Starting phenix.real_space_refine on Sun Jun 15 10:23:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5va2_8651/06_2025/5va2_8651.cif Found real_map, /net/cci-nas-00/data/ceres_data/5va2_8651/06_2025/5va2_8651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5va2_8651/06_2025/5va2_8651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5va2_8651/06_2025/5va2_8651.map" model { file = "/net/cci-nas-00/data/ceres_data/5va2_8651/06_2025/5va2_8651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5va2_8651/06_2025/5va2_8651.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.436 sd= 0.853 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 11456 2.51 5 N 2996 2.21 5 O 3016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17576 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4394 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 536} Chain breaks: 5 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Restraints were copied for chains: C, B, D Time building chain proxies: 9.79, per 1000 atoms: 0.56 Number of scatterers: 17576 At special positions: 0 Unit cell: (149.566, 149.566, 120.569, 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 3016 8.00 N 2996 7.00 C 11456 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 2.2 seconds 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4184 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 12 sheets defined 59.5% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 13 through 26 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.684A pdb=" N CYS A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.696A pdb=" N GLN A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 433 removed outlier: 3.967A pdb=" N VAL A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Proline residue: A 426 - end of helix removed outlier: 3.579A pdb=" N PHE A 431 " --> pdb=" O TYR A 427 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 473 removed outlier: 4.317A pdb=" N LEU A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 498 removed outlier: 3.993A pdb=" N HIS A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A 498 " --> pdb=" O PHE A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 505 removed outlier: 3.792A pdb=" N VAL A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.688A pdb=" N ALA A 527 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 538 through 543 removed outlier: 4.030A pdb=" N TYR A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 543' Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 547 through 575 removed outlier: 4.146A pdb=" N PHE A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 558 " --> pdb=" O MET A 554 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 572 " --> pdb=" O TRP A 568 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU A 575 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 593 removed outlier: 3.630A pdb=" N ASN A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 removed outlier: 3.539A pdb=" N ALA A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 667 removed outlier: 3.655A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 688 removed outlier: 3.615A pdb=" N HIS A 674 " --> pdb=" O THR A 670 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 709 removed outlier: 3.880A pdb=" N ARG A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 Processing helix chain 'A' and resid 721 through 733 Processing helix chain 'A' and resid 733 through 738 Processing helix chain 'A' and resid 740 through 745 removed outlier: 3.767A pdb=" N GLY A 745 " --> pdb=" O LYS A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 758 removed outlier: 3.614A pdb=" N ARG A 752 " --> pdb=" O LYS A 748 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 845 removed outlier: 3.830A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 841 " --> pdb=" O ASP A 837 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 856 Processing helix chain 'B' and resid 13 through 26 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.684A pdb=" N CYS B 49 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 75 through 89 removed outlier: 3.696A pdb=" N GLN B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 433 removed outlier: 3.967A pdb=" N VAL B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Proline residue: B 426 - end of helix removed outlier: 3.579A pdb=" N PHE B 431 " --> pdb=" O TYR B 427 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 473 removed outlier: 4.317A pdb=" N LEU B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 498 removed outlier: 3.993A pdb=" N HIS B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE B 498 " --> pdb=" O PHE B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 505 removed outlier: 3.792A pdb=" N VAL B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 531 removed outlier: 3.688A pdb=" N ALA B 527 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 538 through 543 removed outlier: 4.030A pdb=" N TYR B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 538 through 543' Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 547 through 575 removed outlier: 4.146A pdb=" N PHE B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 558 " --> pdb=" O MET B 554 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY B 572 " --> pdb=" O TRP B 568 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 593 removed outlier: 3.630A pdb=" N ASN B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN B 592 " --> pdb=" O ASN B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 623 removed outlier: 3.539A pdb=" N ALA B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 667 removed outlier: 3.655A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 688 removed outlier: 3.615A pdb=" N HIS B 674 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 709 removed outlier: 3.880A pdb=" N ARG B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 Processing helix chain 'B' and resid 721 through 733 Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 740 through 745 removed outlier: 3.767A pdb=" N GLY B 745 " --> pdb=" O LYS B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 758 removed outlier: 3.614A pdb=" N ARG B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 753 " --> pdb=" O GLY B 749 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 845 removed outlier: 3.830A pdb=" N GLU B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 841 " --> pdb=" O ASP B 837 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET B 844 " --> pdb=" O GLU B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 856 Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.684A pdb=" N CYS C 49 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 75 through 89 removed outlier: 3.696A pdb=" N GLN C 81 " --> pdb=" O ARG C 77 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 433 removed outlier: 3.967A pdb=" N VAL C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Proline residue: C 426 - end of helix removed outlier: 3.579A pdb=" N PHE C 431 " --> pdb=" O TYR C 427 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 432 " --> pdb=" O SER C 428 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU C 433 " --> pdb=" O ALA C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 473 removed outlier: 4.317A pdb=" N LEU C 457 " --> pdb=" O ALA C 453 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 459 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 471 " --> pdb=" O ILE C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 498 removed outlier: 3.993A pdb=" N HIS C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE C 498 " --> pdb=" O PHE C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 505 removed outlier: 3.792A pdb=" N VAL C 503 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 531 removed outlier: 3.688A pdb=" N ALA C 527 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 538 through 543 removed outlier: 4.030A pdb=" N TYR C 542 " --> pdb=" O LYS C 538 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 538 through 543' Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 547 through 575 removed outlier: 4.146A pdb=" N PHE C 551 " --> pdb=" O ALA C 547 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 558 " --> pdb=" O MET C 554 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY C 572 " --> pdb=" O TRP C 568 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU C 575 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 593 removed outlier: 3.630A pdb=" N ASN C 588 " --> pdb=" O GLY C 584 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN C 592 " --> pdb=" O ASN C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 623 removed outlier: 3.539A pdb=" N ALA C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 667 removed outlier: 3.655A pdb=" N ALA C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE C 656 " --> pdb=" O TYR C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 688 removed outlier: 3.615A pdb=" N HIS C 674 " --> pdb=" O THR C 670 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 709 removed outlier: 3.880A pdb=" N ARG C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 Processing helix chain 'C' and resid 721 through 733 Processing helix chain 'C' and resid 733 through 738 Processing helix chain 'C' and resid 740 through 745 removed outlier: 3.767A pdb=" N GLY C 745 " --> pdb=" O LYS C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 758 removed outlier: 3.614A pdb=" N ARG C 752 " --> pdb=" O LYS C 748 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 753 " --> pdb=" O GLY C 749 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 845 removed outlier: 3.830A pdb=" N GLU C 840 " --> pdb=" O ASP C 836 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 841 " --> pdb=" O ASP C 837 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET C 844 " --> pdb=" O GLU C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 856 Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 45 through 53 removed outlier: 3.684A pdb=" N CYS D 49 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 75 through 89 removed outlier: 3.696A pdb=" N GLN D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 433 removed outlier: 3.967A pdb=" N VAL D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 415 " --> pdb=" O ASP D 411 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 420 " --> pdb=" O LEU D 416 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 421 " --> pdb=" O LEU D 417 " (cutoff:3.500A) Proline residue: D 426 - end of helix removed outlier: 3.579A pdb=" N PHE D 431 " --> pdb=" O TYR D 427 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 432 " --> pdb=" O SER D 428 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU D 433 " --> pdb=" O ALA D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 473 removed outlier: 4.317A pdb=" N LEU D 457 " --> pdb=" O ALA D 453 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE D 458 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL D 459 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE D 463 " --> pdb=" O VAL D 459 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE D 464 " --> pdb=" O ASP D 460 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU D 468 " --> pdb=" O ILE D 464 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 498 removed outlier: 3.993A pdb=" N HIS D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE D 498 " --> pdb=" O PHE D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 505 removed outlier: 3.792A pdb=" N VAL D 503 " --> pdb=" O LEU D 499 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 505 " --> pdb=" O ASP D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 531 removed outlier: 3.688A pdb=" N ALA D 527 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 537 Processing helix chain 'D' and resid 538 through 543 removed outlier: 4.030A pdb=" N TYR D 542 " --> pdb=" O LYS D 538 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 543' Processing helix chain 'D' and resid 544 through 546 No H-bonds generated for 'chain 'D' and resid 544 through 546' Processing helix chain 'D' and resid 547 through 575 removed outlier: 4.146A pdb=" N PHE D 551 " --> pdb=" O ALA D 547 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 558 " --> pdb=" O MET D 554 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY D 572 " --> pdb=" O TRP D 568 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 593 removed outlier: 3.630A pdb=" N ASN D 588 " --> pdb=" O GLY D 584 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 592 " --> pdb=" O ASN D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 623 removed outlier: 3.539A pdb=" N ALA D 614 " --> pdb=" O LYS D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 667 removed outlier: 3.655A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE D 656 " --> pdb=" O TYR D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 688 removed outlier: 3.615A pdb=" N HIS D 674 " --> pdb=" O THR D 670 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 709 removed outlier: 3.880A pdb=" N ARG D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 718 Processing helix chain 'D' and resid 721 through 733 Processing helix chain 'D' and resid 733 through 738 Processing helix chain 'D' and resid 740 through 745 removed outlier: 3.767A pdb=" N GLY D 745 " --> pdb=" O LYS D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 758 removed outlier: 3.614A pdb=" N ARG D 752 " --> pdb=" O LYS D 748 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 753 " --> pdb=" O GLY D 749 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 845 removed outlier: 3.830A pdb=" N GLU D 840 " --> pdb=" O ASP D 836 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 841 " --> pdb=" O ASP D 837 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET D 844 " --> pdb=" O GLU D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 856 Processing sheet with id=1, first strand: chain 'A' and resid 41 through 44 removed outlier: 7.182A pdb=" N VAL A 41 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASN A 33 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 43 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET A 124 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 115 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 126 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 113 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 106 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE A 98 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS A 108 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE A 96 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 112 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG A 92 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 803 through 805 removed outlier: 3.706A pdb=" N ASP A 803 " --> pdb=" O ILE A 782 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 805 " --> pdb=" O TYR A 780 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 779 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.232A pdb=" N ILE A 787 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 798 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 789 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 41 through 44 removed outlier: 7.182A pdb=" N VAL B 41 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASN B 33 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR B 43 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET B 124 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 115 " --> pdb=" O MET B 124 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 126 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 113 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 106 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE B 98 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS B 108 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 96 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 112 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG B 92 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 803 through 805 removed outlier: 3.706A pdb=" N ASP B 803 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 805 " --> pdb=" O TYR B 780 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 779 " --> pdb=" O ILE B 833 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 787 through 790 removed outlier: 6.232A pdb=" N ILE B 787 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE B 798 " --> pdb=" O ILE B 787 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 789 " --> pdb=" O VAL B 796 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'C' and resid 41 through 44 removed outlier: 7.182A pdb=" N VAL C 41 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASN C 33 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR C 43 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET C 124 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 115 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE C 126 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 113 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C 106 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE C 98 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS C 108 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE C 96 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 112 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG C 92 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 803 through 805 removed outlier: 3.706A pdb=" N ASP C 803 " --> pdb=" O ILE C 782 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 805 " --> pdb=" O TYR C 780 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 779 " --> pdb=" O ILE C 833 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 787 through 790 removed outlier: 6.232A pdb=" N ILE C 787 " --> pdb=" O ILE C 798 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE C 798 " --> pdb=" O ILE C 787 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE C 789 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'D' and resid 41 through 44 removed outlier: 7.182A pdb=" N VAL D 41 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASN D 33 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR D 43 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET D 124 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 115 " --> pdb=" O MET D 124 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE D 126 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 113 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE D 106 " --> pdb=" O PHE D 98 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE D 98 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS D 108 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE D 96 " --> pdb=" O CYS D 108 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 112 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG D 92 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'D' and resid 803 through 805 removed outlier: 3.706A pdb=" N ASP D 803 " --> pdb=" O ILE D 782 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 805 " --> pdb=" O TYR D 780 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 779 " --> pdb=" O ILE D 833 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'D' and resid 787 through 790 removed outlier: 6.232A pdb=" N ILE D 787 " --> pdb=" O ILE D 798 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE D 798 " --> pdb=" O ILE D 787 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 789 " --> pdb=" O VAL D 796 " (cutoff:3.500A) 784 hydrogen bonds defined for protein. 2280 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: 6.01 Time building geometry restraints manager: 4.84 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: 5492 1.34 - 1.46: 2324 1.46 - 1.58: 10032 1.58 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 18000 Sorted by residual: bond pdb=" CA PRO A 764 " pdb=" C PRO A 764 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.32e+00 bond pdb=" CA PRO D 764 " pdb=" C PRO D 764 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.32e+00 bond pdb=" CA PRO C 764 " pdb=" C PRO C 764 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.32e+00 bond pdb=" CA PRO B 764 " pdb=" C PRO B 764 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.32e+00 bond pdb=" N GLY C 603 " pdb=" CA GLY C 603 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.86e+00 ... (remaining 17995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 22164 1.87 - 3.75: 2120 3.75 - 5.62: 132 5.62 - 7.50: 12 7.50 - 9.37: 4 Bond angle restraints: 24432 Sorted by residual: angle pdb=" C VAL A 8 " pdb=" CA VAL A 8 " pdb=" CB VAL A 8 " ideal model delta sigma weight residual 111.74 107.32 4.42 9.40e-01 1.13e+00 2.21e+01 angle pdb=" C VAL D 8 " pdb=" CA VAL D 8 " pdb=" CB VAL D 8 " ideal model delta sigma weight residual 111.74 107.32 4.42 9.40e-01 1.13e+00 2.21e+01 angle pdb=" C VAL C 8 " pdb=" CA VAL C 8 " pdb=" CB VAL C 8 " ideal model delta sigma weight residual 111.74 107.32 4.42 9.40e-01 1.13e+00 2.21e+01 angle pdb=" C VAL B 8 " pdb=" CA VAL B 8 " pdb=" CB VAL B 8 " ideal model delta sigma weight residual 111.74 107.32 4.42 9.40e-01 1.13e+00 2.21e+01 angle pdb=" N ALA A 813 " pdb=" CA ALA A 813 " pdb=" C ALA A 813 " ideal model delta sigma weight residual 112.24 117.27 -5.03 1.28e+00 6.10e-01 1.54e+01 ... (remaining 24427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.46: 9124 12.46 - 24.92: 1048 24.92 - 37.38: 248 37.38 - 49.83: 92 49.83 - 62.29: 28 Dihedral angle restraints: 10540 sinusoidal: 4056 harmonic: 6484 Sorted by residual: 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 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA GLY A 628 " pdb=" C GLY A 628 " pdb=" N ASN A 629 " pdb=" CA ASN A 629 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 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 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 10537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1856 0.052 - 0.104: 608 0.104 - 0.156: 240 0.156 - 0.208: 76 0.208 - 0.260: 8 Chirality restraints: 2788 Sorted by residual: chirality pdb=" CA ILE D 593 " pdb=" N ILE D 593 " pdb=" C ILE D 593 " pdb=" CB ILE D 593 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ILE C 593 " pdb=" N ILE C 593 " pdb=" C ILE C 593 " pdb=" CB ILE C 593 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ILE B 593 " pdb=" N ILE B 593 " pdb=" C ILE B 593 " pdb=" CB ILE B 593 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2785 not shown) Planarity restraints: 3064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 113 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO B 114 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 114 