Starting phenix.real_space_refine on Thu Sep 18 13:47:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5va2_8651/09_2025/5va2_8651.cif Found real_map, /net/cci-nas-00/data/ceres_data/5va2_8651/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/5va2_8651/09_2025/5va2_8651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5va2_8651/09_2025/5va2_8651.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5va2_8651/09_2025/5va2_8651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5va2_8651/09_2025/5va2_8651.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.436 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'ASP:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 63 Restraints were copied for chains: B, C, D Time building chain proxies: 3.76, per 1000 atoms: 0.21 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: 1.27 Conformation dependent library (CDL) restraints added in 669.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.60 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: 2.68 Time building geometry restraints manager: 1.64 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.000 Extract box with map and model: 0.900 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.710 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.690 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.86 (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 ARG 0.003 0.000 ARG A 694 TYR 0.013 0.001 TYR D 652 PHE 0.011 0.001 PHE D 494 TRP 0.008 0.001 TRP D 705 HIS 0.005 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00785 (18000) covalent geometry : angle 1.08056 (24432) hydrogen bonds : bond 0.28900 ( 784) hydrogen bonds : angle 8.66493 ( 2280) 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 : 0.602 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: 0.1264 time to fit residues: 167.9794 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 : 0.645 ------------------------------------------------------------------------------- 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 216 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 470 ASN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN A 731 HIS A 834 HIS B 12 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.067806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.055008 restraints weight = 91333.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.056560 restraints weight = 58130.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.057697 restraints weight = 41868.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.058552 restraints weight = 32498.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.059174 restraints weight = 26665.955| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18004 Z= 0.186 Angle : 0.825 9.713 24432 Z= 0.419 Chirality : 0.047 0.187 2788 Planarity : 0.005 0.057 3064 Dihedral : 5.412 34.379 2424 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.76 % Favored : 94.51 % Rotamer: Outliers : 4.44 % Allowed : 18.18 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.17), residues: 2184 helix: -0.72 (0.14), residues: 1192 sheet: -2.37 (0.36), residues: 152 loop : -2.02 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 694 TYR 0.023 0.002 TYR B 700 PHE 0.017 0.002 PHE B 617 TRP 0.028 0.002 TRP B 497 HIS 0.008 0.002 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00394 (18000) covalent geometry : angle 0.82529 (24432) hydrogen bonds : bond 0.05979 ( 784) hydrogen bonds : angle 5.41641 ( 2280) Misc. bond : bond 0.00137 ( 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 676 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 594 time to evaluate : 0.508 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 43 TYR cc_start: 0.9268 (t80) cc_final: 0.8923 (t80) REVERT: A 424 PHE cc_start: 0.9259 (m-80) cc_final: 0.8963 (m-80) REVERT: A 533 VAL cc_start: 0.9723 (t) cc_final: 0.9413 (p) REVERT: A 574 MET cc_start: 0.8029 (mtt) cc_final: 0.7707 (ppp) REVERT: A 677 MET cc_start: 0.9692 (tpp) cc_final: 0.9236 (mmm) REVERT: A 678 LEU cc_start: 0.9727 (mt) cc_final: 0.9511 (mt) REVERT: A 711 ILE cc_start: 0.8397 (mt) cc_final: 0.5772 (mm) REVERT: A 737 LEU cc_start: 0.9645 (mp) cc_final: 0.9439 (mp) REVERT: A 768 THR cc_start: 0.8209 (p) cc_final: 0.7977 (p) REVERT: A 823 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7744 (mmp80) REVERT: A 832 LYS cc_start: 0.9701 (tttt) cc_final: 0.9465 (ttpp) REVERT: A 833 ILE cc_start: 0.9630 (pt) cc_final: 0.9357 (tp) REVERT: A 840 GLU cc_start: 0.9555 (mt-10) cc_final: 0.9295 (tm-30) REVERT: B 424 PHE cc_start: 0.9290 (m-80) cc_final: 0.9005 (m-80) REVERT: B 533 VAL cc_start: 0.9706 (t) cc_final: 0.9489 (p) REVERT: B 563 TRP cc_start: 0.9548 (m-10) cc_final: 0.9226 (m-10) REVERT: B 574 MET cc_start: 0.8033 (mtt) cc_final: 0.7657 (ppp) REVERT: B 651 MET cc_start: 0.9388 (mmm) cc_final: 0.9166 (mmm) REVERT: B 677 MET cc_start: 0.9701 (tpp) cc_final: 0.9277 (mmm) REVERT: B 678 LEU cc_start: 0.9732 (mt) cc_final: 0.9330 (mt) REVERT: B 712 ASP cc_start: 0.9449 (m-30) cc_final: 0.9244 (p0) REVERT: B 729 CYS cc_start: 0.9664 (m) cc_final: 0.9458 (m) REVERT: B 768 THR cc_start: 0.8230 (p) cc_final: 0.7964 (p) REVERT: B 804 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9146 (mm) REVERT: B 832 LYS cc_start: 0.9673 (tttt) cc_final: 0.9445 (ttpp) REVERT: B 833 ILE cc_start: 0.9654 (pt) cc_final: 0.9431 (tp) REVERT: B 843 ASP cc_start: 0.9348 (m-30) cc_final: 0.9130 (m-30) REVERT: C 12 ASN cc_start: 0.9278 (OUTLIER) cc_final: 0.8972 (t0) REVERT: C 43 TYR cc_start: 0.9278 (t80) cc_final: 0.8967 (t80) REVERT: C 59 VAL cc_start: 0.9406 (t) cc_final: 0.9161 (m) REVERT: C 60 MET cc_start: 0.7822 (mmm) cc_final: 0.7524 (mmm) REVERT: C 424 PHE cc_start: 0.9350 (m-80) cc_final: 0.9086 (m-80) REVERT: C 533 VAL cc_start: 0.9704 (t) cc_final: 0.9201 (p) REVERT: C 534 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8957 (mmm160) REVERT: C 563 TRP cc_start: 0.9520 (m-10) cc_final: 0.9281 (m-10) REVERT: C 574 MET cc_start: 0.8002 (mtt) cc_final: 0.7599 (ppp) REVERT: C 575 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7727 (tp30) REVERT: C 651 MET cc_start: 0.9370 (mmm) cc_final: 0.9141 (mmm) REVERT: C 677 MET cc_start: 0.9706 (tpp) cc_final: 0.9290 (mmm) REVERT: C 712 ASP cc_start: 0.9398 (m-30) cc_final: 0.9175 (p0) REVERT: C 729 CYS cc_start: 0.9624 (m) cc_final: 0.9383 (m) REVERT: C 737 LEU cc_start: 0.9648 (mp) cc_final: 0.9420 (mp) REVERT: C 804 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9196 (mm) REVERT: C 821 ASP cc_start: 0.8881 (m-30) cc_final: 0.8633 (p0) REVERT: C 823 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7882 (mmp80) REVERT: C 832 LYS cc_start: 0.9668 (tttt) cc_final: 0.9450 (ttpp) REVERT: C 833 ILE cc_start: 0.9685 (pt) cc_final: 0.9434 (tp) REVERT: C 840 GLU cc_start: 0.9546 (mt-10) cc_final: 0.9253 (tm-30) REVERT: D 12 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.9017 (t0) REVERT: D 43 TYR cc_start: 0.9178 (t80) cc_final: 0.8937 (t80) REVERT: D 424 PHE cc_start: 0.9355 (m-80) cc_final: 0.9018 (m-80) REVERT: D 533 VAL cc_start: 0.9694 (t) cc_final: 0.9355 (p) REVERT: D 574 MET cc_start: 0.7962 (mtt) cc_final: 0.7540 (ppp) REVERT: D 619 PHE cc_start: 0.9640 (OUTLIER) cc_final: 0.9008 (t80) REVERT: D 677 MET cc_start: 0.9691 (tpp) cc_final: 0.9214 (tmm) REVERT: D 729 CYS cc_start: 0.9582 (m) cc_final: 0.9339 (m) REVERT: D 784 ARG cc_start: 0.9151 (mtp85) cc_final: 0.8516 (ptm160) REVERT: D 823 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.7982 (mmp80) REVERT: D 827 TYR cc_start: 0.8567 (m-80) cc_final: 0.8110 (m-80) REVERT: D 832 LYS cc_start: 0.9696 (tttt) cc_final: 0.9487 (ttpp) REVERT: D 833 ILE cc_start: 0.9688 (pt) cc_final: 0.9424 (tp) REVERT: D 840 GLU cc_start: 0.9570 (mt-10) cc_final: 0.9284 (tm-30) outliers start: 82 outliers final: 45 residues processed: 645 average time/residue: 0.1156 time to fit residues: 111.7039 Evaluate side-chains 543 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 489 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 421 THR 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 698 GLU 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 A residue 858 ILE Chi-restraints excluded: chain B residue 7 HIS Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 698 GLU 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 858 ILE Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 534 ARG 