0.9212 (mppt) REVERT: A 542 TYR cc_start: 0.9085 (m-80) cc_final: 0.8590 (m-80) REVERT: A 574 MET cc_start: 0.8538 (ppp) cc_final: 0.8272 (mmt) REVERT: A 651 MET cc_start: 0.9593 (mmp) cc_final: 0.9393 (mmp) REVERT: A 677 MET cc_start: 0.9794 (tpp) cc_final: 0.9480 (tpp) REVERT: A 691 ASN cc_start: 0.9753 (m-40) cc_final: 0.9310 (t0) REVERT: A 699 GLU cc_start: 0.9576 (pt0) cc_final: 0.9352 (pp20) REVERT: A 705 TRP cc_start: 0.9324 (t60) cc_final: 0.8981 (t60) REVERT: A 729 CYS cc_start: 0.9193 (m) cc_final: 0.8620 (m) REVERT: A 748 LYS cc_start: 0.9845 (mttt) cc_final: 0.9641 (ttpp) REVERT: A 756 MET cc_start: 0.8869 (mmm) cc_final: 0.8408 (mmm) REVERT: B 4 ARG cc_start: 0.9480 (ttp-170) cc_final: 0.8894 (ttm-80) REVERT: B 124 MET cc_start: 0.9704 (mmm) cc_final: 0.9498 (mmm) REVERT: B 538 LYS cc_start: 0.9651 (mmtt) cc_final: 0.9171 (mppt) REVERT: B 542 TYR cc_start: 0.9092 (m-80) cc_final: 0.8640 (m-80) REVERT: B 677 MET cc_start: 0.9700 (tpp) cc_final: 0.9318 (tpp) REVERT: B 691 ASN cc_start: 0.9736 (m-40) cc_final: 0.9279 (t0) REVERT: B 729 CYS cc_start: 0.9250 (m) cc_final: 0.8689 (m) REVERT: B 756 MET cc_start: 0.8840 (mmm) cc_final: 0.8409 (mmm) REVERT: B 840 GLU cc_start: 0.9529 (mt-10) cc_final: 0.9306 (mt-10) REVERT: C 4 ARG cc_start: 0.9444 (ttp-170) cc_final: 0.9017 (ttm-80) REVERT: C 60 MET cc_start: 0.9181 (mmp) cc_final: 0.8899 (mmm) REVERT: C 124 MET cc_start: 0.9654 (mmm) cc_final: 0.9126 (tpp) REVERT: C 462 MET cc_start: 0.9661 (tpt) cc_final: 0.9360 (tpt) REVERT: C 542 TYR cc_start: 0.9175 (m-80) cc_final: 0.8771 (m-80) REVERT: C 574 MET cc_start: 0.8586 (ppp) cc_final: 0.8316 (mmt) REVERT: C 638 LYS cc_start: 0.9761 (mttt) cc_final: 0.9380 (mttm) REVERT: C 651 MET cc_start: 0.9624 (mmp) cc_final: 0.9349 (mmp) REVERT: C 677 MET cc_start: 0.9652 (tpp) cc_final: 0.9353 (tpp) REVERT: C 691 ASN cc_start: 0.9737 (m-40) cc_final: 0.9302 (t0) REVERT: C 756 MET cc_start: 0.8958 (mmm) cc_final: 0.8699 (mmm) REVERT: D 4 ARG cc_start: 0.9430 (ttp-170) cc_final: 0.8926 (ttt180) REVERT: D 60 MET cc_start: 0.9332 (mmp) cc_final: 0.9007 (mmm) REVERT: D 542 TYR cc_start: 0.9140 (m-80) cc_final: 0.8851 (m-80) REVERT: D 574 MET cc_start: 0.8512 (ppp) cc_final: 0.8303 (mmt) REVERT: D 638 LYS cc_start: 0.9762 (mttt) cc_final: 0.9296 (mmtm) REVERT: D 677 MET cc_start: 0.9628 (tpp) cc_final: 0.9254 (tpp) REVERT: D 691 ASN cc_start: 0.9750 (m-40) cc_final: 0.9377 (t0) REVERT: D 695 GLN cc_start: 0.9785 (mt0) cc_final: 0.9382 (mm-40) REVERT: D 729 CYS cc_start: 0.9206 (m) cc_final: 0.8422 (m) REVERT: D 748 LYS cc_start: 0.9839 (mttt) cc_final: 0.9632 (ttpp) REVERT: D 756 MET cc_start: 0.8844 (mmm) cc_final: 0.8383 (mmm) outliers start: 57 outliers final: 47 residues processed: 446 average time/residue: 0.1139 time to fit residues: 79.3689 Evaluate side-chains 433 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 386 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 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 716 VAL Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 822 VAL 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 676 GLN Chi-restraints excluded: chain B residue 680 VAL 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 468 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 535 VAL 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 676 GLN Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 722 GLU 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 550 LEU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 722 GLU 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 20 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 40.0000 chunk 137 optimal weight: 0.0570 chunk 77 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 112 optimal weight: 60.0000 chunk 71 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 overall best weight: 3.