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 114 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 113 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 114 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 113 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO D 114 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 114 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 114 " -0.019 5.00e-02 4.00e+02 ... (remaining 3061 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 48 2.50 - 3.10: 10648 3.10 - 3.70: 25794 3.70 - 4.30: 36232 4.30 - 4.90: 59924 Nonbonded interactions: 132646 Sorted by model distance: nonbonded pdb=" CE1 HIS C 7 " pdb=" CG2 VAL C 8 " model vdw 1.897 3.680 nonbonded pdb=" CE1 HIS D 7 " pdb=" CG2 VAL D 8 " model vdw 1.897 3.680 nonbonded pdb=" CE1 HIS B 7 " pdb=" CG2 VAL B 8 " model vdw 1.897 3.680 nonbonded pdb=" CE1 HIS A 7 " pdb=" CG2 VAL A 8 " model vdw 1.897 3.680 nonbonded pdb=" CB SER A 631 " pdb=" OD1 ASN B 629 " model vdw 1.998 3.440 ... (remaining 132641 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.250 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 38.770 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 0.177 18004 Z= 0.614 Angle : 1.081 9.371 24432 Z= 0.725 Chirality : 0.064 0.260 2788 Planarity : 0.004 0.034 3064 Dihedral : 12.468 62.292 6356 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 1.65 % Allowed : 7.69 % Favored : 90.66 % Rotamer: Outliers : 1.08 % Allowed : 6.49 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.14), residues: 2184 helix: -2.20 (0.11), residues: 1104 sheet: -4.06 (0.30), residues: 128 loop : -2.67 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 705 HIS 0.005 0.001 HIS A 587 PHE 0.011 0.001 PHE D 494 TYR 0.013 0.001 TYR D 652 ARG 0.003 0.000 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.28900 ( 784) hydrogen bonds : angle 8.66493 ( 2280) covalent geometry : bond 0.00785 (18000) covalent geometry : angle 1.08056 (24432) Misc. bond : bond 0.17654 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 896 time to evaluate : 2.028 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 30 ILE cc_start: 0.9743 (pt) cc_final: 0.9540 (mm) REVERT: A 31 ILE cc_start: 0.9799 (mt) cc_final: 0.9576 (mp) REVERT: A 42 ILE cc_start: 0.9629 (pt) cc_final: 0.9355 (pt) REVERT: A 43 TYR cc_start: 0.9498 (t80) cc_final: 0.9249 (t80) REVERT: A 59 VAL cc_start: 0.9734 (t) cc_final: 0.9390 (p) REVERT: A 95 GLU cc_start: 0.9575 (tt0) cc_final: 0.9160 (tm-30) REVERT: A 109 LEU cc_start: 0.9510 (tp) cc_final: 0.8919 (pp) REVERT: A 400 ILE cc_start: 0.9078 (mm) cc_final: 0.8875 (tp) REVERT: A 506 ILE cc_start: 0.9200 (mt) cc_final: 0.8911 (pt) REVERT: A 524 LEU cc_start: 0.9527 (mt) cc_final: 0.9213 (mt) REVERT: A 533 VAL cc_start: 0.9449 (t) cc_final: 0.9165 (p) REVERT: A 574 MET cc_start: 0.8306 (mtt) cc_final: 0.7818 (ppp) REVERT: A 575 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8233 (tp30) REVERT: A 588 ASN cc_start: 0.9626 (t0) cc_final: 0.9252 (m-40) REVERT: A 612 VAL cc_start: 0.9734 (t) cc_final: 0.9465 (p) REVERT: A 638 LYS cc_start: 0.9677 (mttt) cc_final: 0.9245 (mtpp) REVERT: A 644 VAL cc_start: 0.9597 (t) cc_final: 0.9359 (p) REVERT: A 645 MET cc_start: 0.9538 (mtp) cc_final: 0.9198 (ttp) REVERT: A 677 MET cc_start: 0.9866 (tpp) cc_final: 0.9405 (tmm) REVERT: A 681 ARG cc_start: 0.9618 (mtt180) cc_final: 0.9361 (mtm180) REVERT: A 689 ILE cc_start: 0.8779 (mt) cc_final: 0.8465 (mt) REVERT: A 691 ASN cc_start: 0.9641 (m-40) cc_final: 0.9367 (m110) REVERT: A 711 ILE cc_start: 0.7764 (mt) cc_final: 0.5323 (mm) REVERT: A 712 ASP cc_start: 0.9388 (m-30) cc_final: 0.9017 (p0) REVERT: A 729 CYS cc_start: 0.9708 (m) cc_final: 0.9485 (m) REVERT: A 737 LEU cc_start: 0.9780 (mp) cc_final: 0.9454 (mp) REVERT: A 751 LEU cc_start: 0.9559 (mt) cc_final: 0.9228 (pp) REVERT: A 761 THR cc_start: 0.8837 (p) cc_final: 0.8602 (t) REVERT: A 775 LEU cc_start: 0.8759 (mt) cc_final: 0.8371 (mm) REVERT: A 782 ILE cc_start: 0.9569 (mt) cc_final: 0.9027 (tt) REVERT: A 798 ILE cc_start: 0.9816 (mp) cc_final: 0.9421 (mm) REVERT: A 832 LYS cc_start: 0.9711 (tttt) cc_final: 0.9448 (ttpp) REVERT: A 833 ILE cc_start: 0.9586 (pt) cc_final: 0.9113 (pt) REVERT: A 840 GLU cc_start: 0.9734 (mt-10) cc_final: 0.9462 (tp30) REVERT: A 844 MET cc_start: 0.9629 (mmp) cc_final: 0.9410 (mtm) REVERT: B 42 ILE cc_start: 0.9570 (pt) cc_final: 0.9276 (pt) REVERT: B 59 VAL cc_start: 0.9741 (t) cc_final: 0.9393 (p) REVERT: B 95 GLU cc_start: 0.9597 (tt0) cc_final: 0.9227 (tm-30) REVERT: B 109 LEU cc_start: 0.9500 (tp) cc_final: 0.8926 (pp) REVERT: B 400 ILE cc_start: 0.9068 (mm) cc_final: 0.8859 (tp) REVERT: B 501 ASP cc_start: 0.9307 (m-30) cc_final: 0.7205 (m-30) REVERT: B 506 ILE cc_start: 0.9277 (mt) cc_final: 0.8934 (pt) REVERT: B 524 LEU cc_start: 0.9525 (mt) cc_final: 0.9257 (mm) REVERT: B 533 VAL cc_start: 0.9473 (t) cc_final: 0.9182 (p) REVERT: B 574 MET cc_start: 0.8332 (mtt) cc_final: 0.7826 (ppp) REVERT: B 575 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8138 (tp30) REVERT: B 612 VAL cc_start: 0.9714 (t) cc_final: 0.9433 (p) REVERT: B 638 LYS cc_start: 0.9638 (mttt) cc_final: 0.9186 (mtpp) REVERT: B 644 VAL cc_start: 0.9566 (t) cc_final: 0.9334 (p) REVERT: B 645 MET cc_start: 0.9529 (mtp) cc_final: 0.9242 (ttp) REVERT: B 677 MET cc_start: 0.9877 (tpp) cc_final: 0.9454 (tmm) REVERT: B 681 ARG cc_start: 0.9622 (mtt180) cc_final: 0.9341 (mtm180) REVERT: B 683 PHE cc_start: 0.9872 (t80) cc_final: 0.9622 (t80) REVERT: B 691 ASN cc_start: 0.9650 (m-40) cc_final: 0.9367 (m110) REVERT: B 711 ILE cc_start: 0.7861 (mt) cc_final: 0.5538 (mm) REVERT: B 712 ASP cc_start: 0.9455 (m-30) cc_final: 0.9066 (p0) REVERT: B 717 LEU cc_start: 0.9637 (tt) cc_final: 0.9389 (tp) REVERT: B 729 CYS cc_start: 0.9691 (m) cc_final: 0.9462 (m) REVERT: B 737 LEU cc_start: 0.9803 (mp) cc_final: 0.9488 (mp) REVERT: B 748 LYS cc_start: 0.9875 (mttt) cc_final: 0.9658 (tmmt) REVERT: B 751 LEU cc_start: 0.9564 (mt) cc_final: 0.9274 (pp) REVERT: B 781 PHE cc_start: 0.9775 (m-80) cc_final: 0.9563 (m-80) REVERT: B 782 ILE cc_start: 0.9566 (mt) cc_final: 0.9090 (tt) REVERT: B 798 ILE cc_start: 0.9804 (mp) cc_final: 0.9571 (tp) REVERT: B 804 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.9008 (tp) REVERT: B 832 LYS cc_start: 0.9685 (tttt) cc_final: 0.9437 (ttpp) REVERT: B 833 ILE cc_start: 0.9531 (pt) cc_final: 0.9082 (pt) REVERT: C 31 ILE cc_start: 0.9779 (mt) cc_final: 0.9548 (mp) REVERT: C 42 ILE cc_start: 0.9575 (pt) cc_final: 0.9309 (pt) REVERT: C 43 TYR cc_start: 0.9460 (t80) cc_final: 0.9236 (t80) REVERT: C 59 VAL cc_start: 0.9750 (t) cc_final: 0.9237 (p) REVERT: C 95 GLU cc_start: 0.9586 (tt0) cc_final: 0.9208 (tm-30) REVERT: C 109 LEU cc_start: 0.9495 (tp) cc_final: 0.8928 (pp) REVERT: C 400 ILE cc_start: 0.9033 (mm) cc_final: 0.8819 (tp) REVERT: C 501 ASP cc_start: 0.9336 (m-30) cc_final: 0.6770 (m-30) REVERT: C 533 VAL cc_start: 0.9413 (t) cc_final: 0.9050 (p) REVERT: C 574 MET cc_start: 0.8278 (mtt) cc_final: 0.7700 (ppp) REVERT: C 575 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8113 (tp30) REVERT: C 588 ASN cc_start: 0.9632 (t0) cc_final: 0.9260 (m-40) REVERT: C 638 LYS cc_start: 0.9663 (mttt) cc_final: 0.9225 (mtpp) REVERT: C 645 MET cc_start: 0.9522 (mtp) cc_final: 0.9277 (ttp) REVERT: C 677 MET cc_start: 0.9890 (tpp) cc_final: 0.9456 (tmm) REVERT: C 681 ARG cc_start: 0.9614 (mtt180) cc_final: 0.9345 (mtm180) REVERT: C 683 PHE cc_start: 0.9880 (t80) cc_final: 0.9624 (t80) REVERT: C 691 ASN cc_start: 0.9652 (m-40) cc_final: 0.9232 (m110) REVERT: C 695 GLN cc_start: 0.9770 (mt0) cc_final: 0.9463 (mp10) REVERT: C 698 GLU cc_start: 0.9737 (mt-10) cc_final: 0.9501 (mp0) REVERT: C 711 ILE cc_start: 0.7694 (mt) cc_final: 0.5422 (mm) REVERT: C 712 ASP cc_start: 0.9354 (m-30) cc_final: 0.8987 (p0) REVERT: C 717 LEU cc_start: 0.9607 (tt) cc_final: 0.9321 (tp) REVERT: C 729 CYS cc_start: 0.9703 (m) cc_final: 0.9482 (m) REVERT: C 737 LEU cc_start: 0.9812 (mp) cc_final: 0.9520 (mp) REVERT: C 748 LYS cc_start: 0.9876 (mttt) cc_final: 0.9653 (tmmt) REVERT: C 751 LEU cc_start: 0.9561 (mt) cc_final: 0.9250 (pp) REVERT: C 781 PHE cc_start: 0.9767 (m-80) cc_final: 0.9548 (m-80) REVERT: C 782 ILE cc_start: 0.9528 (mt) cc_final: 0.9016 (tt) REVERT: C 798 ILE cc_start: 0.9782 (mp) cc_final: 0.9542 (tp) REVERT: C 804 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9121 (tp) REVERT: C 821 ASP cc_start: 0.9207 (m-30) cc_final: 0.8960 (p0) REVERT: C 825 LEU cc_start: 0.9278 (mt) cc_final: 0.9075 (mp) REVERT: C 832 LYS cc_start: 0.9699 (tttt) cc_final: 0.9452 (ttpp) REVERT: C 833 ILE cc_start: 0.9589 (pt) cc_final: 0.9154 (pt) REVERT: C 840 GLU cc_start: 0.9716 (mt-10) cc_final: 0.9504 (tp30) REVERT: D 42 ILE cc_start: 0.9645 (pt) cc_final: 0.9201 (pt) REVERT: D 43 TYR cc_start: 0.9485 (t80) cc_final: 0.9157 (t80) REVERT: D 59 VAL cc_start: 0.9735 (t) cc_final: 0.9532 (p) REVERT: D 95 GLU cc_start: 0.9551 (tt0) cc_final: 0.9132 (tm-30) REVERT: D 109 LEU cc_start: 0.9506 (tp) cc_final: 0.8928 (pp) REVERT: D 400 ILE cc_start: 0.9036 (mm) cc_final: 0.8829 (tp) REVERT: D 506 ILE cc_start: 0.9299 (mt) cc_final: 0.9097 (pt) REVERT: D 524 LEU cc_start: 0.9498 (mt) cc_final: 0.9188 (mm) REVERT: D 533 VAL cc_start: 0.9391 (t) cc_final: 0.9099 (p) REVERT: D 574 MET cc_start: 0.8187 (mtt) cc_final: 0.7661 (ppp) REVERT: D 575 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8182 (tp30) REVERT: D 612 VAL cc_start: 0.9742 (t) cc_final: 0.9492 (p) REVERT: D 638 LYS cc_start: 0.9703 (mttt) cc_final: 0.9266 (mtpp) REVERT: D 644 VAL cc_start: 0.9665 (t) cc_final: 0.9456 (p) REVERT: D 645 MET cc_start: 0.9528 (mtp) cc_final: 0.9228 (ttp) REVERT: D 677 MET cc_start: 0.9880 (tpp) cc_final: 0.9468 (tmm) REVERT: D 681 ARG cc_start: 0.9618 (mtt180) cc_final: 0.9402 (mtm180) REVERT: D 689 ILE cc_start: 0.8657 (mt) cc_final: 0.8312 (mt) REVERT: D 691 ASN cc_start: 0.9642 (m-40) cc_final: 0.9233 (m110) REVERT: D 695 GLN cc_start: 0.9763 (mt0) cc_final: 0.9464 (mp10) REVERT: D 698 GLU cc_start: 0.9728 (mt-10) cc_final: 0.9472 (mp0) REVERT: D 711 ILE cc_start: 0.7572 (mt) cc_final: 0.5168 (mm) REVERT: D 712 ASP cc_start: 0.9278 (m-30) cc_final: 0.8888 (p0) REVERT: D 729 CYS cc_start: 0.9716 (m) cc_final: 0.9468 (m) REVERT: D 737 LEU cc_start: 0.9790 (mp) cc_final: 0.9439 (mp) REVERT: D 748 LYS cc_start: 0.9882 (mttt) cc_final: 0.9666 (tmmt) REVERT: D 751 LEU cc_start: 0.9570 (mt) cc_final: 0.9067 (pp) REVERT: D 775 LEU cc_start: 0.8770 (mt) cc_final: 0.8116 (mm) REVERT: D 781 PHE cc_start: 0.9785 (m-80) cc_final: 0.9585 (m-80) REVERT: D 782 ILE cc_start: 0.9530 (mt) cc_final: 0.9023 (tt) REVERT: D 798 ILE cc_start: 0.9795 (mp) cc_final: 0.9555 (tp) REVERT: D 821 ASP cc_start: 0.9225 (m-30) cc_final: 0.9018 (p0) REVERT: D 832 LYS cc_start: 0.9722 (tttt) cc_final: 0.9449 (ttpp) REVERT: D 833 ILE cc_start: 0.9635 (pt) cc_final: 0.9184 (pt) REVERT: D 840 GLU cc_start: 0.9738 (mt-10) cc_final: 0.9448 (tp30) REVERT: D 844 MET cc_start: 0.9628 (mmp) cc_final: 0.9345 (mtm) outliers start: 20 outliers final: 0 residues processed: 912 average time/residue: 0.3334 time to fit residues: 435.1411 Evaluate side-chains 592 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 590 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain C residue 804 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 199 optimal weight: 20.