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 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 60 MET Chi-restraints excluded: chain D residue 421 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 619 PHE Chi-restraints excluded: chain D residue 641 SER 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 Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 50.0000 chunk 109 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 28 optimal weight: 0.0010 chunk 128 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 71 optimal weight: 40.0000 chunk 141 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- 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 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 ASN A 739 HIS B 12 ASN B 61 GLN B 562 HIS ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 ASN B 739 HIS ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 HIS ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 HIS ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.084347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.071017 restraints weight = 87480.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.072547 restraints weight = 57503.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.073684 restraints weight = 42210.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.074539 restraints weight = 33294.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.075185 restraints weight = 27582.978| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18004 Z= 0.148 Angle : 0.794 12.773 24432 Z= 0.386 Chirality : 0.046 0.253 2788 Planarity : 0.005 0.104 3064 Dihedral : 5.013 36.301 2424 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.35 % Favored : 94.92 % Rotamer: Outliers : 4.33 % Allowed : 20.51 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.17), residues: 2184 helix: -0.48 (0.14), residues: 1204 sheet: -1.42 (0.42), residues: 132 loop : -1.84 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 537 TYR 0.016 0.001 TYR B 700 PHE 0.027 0.002 PHE B 48 TRP 0.022 0.002 TRP A 410 HIS 0.006 0.001 HIS C 831 Details of bonding type rmsd covalent geometry : bond 0.00315 (18000) covalent geometry : angle 0.79359 (24432) hydrogen bonds : bond 0.04962 ( 784) hydrogen bonds : angle 5.05320 ( 2280) Misc. bond : bond 0.00055 ( 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 603 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 523 time to evaluate : 0.570 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: A 424 PHE cc_start: 0.9232 (m-80) cc_final: 0.8899 (m-80) REVERT: A 533 VAL cc_start: 0.9764 (t) cc_final: 0.9403 (p) REVERT: A 537 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8144 (ptp90) REVERT: A 538 LYS cc_start: 0.9278 (mmtm) cc_final: 0.8879 (mmtm) REVERT: A 541 ARG cc_start: 0.9133 (tpp80) cc_final: 0.8907 (tpp80) REVERT: A 574 MET cc_start: 0.8023 (mtt) cc_final: 0.7782 (tpt) REVERT: A 651 MET cc_start: 0.9483 (mmm) cc_final: 0.9260 (mmm) REVERT: A 677 MET cc_start: 0.9515 (tpp) cc_final: 0.8989 (tpp) REVERT: A 768 THR cc_start: 0.8067 (p) cc_final: 0.7835 (p) REVERT: A 779 LEU cc_start: 0.9862 (tp) cc_final: 0.9643 (mm) REVERT: A 784 ARG cc_start: 0.9147 (mtp85) cc_final: 0.8431 (ptm160) REVERT: A 832 LYS cc_start: 0.9677 (tttt) cc_final: 0.9464 (ttpp) REVERT: A 840 GLU cc_start: 0.9696 (mt-10) cc_final: 0.9223 (tp30) REVERT: A 841 VAL cc_start: 0.9856 (t) cc_final: 0.9649 (t) REVERT: B 410 TRP cc_start: 0.9312 (t60) cc_final: 0.9060 (t60) REVERT: B 424 PHE cc_start: 0.9312 (m-80) cc_final: 0.8973 (m-80) REVERT: B 533 VAL cc_start: 0.9752 (t) cc_final: 0.9520 (p) REVERT: B 541 ARG cc_start: 0.9111 (tpp80) cc_final: 0.8885 (tpp80) REVERT: B 563 TRP cc_start: 0.9508 (m-10) cc_final: 0.9091 (m-10) REVERT: B 574 MET cc_start: 0.8024 (mtt) cc_final: 0.7790 (tpt) REVERT: B 645 MET cc_start: 0.9191 (ttm) cc_final: 0.8613 (ttt) REVERT: B 651 MET cc_start: 0.9435 (mmm) cc_final: 0.9182 (mmm) REVERT: B 729 CYS cc_start: 0.9590 (m) cc_final: 0.9365 (m) REVERT: B 751 LEU cc_start: 0.9773 (mt) cc_final: 0.9558 (pp) REVERT: B 768 THR cc_start: 0.8174 (p) cc_final: 0.7907 (p) REVERT: B 779 LEU cc_start: 0.9869 (tp) cc_final: 0.9600 (mm) REVERT: B 832 LYS cc_start: 0.9676 (tttt) cc_final: 0.9438 (ttpp) REVERT: C 43 TYR cc_start: 0.9199 (t80) cc_final: 0.8839 (t80) REVERT: C 59 VAL cc_start: 0.9282 (t) cc_final: 0.8853 (p) REVERT: C 60 MET cc_start: 0.7882 (mmm) cc_final: 0.7601 (mmm) REVERT: C 411 ASP cc_start: 0.9247 (t70) cc_final: 0.8336 (t0) REVERT: C 424 PHE cc_start: 0.9378 (m-80) cc_final: 0.9054 (m-80) REVERT: C 533 VAL cc_start: 0.9732 (t) cc_final: 0.9513 (p) REVERT: C 541 ARG cc_start: 0.9151 (tpt-90) cc_final: 0.8703 (tpt-90) REVERT: C 563 TRP cc_start: 0.9539 (m-10) cc_final: 0.9111 (m-10) REVERT: C 574 MET cc_start: 0.8040 (mtt) cc_final: 0.7724 (tpt) REVERT: C 619 PHE cc_start: 0.9612 (OUTLIER) cc_final: 0.9043 (t80) REVERT: C 651 MET cc_start: 0.9481 (mmm) cc_final: 0.9201 (mmm) REVERT: C 698 GLU cc_start: 0.9511 (pt0) cc_final: 0.9233 (pp20) REVERT: C 712 ASP cc_start: 0.9398 (m-30) cc_final: 0.9193 (p0) REVERT: C 729 CYS cc_start: 0.9638 (m) cc_final: 0.9427 (m) REVERT: C 751 LEU cc_start: 0.9785 (mt) cc_final: 0.9540 (pp) REVERT: C 779 LEU cc_start: 0.9862 (tp) cc_final: 0.9630 (mm) REVERT: C 821 ASP cc_start: 0.8873 (m-30) cc_final: 0.8518 (p0) REVERT: C 827 TYR cc_start: 0.8575 (m-80) cc_final: 0.8244 (m-80) REVERT: C 840 GLU cc_start: 0.9665 (mt-10) cc_final: 0.9117 (tp30) REVERT: C 841 VAL cc_start: 0.9830 (t) cc_final: 0.9517 (t) REVERT: C 844 MET cc_start: 0.9396 (mtm) cc_final: 0.8095 (mtm) REVERT: D 43 TYR cc_start: 0.9179 (t80) cc_final: 0.8837 (t80) REVERT: D 424 PHE cc_start: 0.9322 (m-80) cc_final: 0.8962 (m-80) REVERT: D 533 VAL cc_start: 0.9743 (t) cc_final: 0.9354 (p) REVERT: D 537 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8053 (ptp90) REVERT: D 538 LYS cc_start: 0.9289 (mmtm) cc_final: 0.8914 (mmtm) REVERT: D 541 ARG cc_start: 0.9234 (tpp80) cc_final: 0.9026 (tpp80) REVERT: D 574 MET cc_start: 0.7952 (mtt) cc_final: 0.7654 (tpt) REVERT: D 651 MET cc_start: 0.9366 (mmm) cc_final: 0.9150 (mmm) REVERT: D 677 MET cc_start: 0.9671 (tpp) cc_final: 0.8790 (tmm) REVERT: D 681 ARG cc_start: 0.9318 (mmm160) cc_final: 0.9073 (mmm-85) REVERT: D 695 GLN cc_start: 0.9652 (mt0) cc_final: 0.9407 (mm110) REVERT: D 698 GLU cc_start: 0.9468 (pt0) cc_final: 0.9149 (pp20) REVERT: D 729 CYS cc_start: 0.9586 (m) cc_final: 0.9354 (m) REVERT: D 784 ARG cc_start: 0.9131 (mtp85) cc_final: 0.8428 (ptm160) REVERT: D 840 GLU cc_start: 0.9684 (mt-10) cc_final: 0.9230 (tp30) REVERT: D 841 VAL cc_start: 0.9851 (t) cc_final: 0.9646 (t) outliers start: 80 outliers final: 46 residues processed: 578 average time/residue: 0.1086 time to fit residues: 96.5723 Evaluate side-chains 528 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 479 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 537 ARG Chi-restraints excluded: chain A residue 539 LEU 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 804 ILE 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 483 VAL Chi-restraints excluded: chain B residue 539 LEU 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 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 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 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 714 ASN 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 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 641 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 711 ILE Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 768 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 98 optimal weight: 0.0000 chunk 173 optimal weight: 50.0000 chunk 16 optimal weight: 0.4980 chunk 180 optimal weight: 5.9990 chunk 146 optimal weight: 50.0000 chunk 218 optimal weight: 0.8980 chunk 2 optimal weight: 50.0000 chunk 27 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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 658 ASN A 676 GLN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 702 GLN ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 61 GLN C 70 HIS ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 691 ASN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 ASN ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.069207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.055832 restraints weight = 90058.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.057407 restraints weight = 58508.