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN A 592 GLN B 33 ASN B 592 GLN ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 592 GLN ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 592 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.060703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.045552 restraints weight = 86235.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.047338 restraints weight = 45940.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.048583 restraints weight = 30270.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.049489 restraints weight = 22356.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.050121 restraints weight = 17829.333| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18056 Z= 0.122 Angle : 0.739 11.388 24512 Z= 0.352 Chirality : 0.046 0.179 2792 Planarity : 0.004 0.050 3080 Dihedral : 4.244 16.090 2428 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.16 % Allowed : 23.65 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.18), residues: 2192 helix: 0.63 (0.15), residues: 1220 sheet: -0.20 (0.40), residues: 168 loop : -0.74 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 681 TYR 0.018 0.001 TYR D 707 PHE 0.024 0.001 PHE A 551 TRP 0.013 0.001 TRP C 585 HIS 0.005 0.001 HIS C 762 Details of bonding type rmsd covalent geometry : bond 0.00266 (18056) covalent geometry : angle 0.73907 (24512) hydrogen bonds : bond 0.03771 ( 940) hydrogen bonds : angle 4.72790 ( 2688) *********************** 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 453 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 413 time to evaluate : 0.735 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: A 4 ARG cc_start: 0.9461 (ttp-170) cc_final: 0.8845 (ttm-80) REVERT: A 124 MET cc_start: 0.9680 (mmm) cc_final: 0.9157 (tpp) REVERT: A 538 LYS cc_start: 0.9662 (mmtt) cc_final: 0.9219 (mppt) REVERT: A 541 ARG cc_start: 0.9211 (tpp80) cc_final: 0.8596 (ttp80) REVERT: A 542 TYR cc_start: 0.9040 (m-80) cc_final: 0.8521 (m-80) REVERT: A 574 MET cc_start: 0.8457 (ppp) cc_final: 0.8167 (mmt) REVERT: A 638 LYS cc_start: 0.9749 (mttt) cc_final: 0.9348 (mmtm) REVERT: A 677 MET cc_start: 0.9803 (tpp) cc_final: 0.9410 (tpp) REVERT: A 681 ARG cc_start: 0.9517 (ptp-110) cc_final: 0.9028 (mtm110) REVERT: A 691 ASN cc_start: 0.9750 (m-40) cc_final: 0.9312 (t0) REVERT: A 698 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9191 (pp20) REVERT: A 699 GLU cc_start: 0.9578 (pt0) cc_final: 0.9177 (pp20) REVERT: A 705 TRP cc_start: 0.9258 (t60) cc_final: 0.8940 (t60) REVERT: A 729 CYS cc_start: 0.9081 (m) cc_final: 0.8496 (m) REVERT: A 748 LYS cc_start: 0.9855 (mttt) cc_final: 0.9621 (ttpp) REVERT: A 756 MET cc_start: 0.8817 (mmm) cc_final: 0.8360 (mmm) REVERT: A 768 THR cc_start: 0.8702 (p) cc_final: 0.8198 (t) REVERT: A 832 LYS cc_start: 0.9662 (OUTLIER) cc_final: 0.9383 (mtpp) REVERT: B 4 ARG cc_start: 0.9480 (ttp-170) cc_final: 0.8805 (ttt90) REVERT: B 542 TYR cc_start: 0.9059 (m-80) cc_final: 0.8671 (m-80) REVERT: B 571 ILE cc_start: 0.9695 (mm) cc_final: 0.9486 (mm) REVERT: B 677 MET cc_start: 0.9721 (tpp) cc_final: 0.9293 (mmm) REVERT: B 691 ASN cc_start: 0.9738 (m-40) cc_final: 0.9262 (t0) REVERT: B 756 MET cc_start: 0.8790 (mmm) cc_final: 0.8544 (mmm) REVERT: B 768 THR cc_start: 0.8645 (p) cc_final: 0.8116 (t) REVERT: B 832 LYS cc_start: 0.9672 (OUTLIER) cc_final: 0.9371 (mtpp) REVERT: B 840 GLU cc_start: 0.9513 (mt-10) cc_final: 0.9282 (mt-10) REVERT: C 4 ARG cc_start: 0.9452 (ttp-170) cc_final: 0.9023 (ttm-80) REVERT: C 31 ILE cc_start: 