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 470 ASN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS B 12 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 GLN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS B 834 HIS C 12 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN C 676 GLN C 762 HIS C 834 HIS D 12 ASN D 470 ASN ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 GLN D 834 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.067575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.054194 restraints weight = 89621.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055799 restraints weight = 57481.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056967 restraints weight = 41390.361| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18004 Z= 0.168 Angle : 0.821 9.541 24432 Z= 0.413 Chirality : 0.047 0.188 2788 Planarity : 0.005 0.062 3064 Dihedral : 5.353 32.943 2424 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.85 % Favored : 94.41 % Rotamer: Outliers : 4.00 % Allowed : 18.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.17), residues: 2184 helix: -0.80 (0.14), residues: 1192 sheet: -2.17 (0.40), residues: 132 loop : -2.10 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 497 HIS 0.008 0.002 HIS C 7 PHE 0.018 0.002 PHE B 617 TYR 0.023 0.002 TYR B 700 ARG 0.007 0.001 ARG B 694 Details of bonding type rmsd hydrogen bonds : bond 0.06057 ( 784) hydrogen bonds : angle 5.37488 ( 2280) covalent geometry : bond 0.00355 (18000) covalent geometry : angle 0.82099 (24432) Misc. bond : bond 0.00079 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 610 time to evaluate : 2.107 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: symmetry clash revert: 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 43 TYR cc_start: 0.9297 (t80) cc_final: 0.8892 (t80) REVERT: A 424 PHE cc_start: 0.9247 (m-80) cc_final: 0.8946 (m-80) REVERT: A 533 VAL cc_start: 0.9718 (t) cc_final: 0.9494 (p) REVERT: A 574 MET cc_start: 0.8119 (mtt) cc_final: 0.7744 (ppp) REVERT: A 677 MET cc_start: 0.9722 (tpp) cc_final: 0.9317 (mmm) REVERT: A 711 ILE cc_start: 0.8343 (mt) cc_final: 0.5662 (mm) REVERT: A 729 CYS cc_start: 0.9683 (m) cc_final: 0.9479 (m) REVERT: A 768 THR cc_start: 0.8179 (p) cc_final: 0.7962 (p) REVERT: A 798 ILE cc_start: 0.9747 (mp) cc_final: 0.9487 (mm) REVERT: A 823 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7752 (mmp80) REVERT: A 832 LYS cc_start: 0.9697 (tttt) cc_final: 0.9455 (ttpp) REVERT: A 833 ILE cc_start: 0.9605 (pt) cc_final: 0.9351 (tp) REVERT: A 840 GLU cc_start: 0.9590 (mt-10) cc_final: 0.9321 (tm-30) REVERT: B 424 PHE cc_start: 0.9265 (m-80) cc_final: 0.8992 (m-80) REVERT: B 563 TRP cc_start: 0.9517 (m-10) cc_final: 0.9254 (m-10) REVERT: B 574 MET cc_start: 0.8118 (mtt) cc_final: 0.7698 (ppp) REVERT: B 651 MET cc_start: 0.9355 (mmm) cc_final: 0.9130 (mmm) REVERT: B 677 MET cc_start: 0.9734 (tpp) cc_final: 0.9349 (mmm) REVERT: B 678 LEU cc_start: 0.9753 (mt) cc_final: 0.9353 (mt) REVERT: B 712 ASP cc_start: 0.9470 (m-30) cc_final: 0.9232 (p0) REVERT: B 729 CYS cc_start: 0.9667 (m) cc_final: 0.9458 (m) REVERT: B 804 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9132 (mm) REVERT: B 823 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7676 (mmp80) REVERT: B 832 LYS cc_start: 0.9656 (tttt) cc_final: 0.9412 (ttpp) REVERT: B 833 ILE cc_start: 0.9621 (pt) cc_final: 0.9362 (tp) REVERT: C 43 TYR cc_start: 0.9295 (t80) cc_final: 0.8948 (t80) REVERT: C 59 VAL cc_start: 0.9434 (t) cc_final: 0.9152 (m) REVERT: C 60 MET cc_start: 0.7900 (mmm) cc_final: 0.7592 (mmm) REVERT: C 424 PHE cc_start: 0.9323 (m-80) cc_final: 0.9067 (m-80) REVERT: C 533 VAL cc_start: 0.9699 (t) cc_final: 0.9450 (p) REVERT: C 574 MET cc_start: 0.8096 (mtt) cc_final: 0.7642 (ppp) REVERT: C 575 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7768 (tp30) REVERT: C 677 MET cc_start: 0.9739 (tpp) cc_final: 0.9365 (mmm) REVERT: C 711 ILE cc_start: 0.8326 (mt) cc_final: 0.5713 (mm) REVERT: C 712 ASP cc_start: 0.9406 (m-30) cc_final: 0.9176 (p0) REVERT: C 729 CYS cc_start: 0.9629 (m) cc_final: 0.9383 (m) REVERT: C 737 LEU cc_start: 0.9643 (mp) cc_final: 0.9428 (mp) REVERT: C 804 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9195 (mm) REVERT: C 821 ASP cc_start: 0.8964 (m-30) cc_final: 0.8619 (p0) REVERT: C 823 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7748 (mmp80) REVERT: C 832 LYS cc_start: 0.9655 (tttt) cc_final: 0.9439 (ttpp) REVERT: C 833 ILE cc_start: 0.9658 (pt) cc_final: 0.9414 (tp) REVERT: C 840 GLU cc_start: 0.9580 (mt-10) cc_final: 0.9272 (tm-30) REVERT: D 12 ASN cc_start: 0.9311 (OUTLIER) cc_final: 0.9029 (t0) REVERT: D 43 TYR cc_start: 0.9212 (t80) cc_final: 0.8950 (t80) REVERT: D 424 PHE cc_start: 0.9337 (m-80) cc_final: 0.9020 (m-80) REVERT: D 533 VAL cc_start: 0.9688 (t) cc_final: 0.9365 (p) REVERT: D 574 MET cc_start: 0.8028 (mtt) cc_final: 0.7635 (ppp) REVERT: D 575 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7822 (tp30) REVERT: D 677 MET cc_start: 0.9723 (tpp) cc_final: 0.9337 (tmm) REVERT: D 678 LEU cc_start: 0.9715 (mt) cc_final: 0.9467 (pp) REVERT: D 729 CYS cc_start: 0.9599 (m) cc_final: 0.9358 (m) REVERT: D 768 THR cc_start: 0.8072 (p) cc_final: 0.7817 (p) REVERT: D 821 ASP cc_start: 0.8972 (m-30) cc_final: 0.8669 (p0) REVERT: D 827 TYR cc_start: 0.8563 (m-80) cc_final: 0.8142 (m-80) REVERT: D 832 LYS cc_start: 0.9685 (tttt) cc_final: 0.9476 (ttpp) REVERT: D 833 ILE cc_start: 0.9669 (pt) cc_final: 0.9400 (tp) REVERT: D 840 GLU cc_start: 0.9605 (mt-10) cc_final: 0.9287 (tm-30) outliers start: 74 outliers final: 44 residues processed: 656 average time/residue: 0.2928 time to fit residues: 285.4472 Evaluate side-chains 543 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 493 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 HIS Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 823 ARG Chi-restraints excluded: chain B residue 7 HIS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 804 ILE Chi-restraints excluded: chain C residue 823 ARG Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 7 HIS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 789 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 804 ILE Chi-restraints excluded: chain D residue 823 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 82 optimal weight: 20.0000 chunk 32 optimal weight: 40.0000 chunk 116 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 40.0000 chunk 180 optimal weight: 7.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 HIS ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 ASN A 739 HIS ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 HIS B 691 ASN B 739 HIS ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 HIS ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 HIS ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.084494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.071411 restraints weight = 87942.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.072980 restraints weight = 57233.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.074139 restraints weight = 41683.945| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18004 Z= 0.145 Angle : 0.800 13.205 24432 Z= 0.389 Chirality : 0.047 0.270 2788 Planarity : 0.005 0.081 3064 Dihedral : 5.051 34.278 2424 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.35 % Favored : 94.92 % Rotamer: Outliers : 4.60 % Allowed : 19.91 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.17), residues: 2184 helix: -0.58 (0.14), residues: 1204 sheet: -1.57 (0.41), residues: 136 loop : -1.91 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 410 HIS 0.006 0.001 HIS B 731 PHE 0.025 0.002 PHE C 48 TYR 0.015 0.001 TYR B 700 ARG 0.012 0.001 ARG C 537 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 784) hydrogen bonds : angle 5.12455 ( 2280) covalent geometry : bond 0.00313 (18000) covalent geometry : angle 0.80034 (24432) Misc. bond : bond 0.00039 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 523 time to evaluate : 2.186 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 424 PHE cc_start: 0.9261 (m-80) cc_final: 0.8918 (m-80) REVERT: A 541 ARG cc_start: 0.9158 (tpp80) cc_final: 0.8956 (tpp80) REVERT: A 574 MET cc_start: 0.8097 (mtt) cc_final: 0.7842 (tpt) REVERT: A 645 MET cc_start: 0.9429 (ttm) cc_final: 0.9201 (ptm) REVERT: A 729 CYS cc_start: 0.9629 (m) cc_final: 0.9411 (m) REVERT: A 768 THR cc_start: 0.8092 (p) cc_final: 0.7871 (p) REVERT: A 779 LEU cc_start: 0.9862 (tp) cc_final: 0.9588 (mm) REVERT: A 832 LYS cc_start: 0.9684 (tttt) cc_final: 0.9465 (ttpp) REVERT: A 840 GLU cc_start: 0.9717 (mt-10) cc_final: 0.9267 (tp30) REVERT: B 410 TRP cc_start: 0.9350 (t60) cc_final: 0.9055 (t60) REVERT: B 424 PHE cc_start: 0.9335 (m-80) cc_final: 0.8995 (m-80) REVERT: B 541 ARG cc_start: 0.9132 (tpp80) cc_final: 0.8919 (tpp80) REVERT: B 563 TRP cc_start: 0.9526 (m-10) cc_final: 0.9114 (m-10) REVERT: B 574 MET cc_start: 0.8169 (mtt) cc_final: 0.7907 (tpt) REVERT: B 619 PHE cc_start: 0.9602 (OUTLIER) cc_final: 0.9136 (t80) REVERT: B 645 MET cc_start: 0.9221 (ttm) cc_final: 0.8569 (ttm) REVERT: B 651 MET cc_start: 0.9460 (mmm) cc_final: 0.9217 (mmm) REVERT: B 677 MET cc_start: 0.9624 (tpp) cc_final: 0.9289 (mtm) REVERT: B 712 ASP cc_start: 0.9481 (m-30) cc_final: 0.9280 (p0) REVERT: B 729 CYS cc_start: 0.9603 (m) cc_final: 0.9384 (m) REVERT: B 779 LEU cc_start: 0.9870 (tp) cc_final: 0.9608 (mm) REVERT: B 832 LYS cc_start: 0.9671 (tttt) cc_final: 0.9449 (ttpp) REVERT: B 833 ILE cc_start: 0.9582 (pt) cc_final: 0.9370 (tp) REVERT: C 43 TYR cc_start: 0.9196 (t80) cc_final: 0.8797 (t80) REVERT: C 59 VAL cc_start: 0.9266 (t) cc_final: 0.8835 (p) REVERT: C 60 MET cc_start: 0.7950 (mmm) cc_final: 0.7681 (mmm) REVERT: C 411 ASP cc_start: 0.9380 (t70) cc_final: 0.8262 (t0) REVERT: C 424 PHE cc_start: 0.9398 (m-80) cc_final: 0.9068 (m-80) REVERT: C 541 ARG cc_start: 0.9174 (tpt-90) cc_final: 0.8777 (mmm160) REVERT: C 574 MET cc_start: 0.8071 (mtt) cc_final: 0.7762 (tpt) REVERT: C 619 PHE cc_start: 0.9608 (OUTLIER) cc_final: 0.8964 (t80) REVERT: C 640 PHE cc_start: 0.9662 (t80) cc_final: 0.9443 (t80) REVERT: C 645 MET cc_start: 0.9480 (ttm) cc_final: 0.8903 (ttm) REVERT: C 651 MET cc_start: 0.9419 (mmm) cc_final: 0.9191 (mmm) REVERT: C 691 ASN cc_start: 0.9676 (p0) cc_final: 0.9456 (m110) REVERT: C 695 GLN cc_start: 0.9673 (mt0) cc_final: 0.9450 (mm110) REVERT: C 698 GLU cc_start: 0.9533 (pt0) cc_final: 0.9189 (pp20) REVERT: C 712 ASP cc_start: 0.9491 (m-30) cc_final: 0.9245 (p0) REVERT: C 751 LEU cc_start: 0.9789 (mt) cc_final: 0.9542 (pp) REVERT: C 779 LEU cc_start: 0.9861 (tp) cc_final: 0.9636 (mm) REVERT: C 804 ILE cc_start: 0.9543 (OUTLIER) cc_final: 0.9297 (mm) REVERT: C 821 ASP cc_start: 0.8946 (m-30) cc_final: 0.8604 (p0) REVERT: C 827 TYR cc_start: 0.8614 (m-80) cc_final: 0.8280 (m-80) REVERT: C 840 GLU cc_start: 0.9692 (mt-10) cc_final: 0.9185 (tp30) REVERT: C 841 VAL cc_start: 0.9843 (t) cc_final: 0.9558 (t) REVERT: C 844 MET cc_start: 0.9470 (mtm) cc_final: 0.8239 (mtm) REVERT: D 43 TYR cc_start: 0.9207 (t80) cc_final: 0.8848 (t80) REVERT: D 410 TRP cc_start: 0.9389 (t60) cc_final: 0.9173 (t60) REVERT: D 424 PHE cc_start: 0.9334 (m-80) cc_final: 0.8975 (m-80) REVERT: D 533 VAL cc_start: 0.9727 (t) cc_final: 0.9325 (p) REVERT: D 537 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8021 (ptp90) REVERT: D 538 LYS cc_start: 0.9269 (mmtm) cc_final: 0.8903 (mmtm) REVERT: D 541 ARG