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058576 restraints weight = 42493.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059454 restraints weight = 33139.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.060121 restraints weight = 27189.655| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18004 Z= 0.133 Angle : 0.743 12.416 24432 Z= 0.360 Chirality : 0.044 0.164 2788 Planarity : 0.004 0.035 3064 Dihedral : 4.666 19.149 2420 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.69 % Allowed : 4.17 % Favored : 95.15 % Rotamer: Outliers : 3.57 % Allowed : 20.29 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.17), residues: 2184 helix: -0.50 (0.15), residues: 1172 sheet: -1.07 (0.46), residues: 112 loop : -1.63 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 537 TYR 0.020 0.001 TYR B 700 PHE 0.021 0.001 PHE C 701 TRP 0.026 0.002 TRP A 410 HIS 0.007 0.001 HIS B 731 Details of bonding type rmsd covalent geometry : bond 0.00285 (18000) covalent geometry : angle 0.74326 (24432) hydrogen bonds : bond 0.04528 ( 784) hydrogen bonds : angle 4.87660 ( 2280) Misc. bond : bond 0.00048 ( 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 571 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 505 time to evaluate : 0.584 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: A 424 PHE cc_start: 0.9194 (m-80) cc_final: 0.8860 (m-80) REVERT: A 533 VAL cc_start: 0.9765 (t) cc_final: 0.9530 (p) REVERT: A 538 LYS cc_start: 0.9385 (mmtm) cc_final: 0.9030 (mmtm) REVERT: A 541 ARG cc_start: 0.9129 (tpp80) cc_final: 0.8815 (tpp80) REVERT: A 651 MET cc_start: 0.9501 (mmm) cc_final: 0.9267 (mmm) REVERT: A 658 ASN cc_start: 0.9339 (m110) cc_final: 0.9010 (m110) REVERT: A 677 MET cc_start: 0.9725 (tpp) cc_final: 0.9236 (tpp) REVERT: A 779 LEU cc_start: 0.9868 (tp) cc_final: 0.9574 (mm) REVERT: A 840 GLU cc_start: 0.9684 (mt-10) cc_final: 0.9128 (tp30) REVERT: A 841 VAL cc_start: 0.9857 (t) cc_final: 0.9617 (t) REVERT: A 844 MET cc_start: 0.9131 (mtm) cc_final: 0.7943 (ptp) REVERT: B 411 ASP cc_start: 0.9357 (t70) cc_final: 0.8762 (t0) REVERT: B 424 PHE cc_start: 0.9242 (m-80) cc_final: 0.8887 (m-80) REVERT: B 541 ARG cc_start: 0.9125 (tpp80) cc_final: 0.8708 (tpp80) REVERT: B 563 TRP cc_start: 0.9467 (m-10) cc_final: 0.9051 (m-10) REVERT: B 645 MET cc_start: 0.9185 (ttm) cc_final: 0.8550 (ttt) REVERT: B 651 MET cc_start: 0.9462 (mmm) cc_final: 0.9250 (mmm) REVERT: B 658 ASN cc_start: 0.9312 (m110) cc_final: 0.8991 (m110) REVERT: B 677 MET cc_start: 0.9417 (mtm) cc_final: 0.8936 (tmm) REVERT: B 729 CYS cc_start: 0.9554 (m) cc_final: 0.9291 (m) REVERT: B 741 LYS cc_start: 0.9481 (mmtt) cc_final: 0.9270 (mmmm) REVERT: B 768 THR cc_start: 0.8211 (p) cc_final: 0.7936 (p) REVERT: B 779 LEU cc_start: 0.9879 (tp) cc_final: 0.9615 (mm) REVERT: B 788 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8763 (mp0) REVERT: B 834 HIS cc_start: 0.9688 (OUTLIER) cc_final: 0.9414 (t-90) REVERT: C 12 ASN cc_start: 0.9450 (OUTLIER) cc_final: 0.8917 (t0) REVERT: C 411 ASP cc_start: 0.9285 (t70) cc_final: 0.8339 (t70) REVERT: C 462 MET cc_start: 0.9524 (tpt) cc_final: 0.9166 (tpp) REVERT: C 466 ASP cc_start: 0.9221 (m-30) cc_final: 0.8733 (m-30) REVERT: C 533 VAL cc_start: 0.9749 (t) cc_final: 0.9541 (p) REVERT: C 538 LYS cc_start: 0.9404 (mmtm) cc_final: 0.9106 (mmtm) REVERT: C 541 ARG cc_start: 0.9206 (tpt-90) cc_final: 0.8749 (tpt-90) REVERT: C 563 TRP cc_start: 0.9496 (m-10) cc_final: 0.9051 (m-10) REVERT: C 574 MET cc_start: 0.8033 (mtt) cc_final: 0.7785 (tpt) REVERT: C 619 PHE cc_start: 0.9589 (OUTLIER) cc_final: 0.9036 (t80) REVERT: C 651 MET cc_start: 0.9467 (mmm) cc_final: 0.9203 (mmm) REVERT: C 658 ASN cc_start: 0.9277 (m110) cc_final: 0.8933 (m110) REVERT: C 677 MET cc_start: 0.9672 (tpp) cc_final: 0.9322 (mmm) REVERT: C 707 TYR cc_start: 0.8977 (t80) cc_final: 0.8305 (t80) REVERT: C 712 ASP cc_start: 0.9405 (m-30) cc_final: 0.9191 (p0) REVERT: C 729 CYS cc_start: 0.9558 (m) cc_final: 0.9325 (m) REVERT: C 751 LEU cc_start: 0.9767 (mt) cc_final: 0.9554 (pp) REVERT: C 762 HIS cc_start: 0.7991 (m-70) cc_final: 0.6984 (m-70) REVERT: C 821 ASP cc_start: 0.8865 (m-30) cc_final: 0.8569 (p0) REVERT: C 827 TYR cc_start: 0.8561 (m-80) cc_final: 0.8206 (m-10) REVERT: C 840 GLU cc_start: 0.9659 (mt-10) cc_final: 0.9131 (tp30) REVERT: C 841 VAL cc_start: 0.9841 (t) cc_final: 0.9553 (t) REVERT: C 844 MET cc_start: 0.9392 (mtm) cc_final: 0.8136 (mtm) REVERT: D 43 TYR cc_start: 0.9201 (t80) cc_final: 0.8869 (t80) REVERT: D 533 VAL cc_start: 0.9756 (t) cc_final: 0.9520 (p) REVERT: D 538 LYS cc_start: 0.9377 (mmtm) cc_final: 0.8994 (mmtm) REVERT: D 541 ARG cc_start: 0.9236 (tpp80) cc_final: 0.8726 (tpp80) REVERT: D 563 TRP cc_start: 0.9661 (m-10) cc_final: 0.9461 (m-10) REVERT: D 574 MET cc_start: 0.8002 (mtt) cc_final: 0.7731 (tpt) REVERT: D 617 PHE cc_start: 0.9471 (t80) cc_final: 0.8920 (t80) REVERT: D 640 PHE cc_start: 0.9647 (t80) cc_final: 0.9417 (t80) REVERT: D 651 MET cc_start: 0.9373 (mmm) cc_final: 0.9123 (mmm) REVERT: D 658 ASN cc_start: 0.9262 (m110) cc_final: 0.8909 (m110) REVERT: D 677 MET cc_start: 0.9685 (tpp) cc_final: 0.8747 (tmm) REVERT: D 681 ARG cc_start: 0.9312 (mmm160) cc_final: 0.8998 (mmm-85) REVERT: D 729 CYS cc_start: 0.9559 (m) cc_final: 0.9329 (m) REVERT: D 751 LEU cc_start: 0.9750 (mt) cc_final: 0.9534 (pp) REVERT: D 779 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9290 (mm) REVERT: D 840 GLU cc_start: 0.9684 (mt-10) cc_final: 0.9241 (tp30) outliers start: 66 outliers final: 50 residues processed: 547 average time/residue: 0.1045 time to fit residues: 89.2722 Evaluate side-chains 525 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 471 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 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 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 646 LEU Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 714 ASN 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 858 ILE Chi-restraints excluded: chain C residue 12 ASN 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 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 646 LEU Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 761 THR 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 817 LYS Chi-restraints excluded: chain C residue 822 VAL 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 593 ILE 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 761 THR Chi-restraints excluded: chain D residue 762 HIS Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 795 VAL 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 8 optimal weight: 0.1980 chunk 148 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 80 optimal weight: 40.0000 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 68 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 HIS ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 HIS C 12 ASN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 HIS D 70 HIS ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.082431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.069096 restraints weight = 88148.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.070607 restraints weight = 58311.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.071717 restraints weight = 43112.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.072566 restraints weight = 34164.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.073209 restraints weight = 28375.751| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.5804 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= 0.133 Angle : 0.732 13.420 24432 Z= 0.356 Chirality : 0.045 0.254 2788 Planarity : 0.003 0.033 3064 Dihedral : 4.557 19.163 2420 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.12 % Favored : 95.51 % Rotamer: Outliers : 3.95 % Allowed : 23.16 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.17), residues: 2184 helix: -0.46 (0.14), residues: 1184 sheet: -1.09 (0.39), residues: 152 loop : -1.48 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 537 TYR 0.016 0.001 TYR B 700 PHE 0.027 0.002 PHE A 640 TRP 0.028 0.002 TRP A 410 HIS 0.008 0.001 HIS D 762 Details of bonding type rmsd covalent geometry : bond 0.00291 (18000) covalent geometry : angle 0.73207 (24432) hydrogen bonds : bond 0.04317 ( 784) hydrogen bonds : angle 4.90225 ( 2280) Misc. bond : bond 0.00030 ( 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 568 