0.9760 (pt) cc_final: 0.9556 (tp) REVERT: C 60 MET cc_start: 0.9195 (mmp) cc_final: 0.8918 (mmm) REVERT: C 462 MET cc_start: 0.9675 (tpt) cc_final: 0.9388 (tpt) REVERT: C 538 LYS cc_start: 0.9650 (mmtt) cc_final: 0.9229 (mppt) REVERT: C 542 TYR cc_start: 0.9131 (m-80) cc_final: 0.8752 (m-80) REVERT: C 574 MET cc_start: 0.8532 (ppp) cc_final: 0.8215 (mmt) REVERT: C 638 LYS cc_start: 0.9745 (mttt) cc_final: 0.9333 (mmtm) REVERT: C 651 MET cc_start: 0.9612 (mmp) cc_final: 0.9400 (mmp) REVERT: C 677 MET cc_start: 0.9656 (tpp) cc_final: 0.9431 (tpp) REVERT: C 681 ARG cc_start: 0.9567 (ttm110) cc_final: 0.9249 (mmm160) REVERT: C 691 ASN cc_start: 0.9732 (m-40) cc_final: 0.9308 (t0) REVERT: C 698 GLU cc_start: 0.9599 (mp0) cc_final: 0.9136 (mm-30) REVERT: C 756 MET cc_start: 0.8919 (mmm) cc_final: 0.8710 (mmm) REVERT: D 4 ARG cc_start: 0.9428 (ttp-170) cc_final: 0.8872 (ttm-80) REVERT: D 60 MET cc_start: 0.9319 (mmp) cc_final: 0.8932 (mmm) REVERT: D 538 LYS cc_start: 0.9653 (mmtt) cc_final: 0.9243 (mppt) REVERT: D 542 TYR cc_start: 0.9092 (m-80) cc_final: 0.8741 (m-80) REVERT: D 574 MET cc_start: 0.8480 (ppp) cc_final: 0.8225 (mmt) REVERT: D 638 LYS cc_start: 0.9741 (mttt) cc_final: 0.9329 (mmtm) REVERT: D 677 MET cc_start: 0.9584 (tpp) cc_final: 0.8818 (tpt) REVERT: D 681 ARG cc_start: 0.9342 (ptp90) cc_final: 0.8714 (ptp90) REVERT: D 691 ASN cc_start: 0.9745 (m-40) cc_final: 0.9361 (t0) REVERT: D 714 ASN cc_start: 0.9816 (m110) cc_final: 0.9468 (p0) REVERT: D 729 CYS cc_start: 0.9105 (m) cc_final: 0.8269 (m) REVERT: D 748 LYS cc_start: 0.9847 (mttt) cc_final: 0.9586 (ttpp) REVERT: D 756 MET cc_start: 0.8793 (mmm) cc_final: 0.8330 (mmm) REVERT: D 799 LEU cc_start: 0.9675 (mm) cc_final: 0.9445 (mm) outliers start: 40 outliers final: 34 residues processed: 432 average time/residue: 0.1257 time to fit residues: 82.9155 Evaluate side-chains 428 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 392 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 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 722 GLU Chi-restraints excluded: chain A residue 832 LYS 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 539 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 832 LYS Chi-restraints excluded: chain C residue 468 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 559 LEU Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 676 GLN 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 491 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 57 optimal weight: 20.0000 chunk 204 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 174 optimal weight: 0.0060 chunk 94 optimal weight: 10.0000 chunk 215 optimal weight: 30.0000 chunk 194 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 overall best weight: 5.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN B 573 ASN B 762 HIS ** C 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.059660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.044727 restraints weight = 86047.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.046462 restraints weight = 46225.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.047689 restraints weight = 30545.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.048556 restraints weight = 22585.