cc_start: 0.9248 (tpp80) cc_final: 0.9036 (tpp80) REVERT: D 574 MET cc_start: 0.8074 (mtt) cc_final: 0.7760 (tpt) REVERT: D 619 PHE cc_start: 0.9623 (OUTLIER) cc_final: 0.9047 (t80) REVERT: D 651 MET cc_start: 0.9395 (mmm) cc_final: 0.9177 (mmm) REVERT: D 677 MET cc_start: 0.9713 (tpp) cc_final: 0.9113 (tmm) REVERT: D 698 GLU cc_start: 0.9485 (pt0) cc_final: 0.9278 (mp0) REVERT: D 707 TYR cc_start: 0.9013 (t80) cc_final: 0.8602 (t80) REVERT: D 729 CYS cc_start: 0.9595 (m) cc_final: 0.9392 (m) REVERT: D 762 HIS cc_start: 0.7929 (m-70) cc_final: 0.6766 (m-70) REVERT: D 768 THR cc_start: 0.8064 (p) cc_final: 0.7818 (p) REVERT: D 821 ASP cc_start: 0.8913 (m-30) cc_final: 0.8625 (p0) REVERT: D 840 GLU cc_start: 0.9710 (mt-10) cc_final: 0.9193 (tp30) REVERT: D 841 VAL cc_start: 0.9866 (t) cc_final: 0.9659 (t) REVERT: D 844 MET cc_start: 0.9486 (mtm) cc_final: 0.8470 (ptp) outliers start: 85 outliers final: 49 residues processed: 580 average time/residue: 0.2751 time to fit residues: 243.5749 Evaluate side-chains 541 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 487 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 817 LYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 534 ARG Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 643 CYS Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 804 ILE Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 537 ARG Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 711 ILE Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 77 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 194 optimal weight: 40.0000 chunk 28 optimal weight: 0.9980 chunk 113 optimal weight: 40.0000 chunk 164 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 209 optimal weight: 50.0000 chunk 147 optimal weight: 7.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS A 851 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 658 ASN B 691 ASN ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 HIS C 61 GLN C 70 HIS ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 HIS ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 ASN D 691 ASN ** D 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.078446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.065433 restraints weight = 87410.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.066978 restraints weight = 56827.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068106 restraints weight = 41305.570| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18004 Z= 0.143 Angle : 0.728 12.791 24432 Z= 0.356 Chirality : 0.044 0.251 2788 Planarity : 0.004 0.035 3064 Dihedral : 4.741 34.092 2422 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.03 % Favored : 95.24 % Rotamer: Outliers : 4.11 % Allowed : 20.35 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2184 helix: -0.48 (0.14), residues: 1196 sheet: -1.14 (0.37), residues: 164 loop : -1.68 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 410 HIS 0.007 0.001 HIS C 731 PHE 0.017 0.001 PHE D 640 TYR 0.023 0.001 TYR B 700 ARG 0.009 0.001 ARG C 537 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 784) hydrogen bonds : angle 4.91727 ( 2280) covalent geometry : bond 0.00309 (18000) covalent geometry : angle 0.72780 (24432) Misc. bond : bond 0.00037 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 498 time to evaluate : 2.285 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 PHE cc_start: 0.9238 (m-80) cc_final: 0.8894 (m-80) REVERT: A 541 ARG cc_start: 0.9155 (tpp80) cc_final: 0.8877 (tpp80) REVERT: A 617 PHE cc_start: 0.9577 (t80) cc_final: 0.9213 (t80) REVERT: A 642 ILE cc_start: 0.9655 (mm) cc_final: 0.9438 (mm) REVERT: A 658 ASN cc_start: 0.9310 (m110) cc_final: 0.9007 (m110) REVERT: A 677 MET cc_start: 0.9555 (tpp) cc_final: 0.9221 (tmm) REVERT: A 681 ARG cc_start: 0.9333 (mmm160) cc_final: 0.8777 (tpm170) REVERT: A 729 CYS cc_start: 0.9591 (m) cc_final: 0.9344 (m) REVERT: A 768 THR cc_start: 0.8062 (p) cc_final: 0.7860 (p) REVERT: A 779 LEU cc_start: 0.9873 (tp) cc_final: 0.9637 (mm) REVERT: A 840 GLU cc_start: 0.9710 (mt-10) cc_final: 0.9173 (tp30) REVERT: A 844 MET cc_start: 0.9157 (mtm) cc_final: 0.8049 (ptp) REVERT: B 424 PHE cc_start: 0.9271 (m-80) cc_final: 0.8913 (m-80) REVERT: B 534 ARG cc_start: 0.9300 (OUTLIER) cc_final: 0.9039 (mmm160) REVERT: B 538 LYS cc_start: 0.9327 (mmtm) cc_final: 0.9112 (mmtm) REVERT: B 563 TRP cc_start: 0.9535 (m-10) cc_final: 0.9031 (m-10) REVERT: B 574 MET cc_start: 0.8210 (mtt) cc_final: 0.8004 (tpt) REVERT: B 645 MET cc_start: 0.9500 (ttm) cc_final: 0.8656 (ttt) REVERT: B 651 MET cc_start: 0.9497 (mmm) cc_final: 0.9280 (mmm) REVERT: B 658 ASN cc_start: 0.9300 (m110) cc_final: 0.9000 (m110) REVERT: B 677 MET cc_start: 0.9608 (tpp) cc_final: 0.9336 (mmt) REVERT: B 712 ASP cc_start: 0.9496 (m-30) cc_final: 0.9224 (p0) REVERT: B 729 CYS cc_start: 0.9560 (m) cc_final: 0.9314 (m) REVERT: B 779 LEU cc_start: 0.9882 (tp) cc_final: 0.9654 (mm) REVERT: B 832 LYS cc_start: 0.9672 (tttt) cc_final: 0.9413 (ttpp) REVERT: B 833 ILE cc_start: 0.9572 (pt) cc_final: 0.9341 (tp) REVERT: C 411 ASP cc_start: 0.9382 (t70) cc_final: 0.8178 (t70) REVERT: C 462 MET cc_start: 0.9541 (tpt) cc_final: 0.9181 (tpp) REVERT: C 466 ASP cc_start: 0.9246 (m-30) cc_final: 0.8778 (m-30) REVERT: C 541 ARG cc_start: 0.9165 (tpt-90) cc_final: 0.8840 (tpt-90) REVERT: C 563 TRP cc_start: 0.9701 (m-10) cc_final: 0.9483 (m-10) REVERT: C 574 MET cc_start: 0.8169 (mtt) cc_final: 0.7893 (tpt) REVERT: C 619 PHE cc_start: 0.9661 (OUTLIER) cc_final: 0.8993 (t80) REVERT: C 645 MET cc_start: 0.9467 (ttm) cc_final: 0.8907 (ttm) REVERT: C 651 MET cc_start: 0.9483 (mmm) cc_final: 0.9255 (mmm) REVERT: C 658 ASN cc_start: 0.9236 (m110) cc_final: 0.8917 (m110) REVERT: C 677 MET cc_start: 0.9690 (tpp) cc_final: 0.9420 (mmm) REVERT: C 698 GLU cc_start: 0.9517 (pt0) cc_final: 0.9240 (pp20) REVERT: C 804 ILE cc_start: 0.9572 (OUTLIER) cc_final: 0.9344 (mm) REVERT: C 821 ASP cc_start: 0.8865 (m-30) cc_final: 0.8521 (p0) REVERT: C 827 TYR cc_start: 0.8690 (m-80) cc_final: 0.8348 (m-10) REVERT: C 840 GLU cc_start: 0.9687 (mt-10) cc_final: 0.9177 (tp30) REVERT: C 841 VAL cc_start: 0.9856 (t) cc_final: 0.9573 (t) REVERT: C 844 MET cc_start: 0.9435 (mtm) cc_final: 0.8215 (mtm) REVERT: D 533 VAL cc_start: 0.9745 (t) cc_final: 0.9301 (p) REVERT: D 537 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7872 (ptp90) REVERT: D 541 ARG cc_start: 0.9230 (tpp80) cc_final: 0.8752 (tpp80) REVERT: D 563 TRP cc_start: 0.9709 (m-10) cc_final: 0.9479 (m-10) REVERT: D 617 PHE cc_start: 0.9596 (t80) cc_final: 0.9090 (t80) REVERT: D 619 PHE cc_start: 0.9659 (OUTLIER) cc_final: 0.9040 (t80) REVERT: D 640 PHE cc_start: 0.9706 (t80) cc_final: 0.9473 (t80) REVERT: D 651 MET cc_start: 0.9454 (mmm) cc_final: 0.9239 (mmm) REVERT: D 658 ASN cc_start: 0.9225 (m110) cc_final: 0.8907 (m110) REVERT: D 677 MET cc_start: 0.9716 (tpp) cc_final: 0.9054 (tmm) REVERT: D 729 CYS cc_start: 0.9575 (m) cc_final: 0.9307 (m) REVERT: D 768 THR cc_start: 0.8112 (p) cc_final: 0.7879 (p) REVERT: D 779 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9314 (mm) REVERT: D 821 ASP cc_start: 0.8832 (m-30) cc_final: 0.8550 (p0) REVERT: D 827 TYR cc_start: 0.8723 (m-80) cc_final: 0.8382 (m-80) REVERT: D 840 GLU cc_start: 0.9708 (mt-10) cc_final: 0.9165 (tp30) REVERT: D 841 VAL cc_start: 0.9865 (t) cc_final: 0.9646 (t) REVERT: D 844 MET cc_start: 0.9455 (mtm) cc_final: 0.8430 (ptp) outliers start: 76 outliers final: 47 residues processed: 549 average time/residue: 0.2729 time to fit residues: 230.5551 Evaluate side-chains 516 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 463 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 804 ILE Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 537 ARG Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 711 ILE Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 804 ILE Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 103 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 51 optimal weight: 50.0000 chunk 186 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 125 optimal weight: 0.0030 chunk 57 optimal weight: 40.0000 chunk 59 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 overall best weight: 4.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 GLN A 691 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 691 ASN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS ** D 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.075318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060743 restraints weight = 73845.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061968 restraints weight = 53734.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.062808 restraints weight = 42854.533| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18004 Z= 0.133 Angle : 0.736 12.697 24432 Z= 0.357 Chirality : 0.045 0.260 2788 Planarity : 0.003 0.040 3064 Dihedral : 4.618 33.596 2422 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.03 % Favored : 95.60 % Rotamer: Outliers : 4.00 % Allowed : 23.00 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2184 helix: -0.44 (0.14), residues: 1176 sheet: -0.94 (0.39), residues: 160 loop : -1.56 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 410 HIS 0.010 0.001 HIS A 834 PHE 0.024 0.001 PHE A 48 TYR 0.016 0.001 TYR B 700 ARG 0.013 0.001 ARG C 537 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 784) hydrogen bonds : angle 4.88626 ( 2280) covalent geometry : bond 0.00288 (18000) covalent geometry : angle 0.73568 (24432) Misc. bond : bond 0.00013 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 496 time to evaluate : 1.960 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 424 PHE cc_start: 0.9334 (m-80) cc_final: 0.8977 (m-80) REVERT: A 538 LYS cc_start: 0.9235 (mmtm) cc_final: 0.8921 (mmtm) REVERT: A 541 ARG cc_start: 0.9068 (tpp80) cc_final: 0.8644 (tpp80) REVERT: A 617 PHE cc_start: 0.9623 (t80) cc_final: 0.9205 (t80) REVERT: A 677 MET cc_start: 0.9642 (tpp) cc_final: 0.8780 (tmm) REVERT: A 681 ARG cc_start: 0.9368 (mmm160) cc_final: 0.8847 (mmm-85) REVERT: A 729 CYS cc_start: 0.9590 (m) cc_final: 0.9331 (m) REVERT: A 779 LEU cc_start: 0.9852 (tp) cc_final: 0.9638 (mm) REVERT: A 840 GLU cc_start: 0.9699 (mt-10) cc_final: 0.9084 (tp30) REVERT: A 844 MET cc_start: 0.9148 (mtm) cc_final: 0.8158 (ptt) REVERT: B 48 PHE cc_start: 0.9619 (t80) cc_final: 0.9412 (t80) REVERT: B 60 MET cc_start: 0.8089 (tpp) cc_final: 0.7884 (tpp) REVERT: B 410 TRP cc_start: 0.9311 (t60) cc_final: 0.9046 (t60) REVERT: B 424 PHE cc_start: 0.9350 (m-80) cc_final: 0.8966 (m-80) REVERT: B 534 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8929 (mmm160) REVERT: B 541 ARG cc_start: 0.9050 (tpp80) cc_final: 0.8619 (tpp80) REVERT: B 645 MET cc_start: 0.9563 (ttm) cc_final: 0.8902 (ttm) REVERT: B 651 MET cc_start: 0.9478 (mmm) cc_final: 0.9238 (mmm) REVERT: B 658 ASN cc_start: 0.9294 (m110) cc_final: 0.8987 (m110) REVERT: B 707 TYR cc_start: 0.9164 (t80) cc_final: 0.8797 (t80) REVERT: B 729 CYS cc_start: 0.9561 (m) cc_final: 0.9300 (m) REVERT: B 784 ARG cc_start: 0.9267 (mtp85) cc_final: 0.9066 (mtp-110) REVERT: B 832 LYS cc_start: 0.9627 (tttt) cc_final: 0.9424 (ttpp) REVERT: B 834 HIS cc_start: 0.9603 (OUTLIER) cc_final: 0.9345 (t-90) REVERT: C 411 ASP cc_start: 0.9180 (t70) cc_final: 0.8175 (t70) REVERT: C 424 PHE cc_start: 0.9343 (m-80) cc_final: 0.8974 (m-80) REVERT: C 538 LYS cc_start: 0.9292 (mmtm) cc_final: 0.8936 (mmtm) REVERT: C 541 ARG cc_start: 0.9099 (tpt-90) cc_final: 0.8852 (tpt-90) REVERT: C 563 TRP cc_start: 0.9681 (m-10) cc_final: 0.9393 (m-10) REVERT: C 574 MET cc_start: 0.8122 (mtt) cc_final: 0.7863 (tpt) REVERT: C 619 PHE cc_start: 0.9711 (OUTLIER) cc_final: 0.9099 (t80) REVERT: C 640 PHE cc_start: 0.9712 (t80) cc_final: 0.9509 (t80) REVERT: C 651 MET cc_start: 0.9479 (mmm) cc_final: 0.9236 (mmm) REVERT: C 658 ASN cc_start: 0.9241 (m110) cc_final: 0.8908 (m110) REVERT: C 677 MET cc_start: 0.9768 (tpp) cc_final: 0.9357 (tmm) REVERT: C 681 ARG cc_start: 0.9314 (mmm160) cc_final: 0.8831 (tpm170) REVERT: C 707 TYR cc_start: 0.9153 (t80) cc_final: 0.8398 (t80) REVERT: C 762 HIS cc_start: 0.8176 (m-70) cc_final: 0.7331 (m-70) REVERT: C 821 ASP cc_start: 0.8768 (m-30) cc_final: 0.8363 (p0) REVERT: C 827 TYR cc_start: 0.8724 (m-80) cc_final: 0.8413 (m-10) REVERT: C 840 GLU cc_start: 0.9701 (mt-10) cc_final: 0.9200 (tp30) REVERT: C 841 VAL cc_start: 0.9857 (t) cc_final: 0.9630 (t) REVERT: C 844 MET cc_start: 0.9468 (mtm) cc_final: 0.8320 (mtm) REVERT: D 533 VAL cc_start: 0.9772 (t) cc_final: 0.9533 (p) REVERT: D 538 LYS cc_start: 0.9393 (mmtm) cc_final: 0.9057 (mmtm) REVERT: D 541 ARG cc_start: 0.9117 (tpp80) cc_final: 0.8727 (tpp80) REVERT: D 563 TRP cc_start: 0.9693 (m-10) cc_final: 0.9423 (m-10) REVERT: D 651 MET cc_start: 0.9464 (mmm) cc_final: 0.9261 (mmm) REVERT: D 658 ASN cc_start: 0.9233 (m110) cc_final: 0.8902 (m110) REVERT: D 677 MET cc_start: 0.9756 (tpp) cc_final: 0.9180 (tmm) REVERT: D 707 TYR cc_start: 0.9244 (t80) cc_final: 0.9004 (t80) REVERT: D 729 CYS cc_start: 0.9529 (m) cc_final: 0.9309 (m) REVERT: D 821 ASP cc_start: 0.8724 (m-30) cc_final: 0.8449 (p0) REVERT: D 840 GLU cc_start: 0.9705 (mt-10) cc_final: 0.9150 (tp30) REVERT: D 841 VAL cc_start: 0.9865 (t) cc_final: 0.9638 (t) REVERT: D 844 MET cc_start: 0.9488 (mtm) cc_final: 0.8518 (ptp) outliers start: 74 outliers final: 51 residues processed: 539 average time/residue: 0.2635 time to fit residues: 218.9370 Evaluate side-chains 522 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 468 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 834 HIS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 711 ILE Chi-restraints excluded: chain D residue 762 HIS Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 123 optimal weight: 0.3980 chunk 112 optimal weight: 50.0000 chunk 160 optimal weight: 30.0000 chunk 10 optimal weight: 30.0000 chunk 17 optimal weight: 40.0000 chunk 135 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 GLN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS ** D 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.067959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.055365 restraints weight = 93062.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.056932 restraints weight = 59853.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058109 restraints weight = 43153.788| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18004 Z= 0.131 Angle : 0.760 14.199 24432 Z= 0.365 Chirality : 0.045 0.268 2788 Planarity : 0.003 0.032 3064 Dihedral : 4.476 21.560 2420 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.08 % Favored : 95.56 % Rotamer: Outliers : 3.46 % Allowed : 25.97 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.17), residues: 2184 helix: -0.44 (0.14), residues: 1176 sheet: -0.64 (0.39), residues: 164 loop : -1.44 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 410 HIS 0.007 0.001 HIS A 834 PHE 0.019 0.001 PHE B 48 TYR 0.014 0.001 TYR B 43 ARG 0.008 0.001 ARG B 537 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 784) hydrogen bonds : angle 4.91648 ( 2280) covalent geometry : bond 0.00289 (18000) covalent geometry : angle 0.76018 (24432) Misc. bond : bond 0.00023 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 488 time to evaluate : 2.121 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 538 LYS cc_start: 0.9319 (mmtm) cc_final: 0.8999 (mmtm) REVERT: A 541 ARG cc_start: 0.9157 (tpp80) cc_final: 0.8766 (tpp80) REVERT: A 617 PHE cc_start: 0.9573 (t80) cc_final: 0.9147 (t80) REVERT: A 677 MET cc_start: 0.9581 (tpp) cc_final: 0.8948 (tmm) REVERT: A 729 CYS cc_start: 0.9596 (m) cc_final: 0.9363 (m) REVERT: A 779 LEU cc_start: 0.9857 (tp) cc_final: 0.9645 (mm) REVERT: A 840 GLU cc_start: 0.9684 (mt-10) cc_final: 0.9064 (tp30) REVERT: A 844 MET cc_start: 0.9118 (mtm) cc_final: 0.8208 (ptt) REVERT: B 48 PHE cc_start: 0.9503 (t80) cc_final: 0.9303 (t80) REVERT: B 411 ASP cc_start: 0.9322 (t70) cc_final: 0.8855 (t0) REVERT: B 424 PHE cc_start: 0.9406 (m-80) cc_final: 0.9002 (m-80) REVERT: B 541 ARG cc_start: 0.9127 (tpp80) cc_final: 0.8669 (tpp80) REVERT: B 563 TRP cc_start: 0.9681 (m-10) cc_final: 0.9391 (m-10) REVERT: B 645 MET cc_start: 0.9562 (ttm) cc_final: 0.8878 (ttm) REVERT: B 651 MET cc_start: 0.9554 (mmm) cc_final: 0.9329 (mmm) REVERT: B 658 ASN cc_start: 0.9238 (m110) cc_final: 0.8943 (m110) REVERT: B 677 MET cc_start: 0.9465 (mtm) cc_final: 0.8917 (tmm) REVERT: B 707 TYR cc_start: 0.9042 (t80) cc_final: 0.8517 (t80) REVERT: B 729 CYS cc_start: 0.9518 (m) cc_final: 0.9271 (m) REVERT: B 762 HIS cc_start: 0.8172 (m-70) cc_final: 0.6695 (m-70) REVERT: B 788 GLU cc_start: 0.9091 (pm20) cc_final: 0.8821 (pm20) REVERT: C 410 TRP cc_start: 0.9388 (t-100) cc_final: 0.9141 (t-100) REVERT: C 411 ASP cc_start: 0.9380 (t70) cc_final: 0.8459 (t70) REVERT: C 424 PHE cc_start: 0.9342 (m-80) cc_final: 0.8945 (m-80) REVERT: C 538 LYS cc_start: 0.9417 (mmtm) cc_final: 0.9034 (mmtm) REVERT: C 541 ARG cc_start: 0.9261 (tpt-90) cc_final: 0.8790 (tpt-90) REVERT: C 563 TRP cc_start: 0.9696 (m-10) cc_final: 0.9406 (m-10) REVERT: C 574 MET cc_start: 0.8084 (mtt) cc_final: 0.7830 (tpt) REVERT: C 617 PHE cc_start: 0.9567 (t80) cc_final: 0.9144 (t80) REVERT: C 619 PHE cc_start: 0.9672 (OUTLIER) cc_final: 0.9035 (t80) REVERT: C 640 PHE cc_start: 0.9669 (t80) cc_final: 0.9445 (t80) REVERT: C 645 MET cc_start: 0.9627 (ttm) cc_final: 0.8935 (ptm) REVERT: C 651 MET cc_start: 0.9557 (mmm) cc_final: 0.9340 (mmm) REVERT: C 658 ASN cc_start: 0.9174 (m110) cc_final: 0.8848 (m110) REVERT: C 677 MET cc_start: 0.9756 (tpp) cc_final: 0.9296 (tmm) REVERT: C 707 TYR cc_start: 0.8999 (t80) cc_final: 0.8282 (t80) REVERT: C 762 HIS cc_start: 0.8166 (m-70) cc_final: 0.7166 (m-70) REVERT: C 821 ASP cc_start: 0.8861 (m-30) cc_final: 0.8484 (p0) REVERT: C 840 GLU cc_start: 0.9679 (mt-10) cc_final: 0.9144 (tp30) REVERT: C 841 VAL cc_start: 0.9858 (t) cc_final: 0.9592 (t) REVERT: C 844 MET cc_start: 0.9436 (mtm) cc_final: 0.8344 (mtm) REVERT: D 12 ASN cc_start: 0.9576 (t0) cc_final: 0.9279 (t0) REVERT: D 411 ASP cc_start: 0.9372 (t70) cc_final: 0.8790 (t0) REVERT: D 533 VAL cc_start: 0.9752 (t) cc_final: 0.9489 (p) REVERT: D 538 LYS cc_start: 0.9473 (mmtm) cc_final: 0.9158 (mmtm) REVERT: D 541 ARG cc_start: 0.9221 (tpp80) cc_final: 0.8744 (ttp80) REVERT: D 563 TRP cc_start: 0.9709 (m-10) cc_final: 0.9418 (m-10) REVERT: D 619 PHE cc_start: 0.9650 (OUTLIER) cc_final: 0.8904 (t80) REVERT: D 651 MET cc_start: 0.9539 (mmm) cc_final: 0.9329 (mmm) REVERT: D 658 ASN cc_start: 0.9196 (m110) cc_final: 0.8875 (m110) REVERT: D 677 MET cc_start: 0.9705 (tpp) cc_final: 0.9091 (tmm) REVERT: D 699 GLU cc_start: 0.9618 (tt0) cc_final: 0.9243 (mt-10) REVERT: D 707 TYR cc_start: 0.9111 (t80) cc_final: 0.8891 (t80) REVERT: D 729 CYS cc_start: 0.9569 (m) cc_final: 0.9308 (m) REVERT: D 821 ASP cc_start: 0.8793 (m-30) cc_final: 0.8524 (p0) REVERT: D 840 GLU cc_start: 0.9689 (mt-10) cc_final: 0.9039 (tp30) REVERT: D 841 VAL cc_start: 0.9846 (t) cc_final: 0.9569 (t) REVERT: D 844 MET cc_start: 0.9435 (mtm) cc_final: 0.8460 (ptt) outliers start: 64 outliers final: 47 residues processed: 526 average time/residue: 0.2637 time to fit residues: 214.1443 Evaluate side-chains 511 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 462 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 834 HIS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 762 HIS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 148 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 50.0000 chunk 86 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 142 optimal weight: 30.0000 chunk 46 optimal weight: 30.0000 chunk 189 optimal weight: 0.9980 chunk 122 optimal weight: 50.0000 chunk 58 optimal weight: 0.6980 overall best weight: 5.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS ** D 834 HIS ** 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 = 0.3320 r_free = 0.3320 target = 0.067524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.055025 restraints weight = 93260.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.056592 restraints weight = 59872.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.057739 restraints weight = 43080.150| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18004 Z= 0.137 Angle : 0.775 13.800 24432 Z= 0.373 Chirality : 0.046 0.308 2788 Planarity : 0.003 0.030 3064 Dihedral : 4.453 21.905 2420 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.03 % Favored : 95.60 % Rotamer: Outliers : 3.41 % Allowed : 27.60 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.17), residues: 2184 helix: -0.46 (0.14), residues: 1176 sheet: -0.58 (0.39), residues: 164 loop : -1.33 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 410 HIS 0.014 0.001 HIS D 762 PHE 0.028 0.001 PHE A 48 TYR 0.015 0.001 TYR B 43 ARG 0.008 0.001 ARG B 681 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 784) hydrogen bonds : angle 4.93938 ( 2280) covalent geometry : bond 0.00300 (18000) covalent geometry : angle 0.77501 (24432) Misc. bond : bond 0.00036 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 494 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.9368 (t70) cc_final: 0.8740 (t0) REVERT: A 538 LYS cc_start: 0.9359 (mmtm) cc_final: 0.9043 (mmtm) REVERT: A 541 ARG cc_start: 0.9166 (tpp80) cc_final: 0.8723 (tpp80) REVERT: A 617 PHE cc_start: 0.9575 (t80) cc_final: 0.9236 (t80) REVERT: A 619 PHE cc_start: 0.9656 (OUTLIER) cc_final: 0.9272 (t80) REVERT: A 645 MET cc_start: 0.9648 (ptm) cc_final: 0.9372 (ptm) REVERT: A 677 MET cc_start: 0.9505 (tpp) cc_final: 0.8881 (tmm) REVERT: A 681 ARG cc_start: 0.9555 (mtm180) cc_final: 0.9035 (mtm180) REVERT: A 729 CYS cc_start: 0.9617 (m) cc_final: 0.9343 (m) REVERT: A 779 LEU cc_start: 0.9856 (tp) cc_final: 0.9655 (mm) REVERT: A 840 GLU cc_start: 0.9667 (mt-10) cc_final: 0.9149 (tp30) REVERT: B 48 PHE cc_start: 0.9535 (t80) cc_final: 0.9327 (t80) REVERT: B 411 ASP cc_start: 0.9327 (t70) cc_final: 0.8813 (t0) REVERT: B 424 PHE cc_start: 0.9420 (m-80) cc_final: 0.9002 (m-80) REVERT: B 538 LYS cc_start: 0.9214 (mmtm) cc_final: 0.8953 (mmtm) REVERT: B 541 ARG cc_start: 0.9178 (tpp80) cc_final: 0.8719 (tpp80) REVERT: B 563 TRP cc_start: 0.9687 (m-10) cc_final: 0.9395 (m-10) REVERT: B 619 PHE cc_start: 0.9681 (OUTLIER) cc_final: 0.9215 (t80) REVERT: B 640 PHE cc_start: 0.9692 (t80) cc_final: 0.9479 (t80) REVERT: B 645 MET cc_start: 0.9575 (ttm) cc_final: 0.8899 (ttm) REVERT: B 651 MET cc_start: 0.9539 (mmm) cc_final: 0.9305 (mmm) REVERT: B 658 ASN cc_start: 0.9218 (m110) cc_final: 0.8920 (m110) REVERT: B 707 TYR cc_start: 0.9039 (t80) cc_final: 0.8537 (t80) REVERT: B 717 LEU cc_start: 0.9753 (tp) cc_final: 0.9479 (pp) REVERT: B 729 CYS cc_start: 0.9535 (m) cc_final: 0.9300 (m) REVERT: B 762 HIS cc_start: 0.8175 (m-70) cc_final: 0.6677 (m-70) REVERT: B 788 GLU cc_start: 0.9107 (pm20) cc_final: 0.8898 (pm20) REVERT: B 821 ASP cc_start: 0.9009 (m-30) cc_final: 0.8530 (p0) REVERT: C 411 ASP cc_start: 0.9406 (t70) cc_final: 0.8390 (t70) REVERT: C 424 PHE cc_start: 0.9343 (m-80) cc_final: 0.8912 (m-80) REVERT: C 538 LYS cc_start: 0.9458 (mmtm) cc_final: 0.9064 (mmtm) REVERT: C 541 ARG cc_start: 0.9257 (tpt-90) cc_final: 0.8796 (tpt-90) REVERT: C 574 MET cc_start: 0.8112 (mtt) cc_final: 0.7821 (tpt) REVERT: C 619 PHE cc_start: 0.9682 (OUTLIER) cc_final: 0.9079 (t80) REVERT: C 645 MET cc_start: 0.9625 (ttm) cc_final: 0.9365 (ptm) REVERT: C 658 ASN cc_start: 0.9165 (m110) cc_final: 0.8843 (m110) REVERT: C 677 MET cc_start: 0.9750 (tpp) cc_final: 0.9316 (tmm) REVERT: C 681 ARG cc_start: 0.9272 (mmm160) cc_final: 0.8823 (tpm170) REVERT: C 694 ARG cc_start: 0.9617 (mtp-110) cc_final: 0.9303 (ttm110) REVERT: C 707 TYR cc_start: 0.9005 (t80) cc_final: 0.8291 (t80) REVERT: C 762 HIS cc_start: 0.8176 (m-70) cc_final: 0.7208 (m-70) REVERT: C 840 GLU cc_start: 0.9681 (mt-10) cc_final: 0.9139 (tp30) REVERT: C 841 VAL cc_start: 0.9859 (t) cc_final: 0.9605 (t) REVERT: C 844 MET cc_start: 0.9435 (mtm) cc_final: 0.8359 (mtm) REVERT: D 12 ASN cc_start: 0.9607 (t0) cc_final: 0.9212 (t0) REVERT: D 411 ASP cc_start: 0.9339 (t70) cc_final: 0.8797 (t0) REVERT: D 424 PHE cc_start: 0.9342 (m-80) cc_final: 0.8926 (m-80) REVERT: D 533 VAL cc_start: 0.9754 (t) cc_final: 0.9342 (p) REVERT: D 537 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8058 (ptp90) REVERT: D 538 LYS cc_start: 0.9502 (mmtm) cc_final: 0.9230 (mmtm) REVERT: D 541 ARG cc_start: 0.9219 (tpp80) cc_final: 0.8787 (tpp80) REVERT: D 617 PHE cc_start: 0.9575 (t80) cc_final: 0.9306 (t80) REVERT: D 658 ASN cc_start: 0.9191 (m110) cc_final: 0.8873 (m110) REVERT: D 677 MET cc_start: 0.9699 (tpp) cc_final: 0.9058 (tmm) REVERT: D 707 TYR cc_start: 0.9158 (t80) cc_final: 0.8928 (t80) REVERT: D 729 CYS cc_start: 0.9555 (m) cc_final: 0.9290 (m) REVERT: D 784 ARG cc_start: 0.9368 (mtp-110) cc_final: 0.8793 (ptm160) REVERT: D 840 GLU cc_start: 0.9691 (mt-10) cc_final: 0.9035 (tp30) REVERT: D 841 VAL cc_start: 0.9858 (t) cc_final: 0.9644 (t) REVERT: D 844 MET cc_start: 0.9438 (mtm) cc_final: 0.8536 (ptp) outliers start: 63 outliers final: 44 residues processed: 528 average time/residue: 0.2556 time to fit residues: 210.2791 Evaluate side-chains 519 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 471 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 537 ARG Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 762 HIS Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 129 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 chunk 62 optimal weight: 40.0000 chunk 99 optimal weight: 7.9990 chunk 155 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 187 optimal weight: 40.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS ** D 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.067811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.055283 restraints weight = 92904.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.056845 restraints weight = 59693.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.058007 restraints weight = 42990.113| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18004 Z= 0.136 Angle : 0.789 13.039 24432 Z= 0.379 Chirality : 0.046 0.324 2788 Planarity : 0.003 0.030 3064 Dihedral : 4.406 22.131 2420 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.94 % Favored : 95.70 % Rotamer: Outliers : 2.98 % Allowed : 28.95 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.17), residues: 2184 helix: -0.45 (0.14), residues: 1176 sheet: -0.40 (0.40), residues: 164 loop : -1.25 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 410 HIS 0.011 0.001 HIS A 834 PHE 0.024 0.001 PHE D 14 TYR 0.014 0.001 TYR B 43 ARG 0.007 0.000 ARG B 681 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 784) hydrogen bonds : angle 4.96746 ( 2280) covalent geometry : bond 0.00299 (18000) covalent geometry : angle 0.78886 (24432) Misc. bond : bond 0.00040 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 489 time to evaluate : 2.114 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: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.9385 (t70) cc_final: 0.8870 (t0) REVERT: A 538 LYS cc_start: 0.9384 (mmtm) cc_final: 0.9044 (mmtm) REVERT: A 541 ARG cc_start: 0.9185 (tpp80) cc_final: 0.8772 (tpp80) REVERT: A 619 PHE cc_start: 0.9677 (OUTLIER) cc_final: 0.9228 (t80) REVERT: A 645 MET cc_start: 0.9659 (ptm) cc_final: 0.9348 (ptm) REVERT: A 658 ASN cc_start: 0.9228 (m110) cc_final: 0.8934 (m110) REVERT: A 677 MET cc_start: 0.9522 (tpp) cc_final: 0.8918 (tmm) REVERT: A 681 ARG cc_start: 0.9565 (mtm180) cc_final: 0.9123 (mtm180) REVERT: A 729 CYS cc_start: 0.9626 (m) cc_final: 0.9371 (m) REVERT: A 821 ASP cc_start: 0.8884 (m-30) cc_final: 0.8559 (p0) REVERT: A 840 GLU cc_start: 0.9673 (mt-10) cc_final: 0.9194 (tp30) REVERT: B 48 PHE cc_start: 0.9566 (t80) cc_final: 0.9353 (t80) REVERT: B 411 ASP cc_start: 0.9349 (t70) cc_final: 0.8841 (t0) REVERT: B 424 PHE cc_start: 0.9437 (m-80) cc_final: 0.9030 (m-80) REVERT: B 538 LYS cc_start: 0.9260 (mmtm) cc_final: 0.8919 (mmtm) REVERT: B 541 ARG cc_start: 0.9207 (tpp80) cc_final: 0.8774 (tpp80) REVERT: B 563 TRP cc_start: 0.9688 (m-10) cc_final: 0.9388 (m-10) REVERT: B 619 PHE cc_start: 0.9718 (OUTLIER) cc_final: 0.9248 (t80) REVERT: B 645 MET cc_start: 0.9606 (ttm) cc_final: 0.9395 (ttm) REVERT: B 651 MET cc_start: 0.9546 (mmm) cc_final: 0.9330 (mmm) REVERT: B 658 ASN cc_start: 0.9200 (m110) cc_final: 0.8907 (m110) REVERT: B 677 MET cc_start: 0.9555 (tpp) cc_final: 0.9006 (tmm) REVERT: B 707 TYR cc_start: 0.9078 (t80) cc_final: 0.8566 (t80) REVERT: B 717 LEU cc_start: 0.9756 (tp) cc_final: 0.9390 (pp) REVERT: B 718 LYS cc_start: 0.9773 (tppt) cc_final: 0.9566 (mppt) REVERT: B 729 CYS cc_start: 0.9525 (m) cc_final: 0.9313 (m) REVERT: B 762 HIS cc_start: 0.8210 (m-70) cc_final: 0.6702 (m-70) REVERT: B 821 ASP cc_start: 0.9089 (m-30) cc_final: 0.8569 (p0) REVERT: C 411 ASP cc_start: 0.9415 (t70) cc_final: 0.8380 (t70) REVERT: C 424 PHE cc_start: 0.9401 (m-80) cc_final: 0.8974 (m-80) REVERT: C 538 LYS cc_start: 0.9481 (mmtm) cc_final: 0.9104 (mmtm) REVERT: C 541 ARG cc_start: 0.9252 (tpt-90) cc_final: 0.8796 (tpt-90) REVERT: C 563 TRP cc_start: 0.9663 (m-10) cc_final: 0.9403 (m-10) REVERT: C 574 MET cc_start: 0.8151 (mtt) cc_final: 0.7838 (tpt) REVERT: C 645 MET cc_start: 0.9653 (ttm) cc_final: 0.9446 (ptm) REVERT: C 658 ASN cc_start: 0.9138 (m110) cc_final: 0.8827 (m110) REVERT: C 677 MET cc_start: 0.9755 (tpp) cc_final: 0.8862 (tmm) REVERT: C 681 ARG cc_start: 0.9269 (mmm160) cc_final: 0.8937 (mmm-85) REVERT: C 694 ARG cc_start: 0.9637 (mtp-110) cc_final: 0.9313 (ttm110) REVERT: C 707 TYR cc_start: 0.9017 (t80) cc_final: 0.8318 (t80) REVERT: C 762 HIS cc_start: 0.8257 (m-70) cc_final: 0.7267 (m-70) REVERT: C 821 ASP cc_start: 0.9016 (m-30) cc_final: 0.8476 (p0) REVERT: C 827 TYR cc_start: 0.8598 (m-80) cc_final: 0.8262 (m-10) REVERT: C 840 GLU cc_start: 0.9688 (mt-10) cc_final: 0.9136 (tp30) REVERT: C 841 VAL cc_start: 0.9855 (t) cc_final: 0.9591 (t) REVERT: C 844 MET cc_start: 0.9464 (mtm) cc_final: 0.8356 (mtm) REVERT: D 12 ASN cc_start: 0.9625 (t0) cc_final: 0.9265 (t0) REVERT: D 411 ASP cc_start: 0.9342 (t70) cc_final: 0.8782 (t0) REVERT: D 424 PHE cc_start: 0.9375 (m-80) cc_final: 0.8950 (m-80) REVERT: D 533 VAL cc_start: 0.9745 (t) cc_final: 0.9341 (p) REVERT: D 537 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8056 (ptp90) REVERT: D 538 LYS cc_start: 0.9522 (mmtm) cc_final: 0.9237 (mmtm) REVERT: D 541 ARG cc_start: 0.9235 (tpp80) cc_final: 0.8805 (tpp80) REVERT: D 563 TRP cc_start: 0.9669 (m-10) cc_final: 0.9427 (m-10) REVERT: D 617 PHE cc_start: 0.9598 (t80) cc_final: 0.9338 (t80) REVERT: D 658 ASN cc_start: 0.9172 (m110) cc_final: 0.8861 (m110) REVERT: D 677 MET cc_start: 0.9712 (tpp) cc_final: 0.9080 (tmm) REVERT: D 707 TYR cc_start: 0.9218 (t80) cc_final: 0.8972 (t80) REVERT: D 729 CYS cc_start: 0.9536 (m) cc_final: 0.9306 (m) REVERT: D 840 GLU cc_start: 0.9697 (mt-10) cc_final: 0.9054 (tp30) REVERT: D 841 VAL cc_start: 0.9859 (t) cc_final: 0.9640 (t) REVERT: D 844 MET cc_start: 0.9442 (mtm) cc_final: 0.8558 (ptp) outliers start: 55 outliers final: 47 residues processed: 518 average time/residue: 0.2669 time to fit residues: 213.8532 Evaluate side-chains 522 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 472 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 537 ARG Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 762 HIS Chi-restraints excluded: chain D residue 787 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 191 optimal weight: 6.9990 chunk 17 optimal weight: 40.0000 chunk 151 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 203 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 65 optimal weight: 50.0000 chunk 40 optimal weight: 20.0000 chunk 2 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.067290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.054891 restraints weight = 94267.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.056459 restraints weight = 60529.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057621 restraints weight = 43469.713| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18004 Z= 0.145 Angle : 0.803 13.884 24432 Z= 0.388 Chirality : 0.047 0.324 2788 Planarity : 0.003 0.031 3064 Dihedral : 4.437 22.561 2420 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.85 % Favored : 95.79 % Rotamer: Outliers : 3.30 % Allowed : 29.44 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.18), residues: 2184 helix: -0.40 (0.15), residues: 1200 sheet: -0.76 (0.34), residues: 212 loop : -1.09 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 410 HIS 0.011 0.001 HIS D 762 PHE 0.045 0.001 PHE B 640 TYR 0.017 0.001 TYR D 569 ARG 0.006 0.001 ARG C 679 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 784) hydrogen bonds : angle 5.03130 ( 2280) covalent geometry : bond 0.00318 (18000) covalent geometry : angle 0.80319 (24432) Misc. bond : bond 0.00054 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 475 time to evaluate : 2.082 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: A 109 LEU cc_start: 0.9313 (tp) cc_final: 0.8641 (pp) REVERT: A 411 ASP cc_start: 0.9370 (t70) cc_final: 0.8818 (t0) REVERT: A 538 LYS cc_start: 0.9403 (mmtm) cc_final: 0.9067 (mmtm) REVERT: A 541 ARG cc_start: 0.9197 (tpp80) cc_final: 0.8792 (tpp80) REVERT: A 619 PHE cc_start: 0.9690 (OUTLIER) cc_final: 0.9363 (t80) REVERT: A 645 MET cc_start: 0.9671 (ptm) cc_final: 0.9339 (ptm) REVERT: A 658 ASN cc_start: 0.9212 (m110) cc_final: 0.8919 (m110) REVERT: A 677 MET cc_start: 0.9526 (tpp) cc_final: 0.8940 (tmm) REVERT: A 681 ARG cc_start: 0.9589 (mtm180) cc_final: 0.9106 (mtm180) REVERT: A 729 CYS cc_start: 0.9602 (m) cc_final: 0.9364 (m) REVERT: A 821 ASP cc_start: 0.8905 (m-30) cc_final: 0.8546 (p0) REVERT: A 840 GLU cc_start: 0.9681 (mt-10) cc_final: 0.9192 (tp30) REVERT: B 48 PHE cc_start: 0.9579 (t80) cc_final: 0.9364 (t80) REVERT: B 411 ASP cc_start: 0.9365 (t70) cc_final: 0.8840 (t0) REVERT: B 424 PHE cc_start: 0.9444 (m-80) cc_final: 0.9022 (m-80) REVERT: B 538 LYS cc_start: 0.9282 (mmtm) cc_final: 0.8913 (mmtm) REVERT: B 541 ARG cc_start: 0.9232 (tpp80) cc_final: 0.8806 (tpp80) REVERT: B 619 PHE cc_start: 0.9725 (OUTLIER) cc_final: 0.9250 (t80) REVERT: B 645 MET