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.049177 restraints weight = 18043.304| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.6677 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= 0.135 Angle : 0.751 10.835 24512 Z= 0.360 Chirality : 0.046 0.260 2792 Planarity : 0.004 0.047 3080 Dihedral : 4.237 17.004 2428 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.01 % Favored : 97.95 % Rotamer: Outliers : 2.48 % Allowed : 23.87 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.18), residues: 2192 helix: 0.65 (0.15), residues: 1216 sheet: -0.02 (0.38), residues: 208 loop : -0.56 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 681 TYR 0.016 0.001 TYR B 673 PHE 0.020 0.001 PHE D 640 TRP 0.030 0.002 TRP B 705 HIS 0.005 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00294 (18056) covalent geometry : angle 0.75112 (24512) hydrogen bonds : bond 0.03770 ( 940) hydrogen bonds : angle 4.78050 ( 2688) *********************** 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 449 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 403 time to evaluate : 0.702 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: A 4 ARG cc_start: 0.9472 (ttp-170) cc_final: 0.8839 (ttm-80) REVERT: A 124 MET cc_start: 0.9685 (mmm) cc_final: 0.9167 (tpp) REVERT: A 538 LYS cc_start: 0.9665 (mmtt) cc_final: 0.9220 (mppt) REVERT: A 541 ARG cc_start: 0.9198 (tpp80) cc_final: 0.8572 (ttp80) REVERT: A 542 TYR cc_start: 0.9062 (m-80) cc_final: 0.8551 (m-80) REVERT: A 574 MET cc_start: 0.8480 (ppp) cc_final: 0.8188 (mmt) REVERT: A 638 LYS cc_start: 0.9748 (mttt) cc_final: 0.9364 (mmtm) REVERT: A 677 MET cc_start: 0.9801 (tpp) cc_final: 0.9395 (tpp) REVERT: A 681 ARG cc_start: 0.9506 (ptp-110) cc_final: 0.9026 (mtm110) REVERT: A 691 ASN cc_start: 0.9752 (m-40) cc_final: 0.9305 (t0) REVERT: A 699 GLU cc_start: 0.9587 (pt0) cc_final: 0.9356 (pp20) REVERT: A 705 TRP cc_start: 0.9260 (t60) cc_final: 0.8932 (t60) REVERT: A 729 CYS cc_start: 0.9106 (m) cc_final: 0.8548 (m) REVERT: A 748 LYS cc_start: 0.9854 (mttt) cc_final: 0.9605 (ttpp) REVERT: A 756 MET cc_start: 0.8830 (mmm) cc_final: 0.8379 (mmm) REVERT: A 768 THR cc_start: 0.8743 (p) cc_final: 0.8249 (t) REVERT: A 832 LYS cc_start: 0.9636 (OUTLIER) cc_final: 0.9431 (ttpp) REVERT: B 4 ARG cc_start: 0.9470 (ttp-170) cc_final: 0.9046 (ptm160) REVERT: B 538 LYS cc_start: 0.9652 (mmtt) cc_final: 0.9211 (mppt) REVERT: B 542 TYR cc_start: 0.9083 (m-80) cc_final: 0.8636 (m-80) REVERT: B 574 MET cc_start: 0.8640 (ppp) cc_final: 0.8309 (mmt) REVERT: B 638 LYS cc_start: 0.9732 (mttt) cc_final: 0.9351 (mmtm) REVERT: B 691 ASN cc_start: 0.9735 (m-40) cc_final: 0.9258 (t0) REVERT: B 756 MET cc_start: 0.8807 (mmm) cc_final: 0.8564 (mmm) REVERT: B 768 THR cc_start: 0.8710 (p) cc_final: 0.8459 (p) REVERT: B 832 LYS cc_start: 0.9664 (OUTLIER) cc_final: 0.9361 (mtpp) REVERT: B 840 GLU cc_start: 0.9517 (mt-10) cc_final: 0.9291 (mt-10) REVERT: C 4 ARG cc_start: 0.9468 (ttp-170) cc_final: 0.8997 (ttm-80) REVERT: C 31 ILE cc_start: 0.9774 (pt) cc_final: 0.9531 (tp) REVERT: C 60 MET cc_start: 0.9250 (mmp) cc_final: 0.8919 (mmm) REVERT: C 462 MET cc_start: 0.9679 (tpt) cc_final: 0.9382 (tpt) REVERT: C 538 LYS cc_start: 0.9650 (mmtt) cc_final: 0.9201 (mppt) REVERT: C 542 TYR cc_start: 0.9163 (m-80) cc_final: 0.8705 (m-80) REVERT: C 574 MET cc_start: 0.8553 (ppp) cc_final: 0.8248 (mmt) REVERT: C 638 LYS cc_start: 0.9755 (mttt) cc_final: 0.9359 (mmtm) REVERT: C 677 MET cc_start: 0.9655 (tpp) cc_final: 0.9384 (tpp) REVERT: C 681 ARG cc_start: 0.9548 (ttm110) cc_final: 0.9229 (mmm160) REVERT: C 691 ASN cc_start: 0.9733 (m-40) cc_final: 0.9311 (t0) REVERT: C 698 GLU cc_start: 0.9601 (mp0) cc_final: 0.9192 (mm-30) REVERT: C 756 MET cc_start: 0.8994 (mmm) cc_final: 0.8781 (mmm) REVERT: C 832 LYS cc_start: 0.9633 (OUTLIER) cc_final: 0.9308 (mtpp) REVERT: D 4 ARG cc_start: 0.9422 (ttp-170) cc_final: 0.8913 (ttt90) REVERT: D 60 MET cc_start: 0.9317 (mmp) cc_final: 0.8929 (mmm) REVERT: D 538 LYS cc_start: 0.9655 (mmtt) cc_final: 0.9235 (mppt) REVERT: D 542 TYR cc_start: 0.9130 (m-80) cc_final: 0.8736 (m-80) REVERT: D 574 MET cc_start: 0.8511 (ppp) cc_final: 