cc_start: 0.9607 (ttm) cc_final: 0.9393 (ttm) REVERT: B 651 MET cc_start: 0.9541 (mmm) cc_final: 0.9326 (mmm) REVERT: B 658 ASN cc_start: 0.9196 (m110) cc_final: 0.8905 (m110) REVERT: B 681 ARG cc_start: 0.9364 (mmm-85) cc_final: 0.9151 (mtm110) REVERT: B 707 TYR cc_start: 0.9094 (t80) cc_final: 0.8775 (t80) REVERT: B 729 CYS cc_start: 0.9530 (m) cc_final: 0.9282 (m) REVERT: B 821 ASP cc_start: 0.9060 (m-30) cc_final: 0.8557 (p0) REVERT: C 12 ASN cc_start: 0.9644 (t0) cc_final: 0.9318 (t0) REVERT: C 109 LEU cc_start: 0.9304 (tp) cc_final: 0.8638 (pp) REVERT: C 411 ASP cc_start: 0.9413 (t70) cc_final: 0.8266 (t70) REVERT: C 424 PHE cc_start: 0.9413 (m-80) cc_final: 0.8981 (m-80) REVERT: C 538 LYS cc_start: 0.9485 (mmtm) cc_final: 0.9119 (mmtm) REVERT: C 541 ARG cc_start: 0.9249 (tpt-90) cc_final: 0.8872 (tpt-90) REVERT: C 563 TRP cc_start: 0.9673 (m-10) cc_final: 0.9436 (m-10) REVERT: C 574 MET cc_start: 0.8210 (mtt) cc_final: 0.7865 (tpt) REVERT: C 645 MET cc_start: 0.9652 (ttm) cc_final: 0.9424 (ptm) REVERT: C 658 ASN cc_start: 0.9132 (m110) cc_final: 0.8827 (m110) REVERT: C 677 MET cc_start: 0.9757 (tpp) cc_final: 0.8871 (tmm) REVERT: C 681 ARG cc_start: 0.9269 (mmm160) cc_final: 0.8931 (mmm-85) REVERT: C 694 ARG cc_start: 0.9634 (mtp-110) cc_final: 0.9319 (ttm110) REVERT: C 707 TYR cc_start: 0.9001 (t80) cc_final: 0.8418 (t80) REVERT: C 762 HIS cc_start: 0.8295 (m-70) cc_final: 0.7009 (m-70) REVERT: C 821 ASP cc_start: 0.9041 (m-30) cc_final: 0.8490 (p0) REVERT: C 827 TYR cc_start: 0.8595 (m-80) cc_final: 0.8306 (m-80) REVERT: C 840 GLU cc_start: 0.9702 (mt-10) cc_final: 0.9152 (tp30) REVERT: C 841 VAL cc_start: 0.9854 (t) cc_final: 0.9589 (t) REVERT: C 844 MET cc_start: 0.9457 (mtm) cc_final: 0.8325 (mtm) REVERT: D 12 ASN cc_start: 0.9630 (t0) cc_final: 0.9263 (t0) REVERT: D 411 ASP cc_start: 0.9351 (t70) cc_final: 0.8783 (t0) REVERT: D 533 VAL cc_start: 0.9742 (t) cc_final: 0.9334 (p) REVERT: D 537 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8070 (ptp90) REVERT: D 538 LYS cc_start: 0.9536 (mmtm) cc_final: 0.9265 (mmtm) REVERT: D 541 ARG cc_start: 0.9246 (tpp80) cc_final: 0.8815 (tpp80) REVERT: D 563 TRP cc_start: 0.9676 (m-10) cc_final: 0.9438 (m-10) REVERT: D 658 ASN cc_start: 0.9166 (m110) cc_final: 0.8858 (m110) REVERT: D 677 MET cc_start: 0.9716 (tpp) cc_final: 0.9079 (tmm) REVERT: D 729 CYS cc_start: 0.9537 (m) cc_final: 0.9288 (m) REVERT: D 784 ARG cc_start: 0.9455 (mtp-110) cc_final: 0.8749 (ptm160) REVERT: D 821 ASP cc_start: 0.8994 (m-30) cc_final: 0.8438 (p0) REVERT: D 840 GLU cc_start: 0.9709 (mt-10) cc_final: 0.9093 (tp30) REVERT: D 841 VAL cc_start: 0.9852 (t) cc_final: 0.9642 (t) REVERT: D 844 MET cc_start: 0.9436 (mtm) cc_final: 0.8518 (ptp) outliers start: 61 outliers final: 50 residues processed: 508 average time/residue: 0.2786 time to fit residues: 219.5641 Evaluate side-chains 519 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 466 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 537 ARG Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 762 HIS Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 787 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 191 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 chunk 64 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 137 optimal weight: 30.0000 chunk 217 optimal weight: 50.0000 chunk 83 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 117 optimal weight: 40.0000 chunk 46 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 GLN ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS ** D 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.068904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.056263 restraints weight = 92068.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.057869 restraints weight = 59082.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059060 restraints weight = 42447.580| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.6764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18004 Z= 0.137 Angle : 0.850 14.964 24432 Z= 0.401 Chirality : 0.047 0.341 2788 Planarity : 0.003 0.044 3064 Dihedral : 4.381 21.047 2420 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.03 % Favored : 95.60 % Rotamer: Outliers : 2.44 % Allowed : 30.63 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.18), residues: 2184 helix: -0.51 (0.15), residues: 1176 sheet: -0.66 (0.34), residues: 212 loop : -1.11 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP D 410 HIS 0.010 0.001 HIS B 674 PHE 0.048 0.002 PHE C 640 TYR 0.036 0.001 TYR B 673 ARG 0.009 0.001 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 784) hydrogen bonds : angle 5.01484 ( 2280) covalent geometry : bond 0.00293 (18000) covalent geometry : angle 0.84990 (24432) Misc. bond : bond 0.00057 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 489 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.9300 (tp) cc_final: 0.8645 (pp) REVERT: A 411 ASP cc_start: 0.9394 (t70) cc_final: 0.8861 (t0) REVERT: A 538 LYS cc_start: 0.9396 (mmtm) cc_final: 0.9056 (mmtm) REVERT: A 541 ARG cc_start: 0.9171 (tpp80) cc_final: 0.8800 (tpp80) REVERT: A 619 PHE cc_start: 0.9674 (OUTLIER) cc_final: 0.9322 (t80) REVERT: A 645 MET cc_start: 0.9648 (ptm) cc_final: 0.9363 (ptm) REVERT: A 658 ASN cc_start: 0.9202 (m110) cc_final: 0.8908 (m110) REVERT: A 677 MET cc_start: 0.9530 (tpp) cc_final: 0.8678 (tmm) REVERT: A 681 ARG cc_start: 0.9576 (mtm180) cc_final: 0.8634 (mmm-85) REVERT: A 729 CYS cc_start: 0.9613 (m) cc_final: 0.9359 (m) REVERT: A 821 ASP cc_start: 0.8925 (m-30) cc_final: 0.8544 (p0) REVERT: A 840 GLU cc_start: 0.9684 (mt-10) cc_final: 0.9203 (tp30) REVERT: B 48 PHE cc_start: 0.9589 (t80) cc_final: 0.9371 (t80) REVERT: B 411 ASP cc_start: 0.9360 (t70) cc_final: 0.8868 (t0) REVERT: B 424 PHE cc_start: 0.9422 (m-80) cc_final: 0.9005 (m-80) REVERT: B 538 LYS cc_start: 0.9291 (mmtm) cc_final: 0.8919 (mmtm) REVERT: B 541 ARG cc_start: 0.9212 (tpp80) cc_final: 0.8822 (tpp80) REVERT: B 563 TRP cc_start: 0.9651 (m-10) cc_final: 0.9414 (m-10) REVERT: B 619 PHE cc_start: 0.9692 (OUTLIER) cc_final: 0.9259 (t80) REVERT: B 645 MET cc_start: 0.9625 (ttm) cc_final: 0.9338 (ttm) REVERT: B 651 MET cc_start: 0.9543 (mmm) cc_final: 0.9319 (mmm) REVERT: B 658 ASN cc_start: 0.9157 (m110) cc_final: 0.8859 (m110) REVERT: B 673 TYR cc_start: 0.9606 (t80) cc_final: 0.9303 (t80) REVERT: B 677 MET cc_start: 0.9640 (mmt) cc_final: 0.9029 (mmt) REVERT: B 681 ARG cc_start: 0.9533 (mmm-85) cc_final: 0.9059 (mtm-85) REVERT: B 707 TYR cc_start: 0.9146 (t80) cc_final: 0.8844 (t80) REVERT: B 717 LEU cc_start: 0.9740 (tp) cc_final: 0.9376 (pp) REVERT: B 718 LYS cc_start: 0.9779 (tppt) cc_final: 0.9563 (mppt) REVERT: B 729 CYS cc_start: 0.9506 (m) cc_final: 0.9257 (m) REVERT: B 821 ASP cc_start: 0.9037 (m-30) cc_final: 0.8568 (p0) REVERT: C 12 ASN cc_start: 0.9644 (t0) cc_final: 0.9307 (t0) REVERT: C 109 LEU cc_start: 0.9286 (tp) cc_final: 0.8625 (pp) REVERT: C 411 ASP cc_start: 0.9402 (t70) cc_final: 0.8408 (t70) REVERT: C 424 PHE cc_start: 0.9400 (m-80) cc_final: 0.8966 (m-80) REVERT: C 538 LYS cc_start: 0.9483 (mmtm) cc_final: 0.9121 (mmtm) REVERT: C 541 ARG cc_start: 0.9212 (tpt-90) cc_final: 0.8696 (tpt-90) REVERT: C 563 TRP cc_start: 0.9658 (m-10) cc_final: 0.9426 (m-10) REVERT: C 574 MET cc_start: 0.8150 (mtt) cc_final: 0.7823 (tpt) REVERT: C 645 MET cc_start: 0.9662 (ttm) cc_final: 0.9453 (ptm) REVERT: C 658 ASN cc_start: 0.9104 (m110) cc_final: 0.8797 (m110) REVERT: C 677 MET cc_start: 0.9749 (tpp) cc_final: 0.8950 (tmm) REVERT: C 681 ARG cc_start: 0.9264 (mmm160) cc_final: 0.8908 (mmm-85) REVERT: C 694 ARG cc_start: 0.9635 (mtp-110) cc_final: 0.9311 (ttm110) REVERT: C 707 TYR cc_start: 0.9005 (t80) cc_final: 0.8309 (t80) REVERT: C 762 HIS cc_start: 0.8381 (m-70) cc_final: 0.7404 (m-70) REVERT: C 788 GLU cc_start: 0.8989 (pm20) cc_final: 0.8701 (pm20) REVERT: C 821 ASP cc_start: 0.9052 (m-30) cc_final: 0.8489 (p0) REVERT: C 827 TYR cc_start: 0.8556 (m-80) cc_final: 0.8265 (m-10) REVERT: C 840 GLU cc_start: 0.9700 (mt-10) cc_final: 0.9155 (tp30) REVERT: C 841 VAL cc_start: 0.9835 (t) cc_final: 0.9577 (t) REVERT: C 844 MET cc_start: 0.9432 (mtm) cc_final: 0.8284 (mtm) REVERT: D 12 ASN cc_start: 0.9638 (t0) cc_final: 0.9271 (t0) REVERT: D 411 ASP cc_start: 0.9330 (t70) cc_final: 0.8766 (t0) REVERT: D 533 VAL cc_start: 0.9730 (t) cc_final: 0.9476 (p) REVERT: D 538 LYS cc_start: 0.9530 (mmtm) cc_final: 0.9218 (mmtm) REVERT: D 541 ARG cc_start: 0.9232 (tpp80) cc_final: 0.8836 (tpp80) REVERT: D 562 HIS cc_start: 0.9186 (t70) cc_final: 0.8931 (t-170) REVERT: D 563 TRP cc_start: 0.9663 (m-10) cc_final: 0.9429 (m-10) REVERT: D 658 ASN cc_start: 0.9140 (m110) cc_final: 0.8831 (m110) REVERT: D 677 MET cc_start: 0.9704 (tpp) cc_final: 0.9076 (tmm) REVERT: D 717 LEU cc_start: 0.9698 (tp) cc_final: 0.9373 (pp) REVERT: D 718 LYS cc_start: 0.9823 (mttt) cc_final: 0.9601 (mmtp) REVERT: D 729 CYS cc_start: 0.9527 (m) cc_final: 0.9304 (m) REVERT: D 821 ASP cc_start: 0.8978 (m-30) cc_final: 0.8385 (p0) REVERT: D 840 GLU cc_start: 0.9707 (mt-10) cc_final: 0.9084 (tp30) REVERT: D 844 MET cc_start: 0.9425 (mtm) cc_final: 0.8537 (ptp) outliers start: 45 outliers final: 38 residues processed: 513 average time/residue: 0.2789 time to fit residues: 223.0582 Evaluate side-chains 512 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 472 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 762 HIS Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 787 ILE Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 102 optimal weight: 0.2980 chunk 94 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 113 optimal weight: 50.0000 chunk 18 optimal weight: 7.9990 chunk 57 optimal weight: 50.0000 chunk 133 optimal weight: 9.9990 chunk 6 optimal weight: 50.0000 chunk 85 optimal weight: 0.8980 chunk 77 optimal weight: 0.0570 chunk 16 optimal weight: 7.9990 overall best weight: 3.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 GLN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS ** D 834 HIS ** 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 = 0.3352 r_free = 0.3352 target = 0.068765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.056158 restraints weight = 94294.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.057742 restraints weight = 60677.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058910 restraints weight = 43657.294| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.6869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18004 Z= 0.137 Angle : 0.862 16.406 24432 Z= 0.404 Chirality : 0.047 0.347 2788 Planarity : 0.003 0.035 3064 Dihedral : 4.375 21.162 2420 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.94 % Favored : 95.70 % Rotamer: Outliers : 2.71 % Allowed : 31.33 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.18), residues: 2184 helix: -0.51 (0.14), residues: 1200 sheet: -0.38 (0.33), residues: 260 loop : -0.97 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP B 410 HIS 0.008 0.001 HIS D 762 PHE 0.043 0.001 PHE C 640 TYR 0.044 0.001 TYR B 673 ARG 0.009 0.001 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.04422 ( 784) hydrogen bonds : angle 5.05649 ( 2280) covalent geometry : bond 0.00301 (18000) covalent geometry : angle 0.86238 (24432) Misc. bond : bond 0.00045 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9273.36 seconds wall clock time: 162 minutes 16.45 seconds (9736.45 seconds total)