0.8253 (mmt) REVERT: D 638 LYS cc_start: 0.9745 (mttt) cc_final: 0.9365 (mmtm) REVERT: D 651 MET cc_start: 0.9573 (mmp) cc_final: 0.9360 (mmp) REVERT: D 677 MET cc_start: 0.9587 (tpp) cc_final: 0.8745 (tpt) REVERT: D 681 ARG cc_start: 0.9340 (ptp90) cc_final: 0.8759 (ptp90) REVERT: D 691 ASN cc_start: 0.9746 (m-40) cc_final: 0.9369 (t0) REVERT: D 729 CYS cc_start: 0.9183 (m) cc_final: 0.8421 (m) REVERT: D 733 ASN cc_start: 0.9189 (m-40) cc_final: 0.8752 (t0) REVERT: D 748 LYS cc_start: 0.9851 (mttt) cc_final: 0.9598 (ttpp) REVERT: D 756 MET cc_start: 0.8794 (mmm) cc_final: 0.8353 (mmm) outliers start: 46 outliers final: 38 residues processed: 422 average time/residue: 0.1270 time to fit residues: 82.8362 Evaluate side-chains 429 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 388 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 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 722 GLU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 832 LYS 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 539 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 832 LYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 832 LYS Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 491 VAL 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 634 THR Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 54 optimal weight: 4.9990 chunk 91 optimal weight: 40.0000 chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 50.0000 chunk 52 optimal weight: 50.0000 chunk 174 optimal weight: 40.0000 chunk 16 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 189 optimal weight: 0.0570 chunk 69 optimal weight: 0.1980 chunk 44 optimal weight: 20.0000 overall best weight: 3.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 ASN B 702 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.060705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.045468 restraints weight = 85486.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.047247 restraints weight = 46698.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.048496 restraints weight = 30935.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.049401 restraints weight = 22957.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.050041 restraints weight = 18345.756| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.6759 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= 0.122 Angle : 0.778 12.231 24512 Z= 0.367 Chirality : 0.047 0.263 2792 Planarity : 0.004 0.035 3080 Dihedral : 4.227 23.210 2428 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.11 % Allowed : 24.14 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.18), residues: 2192 helix: 0.58 (0.15), residues: 1240 sheet: 0.12 (0.38), residues: 208 loop : -0.56 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 681 TYR 0.015 0.001 TYR D 616 PHE 0.027 0.001 PHE A 551 TRP 0.022 0.002 TRP B 705 HIS 0.004 0.001 HIS B 831 Details of bonding type rmsd covalent geometry : bond 0.00268 (18056) covalent geometry : angle 0.77845 (24512) hydrogen bonds : bond 0.03677 ( 940) hydrogen bonds : angle 4.69227 ( 2688) *********************** 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 455 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 416 time to evaluate : 0.610 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: 0.9457 (ttp-170) cc_final: 0.8735 (ttt180) REVERT: A 124 MET cc_start: 0.9684 (mmm) cc_final: 0.9157 (tpp) REVERT: A 538 LYS cc_start: 0.9665 (mmtt) cc_final: 0.9231 (mppt) REVERT: A 541 ARG cc_start: 0.9229 (tpp80) cc_final: 0.8615 (ttp80) REVERT: A 542 TYR cc_start: 0.9036 (m-80) cc_final: 0.8529 (m-80) REVERT: A 574 MET cc_start: 0.8454 (ppp) cc_final: 0.8139 (mmt) REVERT: A 638 LYS cc_start: 0.9724 (mttt) cc_final: 0.9398 (mmtm) REVERT: A 677 MET cc_start: 0.9804 (tpp) cc_final: 0.9413 (tpp) REVERT: A 681 ARG cc_start: 0.9507 (ptp-110) cc_final: 0.9031 (mtm110) REVERT: A 691 ASN cc_start: 0.9756 (m-40) cc_final: 0.9303 (t0) REVERT: A 699 GLU cc_start: 0.9600 (pt0) cc_final: 0.9207 (pp20) REVERT: A 729 CYS cc_start: 0.9085 (m) cc_final: 0.8519 (m) REVERT: A 748 LYS cc_start: 0.9858 (mttt) cc_final: 0.9593 (ttpp) REVERT: A 756 MET cc_start: 0.8830 (mmm) cc_final: 0.8381 (mmm) REVERT: A 768 THR cc_start: 0.8720 (p) cc_final: 0.8219 (t) REVERT: B 4 ARG cc_start: 0.9455 (ttp-170) cc_final: 0.8747 (ttm-80) REVERT: B 466 ASP cc_start: 0.9565 (t0) cc_final: 0.9149 (m-30) REVERT: B 541 ARG cc_start: 0.9189 (tpp80) cc_final: 0.8562 (ttp80) REVERT: B 542 TYR cc_start: 0.9066 (m-80) cc_final: 0.8590 (m-80) REVERT: B 574 MET cc_start: 0.8605 (ppp) cc_final: 0.8235 (mmt) REVERT: B 638 LYS cc_start: 0.9715 (mttt) cc_final: 0.9403 (mmtm) REVERT: B 677 MET cc_start: 0.9490 (mmm) cc_final: 0.9209 (mmm) REVERT: B 681 ARG cc_start: 0.9400 (mtt90) cc_final: 0.9199 (mtt90) REVERT: B 691 ASN cc_start: 0.9728 (m-40) cc_final: 0.9282 (t0) REVERT: B 756 MET cc_start: 0.8782 (mmm) cc_final: 0.8544 (mmm) REVERT: B 768 THR cc_start: 0.8659 (p) cc_final: 0.8398 (p) REVERT: B 832 LYS cc_start: 0.9646 (OUTLIER) cc_final: 0.9385 (mtpp) REVERT: B 840 GLU cc_start: 0.9512 (mt-10) cc_final: 0.9276 (mt-10) REVERT: C 4 ARG cc_start: 0.9473 (ttp-170) cc_final: 0.8962 (ttm-80) REVERT: C 538 LYS cc_start: 0.9651 (mmtt) cc_final: 0.9234 (mppt) REVERT: C 542 TYR cc_start: 0.9140 (m-80) cc_final: 0.8745 (m-80) REVERT: C 574 MET cc_start: 0.8550 (ppp) cc_final: 0.8237 (mmt) REVERT: C 638 LYS cc_start: 0.9753 (mttt) cc_final: 0.9410 (mmtm) REVERT: C 677 MET cc_start: 0.9651 (tpp) cc_final: 0.9344 (tpp) REVERT: C 691 ASN cc_start: 0.9730 (m-40) cc_final: 0.9307 (t0) REVERT: C 693 LEU cc_start: 0.9853 (mm) cc_final: 0.9576 (tt) REVERT: C 733 ASN cc_start: 0.8704 (m-40) cc_final: 0.8419 (t0) REVERT: C 756 MET cc_start: 0.9035 (mmm) cc_final: 0.8827 (mmm) REVERT: C 758 PHE cc_start: 0.8814 (m-80) cc_final: 0.8501 (m-80) REVERT: C 832 LYS cc_start: 0.9585 (OUTLIER) cc_final: 0.9285 (mtpp) REVERT: D 4 ARG cc_start: 0.9412 (ttp-170) cc_final: 0.8885 (ttt90) REVERT: D 60 MET cc_start: 0.9276 (mmp) cc_final: 0.8952 (mmm) REVERT: D 542 TYR cc_start: 0.9122 (m-80) cc_final: 0.8777 (m-80) REVERT: D 574 MET cc_start: 0.8512 (ppp) cc_final: 0.8221 (mmt) REVERT: D 638 LYS cc_start: 0.9729 (mttt) cc_final: 0.9396 (mmtm) REVERT: D 677 MET cc_start: 0.9599 (tpp) cc_final: 0.9113 (tpp) REVERT: D 691 ASN cc_start: 0.9745 (m-40) cc_final: 0.9373 (t0) REVERT: D 729 CYS cc_start: 0.9202 (m) cc_final: 0.8485 (m) REVERT: D 733 ASN cc_start: 0.9126 (m-40) cc_final: 0.8727 (t0) REVERT: D 748 LYS cc_start: 0.9850 (mttt) cc_final: 0.9587 (ttpp) REVERT: D 756 MET cc_start: 0.8812 (mmm) cc_final: 0.8371 (mmm) outliers start: 39 outliers final: 31 residues processed: 436 average time/residue: 0.1347 time to fit residues: 89.4421 Evaluate side-chains 431 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 398 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 539 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 758 PHE 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 539 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 832 LYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 832 LYS 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 634 THR Chi-restraints excluded: chain D residue 758 PHE Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 56 optimal weight: 70.0000 chunk 27 optimal weight: 20.0000 chunk 92 optimal weight: 50.0000 chunk 5 optimal weight: 50.0000 chunk 204 optimal weight: 8.9990 chunk 180 optimal weight: 40.0000 chunk 160 optimal weight: 0.4980 chunk 60 optimal weight: 9.9990 overall best weight: 5.2386 ------------------------------------------------------------------------------- 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 = 0.3188 r_free = 0.3188 target = 0.061915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.046782 restraints weight = 86448.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.048548 restraints weight = 46713.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.049781 restraints weight = 30917.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.050663 restraints weight = 22948.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.051297 restraints weight = 18398.267| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.6887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18056 Z= 0.135 Angle : 0.800 13.340 24512 Z= 0.382 Chirality : 0.047 0.245 2792 Planarity : 0.004 0.035 3080 Dihedral : 4.251 23.095 2428 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % Rotamer: Outliers : 1.94 % Allowed : 24.62 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.18), residues: 2192 helix: 0.57 (0.15), residues: 1240 sheet: 0.16 (0.38), residues: 208 loop : -0.54 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 681 TYR 0.021 0.001 TYR D 707 PHE 0.031 0.001 PHE D 781 TRP 0.019 0.002 TRP C 585 HIS 0.005 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00297 (18056) covalent geometry : angle 0.80023 (24512) hydrogen bonds : bond 0.03740 ( 940) hydrogen bonds : angle 4.80876 ( 2688) ********************** 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 447 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 411 time to evaluate : 0.709 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: 0.9447 (ttp-170) cc_final: 0.8996 (ptm160) REVERT: A 124 MET cc_start: 0.9671 (mmm) cc_final: 0.9121 (tpp) REVERT: A 538 LYS cc_start: 0.9667 (mmtt) cc_final: 0.9227 (mppt) REVERT: A 541 ARG cc_start: 0.9224 (tpp80) cc_final: 0.8606 (ttp80) REVERT: A 542 TYR cc_start: 0.9060 (m-80) cc_final: 0.8560 (m-80) REVERT: A 574 MET cc_start: 0.8481 (ppp) cc_final: 0.8162 (mmt) REVERT: A 638 LYS cc_start: 0.9723 (mttt) cc_final: 0.9415 (mmtm) REVERT: A 677 MET cc_start: 0.9808 (tpp) cc_final: 0.8963 (tpp) REVERT: A 680 VAL cc_start: 0.9838 (t) cc_final: 0.9617 (t) REVERT: A 681 ARG cc_start: 0.9483 (ptp-110) cc_final: 0.9110 (ptp90) REVERT: A 691 ASN cc_start: 0.9752 (m-40) cc_final: 0.9307 (t0) REVERT: A 729 CYS cc_start: 0.9141 (m) cc_final: 0.8581 (m) REVERT: A 748 LYS cc_start: 0.9853 (mttt) cc_final: 0.9594 (ttpp) REVERT: A 756 MET cc_start: 0.8834 (mmm) cc_final: 0.8381 (mmm) REVERT: A 768 THR cc_start: 0.8696 (p) cc_final: 0.8458 (p) REVERT: B 4 ARG cc_start: 0.9432 (ttp-170) cc_final: 0.8952 (ptm160) REVERT: B 538 LYS cc_start: 0.9650 (mmtt) cc_final: 0.9218 (mppt) REVERT: B 541 ARG cc_start: 0.9185 (tpp80) cc_final: 0.8556 (ttp80) REVERT: B 542 TYR cc_start: 0.9076 (m-80) cc_final: 0.8555 (m-80) REVERT: B 574 MET cc_start: 0.8641 (ppp) cc_final: 0.8238 (mmt) REVERT: B 638 LYS cc_start: 0.9717 (mttt) cc_final: 0.9395 (mmtm) REVERT: B 663 ILE cc_start: 0.9745 (tp) cc_final: 0.9527 (tp) REVERT: B 677 MET cc_start: 0.9458 (mmm) cc_final: 0.9108 (mmm) REVERT: B 691 ASN cc_start: 0.9733 (m-40) cc_final: 0.9281 (t0) REVERT: B 759 LYS cc_start: 0.9368 (mmtm) cc_final: 0.9156 (mmtt) REVERT: B 768 THR cc_start: 0.8695 (p) cc_final: 0.8436 (p) REVERT: B 840 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9286 (mt-10) REVERT: C 4 ARG cc_start: 0.9473 (ttp-170) cc_final: 0.8969 (ttm-80) REVERT: C 538 LYS cc_start: 0.9649 (mmtt) cc_final: 0.9201 (mppt) REVERT: C 542 TYR cc_start: 0.9155 (m-80) cc_final: 0.8688 (m-80) REVERT: C 607 ILE cc_start: 0.9564 (mp) cc_final: 0.9295 (tp) REVERT: C 638 LYS cc_start: 0.9762 (mttt) cc_final: 0.9432 (mmtm) REVERT: C 658 ASN cc_start: 0.9009 (m-40) cc_final: 0.8762 (m110) REVERT: C 677 MET cc_start: 0.9642 (tpp) cc_final: 0.9380 (tpp) REVERT: C 691 ASN cc_start: 0.9733 (m-40) cc_final: 0.9319 (t0) REVERT: C 693 LEU cc_start: 0.9858 (mm) cc_final: 0.9612 (tt) REVERT: C 733 ASN cc_start: 0.8765 (m-40) cc_final: 0.8448 (t0) REVERT: C 756 MET cc_start: 0.9077 (mmm) cc_final: 0.8860 (mmm) REVERT: C 832 LYS cc_start: 0.9572 (OUTLIER) cc_final: 0.9287 (mtpp) REVERT: D 4 ARG cc_start: 0.9390 (ttp-170) cc_final: 0.8878 (ttt90) REVERT: D 60 MET cc_start: 0.9246 (mmp) cc_final: 0.8839 (mmm) REVERT: D 542 TYR cc_start: 0.9140 (m-80) cc_final: 0.8787 (m-80) REVERT: D 574 MET cc_start: 0.8528 (ppp) cc_final: 0.8242 (mmt) REVERT: D 638 LYS cc_start: 0.9722 (mttt) cc_final: 0.9417 (mmtm) REVERT: D 691 ASN cc_start: 0.9746 (m-40) cc_final: 0.9370 (t0) REVERT: D 729 CYS cc_start: 0.9215 (m) cc_final: 0.8518 (m) REVERT: D 733 ASN cc_start: 0.9110 (m-40) cc_final: 0.8738 (t0) REVERT: D 748 LYS cc_start: 0.9849 (mttt) cc_final: 0.9590 (ttpp) REVERT: D 756 MET cc_start: 0.8840 (mmm) cc_final: 0.8393 (mmm) outliers start: 36 outliers final: 31 residues processed: 428 average time/residue: 0.1293 time to fit residues: 84.7579 Evaluate side-chains 435 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 403 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 550 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 758 PHE 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 539 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 676 GLN Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 832 LYS 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 758 PHE Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 20.0000 chunk 21 optimal weight: 40.0000 chunk 125 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 103 optimal weight: 30.0000 chunk 130 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 66 optimal weight: 40.0000 chunk 201 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 702 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.059907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.044766 restraints weight = 86330.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.046476 restraints weight = 46968.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.047684 restraints weight = 31280.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.048552 restraints weight = 23307.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.049168 restraints weight = 18694.809| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.6989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18056 Z= 0.153 Angle : 0.822 13.198 24512 Z= 0.395 Chirality : 0.048 0.236 2792 Planarity : 0.004 0.034 3080 Dihedral : 4.320 23.389 2428 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.10 % Favored : 97.81 % Rotamer: Outliers : 2.00 % Allowed : 25.32 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.18), residues: 2192 helix: 0.52 (0.15), residues: 1240 sheet: 0.15 (0.37), residues: 208 loop : -0.53 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 681 TYR 0.020 0.001 TYR D 707 PHE 0.028 0.002 PHE A 551 TRP 0.020 0.002 TRP C 585 HIS 0.005 0.001 HIS D 687 Details of bonding type rmsd covalent geometry : bond 0.00333 (18056) covalent geometry : angle 0.82157 (24512) hydrogen bonds : bond 0.03864 ( 940) hydrogen bonds : angle 4.90076 ( 2688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5225.99 seconds wall clock time: 90 minutes 9.58 seconds (5409.58 seconds total)