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 495 time to evaluate : 0.738 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: A 60 MET cc_start: 0.7945 (tpp) cc_final: 0.7725 (tpp) REVERT: A 424 PHE cc_start: 0.9302 (m-80) cc_final: 0.8948 (m-80) REVERT: A 533 VAL cc_start: 0.9760 (t) cc_final: 0.9269 (p) REVERT: A 537 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7815 (ptp90) REVERT: A 541 ARG cc_start: 0.9101 (tpp80) cc_final: 0.8669 (tpp80) REVERT: A 617 PHE cc_start: 0.9539 (t80) cc_final: 0.9184 (t80) REVERT: A 651 MET cc_start: 0.9548 (mmm) cc_final: 0.9346 (mmm) REVERT: A 658 ASN cc_start: 0.9308 (m110) cc_final: 0.8990 (m110) REVERT: A 677 MET cc_start: 0.9708 (tpp) cc_final: 0.9061 (tmm) REVERT: A 751 LEU cc_start: 0.9733 (mt) cc_final: 0.9524 (pp) REVERT: A 779 LEU cc_start: 0.9852 (tp) cc_final: 0.9592 (mm) REVERT: A 840 GLU cc_start: 0.9667 (mt-10) cc_final: 0.9085 (tp30) REVERT: A 841 VAL cc_start: 0.9841 (t) cc_final: 0.9603 (t) REVERT: A 844 MET cc_start: 0.9027 (mtm) cc_final: 0.7968 (ptp) REVERT: B 410 TRP cc_start: 0.9280 (t60) cc_final: 0.9045 (t60) REVERT: B 411 ASP cc_start: 0.9270 (t70) cc_final: 0.8858 (t0) REVERT: B 424 PHE cc_start: 0.9351 (m-80) cc_final: 0.8973 (m-80) REVERT: B 541 ARG cc_start: 0.9066 (tpp80) cc_final: 0.8549 (tpp80) REVERT: B 645 MET cc_start: 0.9209 (ttm) cc_final: 0.8383 (ttm) REVERT: B 658 ASN cc_start: 0.9273 (m110) cc_final: 0.8965 (m110) REVERT: B 677 MET cc_start: 0.9469 (mtm) cc_final: 0.9262 (ptp) REVERT: B 707 TYR cc_start: 0.8912 (t80) cc_final: 0.8633 (t80) REVERT: B 729 CYS cc_start: 0.9554 (m) cc_final: 0.9301 (m) REVERT: B 768 THR cc_start: 0.8294 (p) cc_final: 0.8050 (p) REVERT: B 779 LEU cc_start: 0.9858 (tp) cc_final: 0.9656 (mm) REVERT: B 834 HIS cc_start: 0.9677 (OUTLIER) cc_final: 0.9437 (t-90) REVERT: C 12 ASN cc_start: 0.9471 (m110) cc_final: 0.9062 (t0) REVERT: C 411 ASP cc_start: 0.9216 (t70) cc_final: 0.8435 (t70) REVERT: C 424 PHE cc_start: 0.9329 (m-80) cc_final: 0.8953 (m-80) REVERT: C 533 VAL cc_start: 0.9763 (t) cc_final: 0.9522 (p) REVERT: C 538 LYS cc_start: 0.9464 (mmtm) cc_final: 0.9159 (mmtm) REVERT: C 541 ARG cc_start: 0.9172 (tpt-90) cc_final: 0.8685 (tpt-90) REVERT: C 563 TRP cc_start: 0.9540 (m-10) cc_final: 0.8991 (m-10) REVERT: C 574 MET cc_start: 0.8032 (mtt) cc_final: 0.7786 (tpt) REVERT: C 619 PHE cc_start: 0.9655 (OUTLIER) cc_final: 0.8939 (t80) REVERT: C 645 MET cc_start: 0.9538 (ttt) cc_final: 0.9164 (ptm) REVERT: C 647 ILE cc_start: 0.9720 (tt) cc_final: 0.9513 (tt) REVERT: C 651 MET cc_start: 0.9550 (mmm) cc_final: 0.9296 (mmm) REVERT: C 658 ASN cc_start: 0.9210 (m110) cc_final: 0.8879 (m110) REVERT: C 677 MET cc_start: 0.9685 (tpp) cc_final: 0.9264 (mmm) REVERT: C 707 TYR cc_start: 0.8914 (t80) cc_final: 0.8320 (t80) REVERT: C 712 ASP cc_start: 0.9436 (m-30) cc_final: 0.9215 (p0) REVERT: C 729 CYS cc_start: 0.9569 (m) cc_final: 0.9331 (m) REVERT: C 762 HIS cc_start: 0.8067 (m-70) cc_final: 0.7033 (m-70) REVERT: C 821 ASP cc_start: 0.8784 (m-30) cc_final: 0.8398 (p0) REVERT: C 827 TYR cc_start: 0.8597 (m-80) cc_final: 0.8280 (m-80) REVERT: C 840 GLU cc_start: 0.9659 (mt-10) cc_final: 0.9131 (tp30) REVERT: C 841 VAL cc_start: 0.9831 (t) cc_final: 0.9582 (t) REVERT: C 844 MET cc_start: 0.9357 (mtm) cc_final: 0.8100 (mtm) REVERT: D 12 ASN cc_start: 0.9566 (t0) cc_final: 0.9157 (t0) REVERT: D 533 VAL cc_start: 0.9754 (t) cc_final: 0.9514 (p) REVERT: D 538 LYS cc_start: 0.9416 (mmtm) cc_final: 0.9103 (mmtm) REVERT: D 541 ARG cc_start: 0.9204 (tpp80) cc_final: 0.8779 (tpp80) REVERT: D 563 TRP cc_start: 0.9685 (m-10) cc_final: 0.9433 (m-10) REVERT: D 574 MET cc_start: 0.8047 (mtt) cc_final: 0.7771 (tpt) REVERT: D 617 PHE cc_start: 0.9500 (t80) cc_final: 0.8970 (t80) REVERT: D 619 PHE cc_start: 0.9532 (OUTLIER) cc_final: 0.9117 (t80) REVERT: D 640 PHE cc_start: 0.9667 (t80) cc_final: 0.9447 (t80) REVERT: D 645 MET cc_start: 0.9534 (ttt) cc_final: 0.9063 (ptm) REVERT: D 647 ILE cc_start: 0.9710 (tt) cc_final: 0.9471 (tt) REVERT: D 651 MET cc_start: 0.9485 (mmm) cc_final: 0.9206 (mmm) REVERT: D 658 ASN cc_start: 0.9226 (m110) cc_final: 0.8891 (m110) REVERT: D 677 MET cc_start: 0.9651 (tpp) cc_final: 0.8914 (tmm) REVERT: D 729 CYS cc_start: 0.9569 (m) cc_final: 0.9302 (m) REVERT: D 741 LYS cc_start: 0.9503 (mmtt) cc_final: 0.9282 (ttpp) REVERT: D 762 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7693 (m170) REVERT: D 840 GLU cc_start: 0.9689 (mt-10) cc_final: 0.9156 (tp30) REVERT: D 844 MET cc_start: 0.9352 (mtm) cc_final: 0.8192 (ptp) outliers start: 73 outliers final: 54 residues processed: 539 average time/residue: 0.1096 time to fit residues: 92.3806 Evaluate side-chains 530 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 471 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 537 ARG Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 623 THR 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 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 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 714 ASN Chi-restraints excluded: chain B residue 761 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 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 646 LEU Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 714 ASN 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 817 LYS Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 413 LEU 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 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 698 GLU Chi-restraints excluded: chain D residue 711 ILE Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 762 HIS Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.7980 chunk 128 optimal weight: 40.0000 chunk 145 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 50.0000 chunk 143 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- 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 A 851 HIS ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 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 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 GLN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 HIS D 831 HIS D 834 HIS D 851 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.067522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.055019 restraints weight = 93660.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.056541 restraints weight = 60826.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057690 restraints weight = 44212.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.058550 restraints weight = 34456.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.059180 restraints weight = 28254.078| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18004 Z= 0.141 Angle : 0.727 13.246 24432 Z= 0.354 Chirality : 0.044 0.286 2788 Planarity : 0.003 0.032 3064 Dihedral : 4.446 19.994 2420 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.12 % Favored : 95.51 % Rotamer: Outliers : 4.33 % Allowed : 24.51 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.17), residues: 2184 helix: -0.38 (0.14), residues: 1208 sheet: -0.56 (0.40), residues: 160 loop : -1.37 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 537 TYR 0.018 0.001 TYR D 707 PHE 0.020 0.001 PHE B 48 TRP 0.033 0.002 TRP A 410 HIS 0.016 0.001 HIS D 762 Details of bonding type rmsd covalent geometry : bond 0.00308 (18000) covalent geometry : angle 0.72702 (24432) hydrogen bonds : bond 0.04259 ( 784) hydrogen bonds : angle 4.90797 ( 2280) Misc. bond : bond 0.00022 ( 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 574 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 494 time to evaluate : 0.486 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 411 ASP cc_start: 0.9387 (t70) cc_final: 0.8787 (t0) REVERT: A 538 LYS cc_start: 0.9506 (mmtm) cc_final: 0.9221 (mmtm) REVERT: A 541 ARG cc_start: 0.9124 (tpp80) cc_final: 0.8598 (tpp80) REVERT: A 617 PHE cc_start: 0.9576 (t80) cc_final: 0.9213 (t80) REVERT: A 645 MET cc_start: 0.9673 (ptm) cc_final: 0.9473 (ptm) REVERT: A 651 MET cc_start: 0.9561 (mmm) cc_final: 0.9349 (mmm) REVERT: A 658 ASN cc_start: 0.9271 (m110) cc_final: 0.8955 (m110) REVERT: A 677 MET cc_start: 0.9734 (tpp) cc_final: 0.8978 (tmm) REVERT: A 681 ARG cc_start: 0.9560 (mmm-85) cc_final: 0.8414 (mmm-85) REVERT: A 779 LEU cc_start: 0.9850 (tp) cc_final: 0.9609 (mm) REVERT: A 784 ARG cc_start: 0.9178 (mtp85) cc_final: 0.8339 (ptm160) REVERT: A 840 GLU cc_start: 0.9672 (mt-10) cc_final: 0.9016 (tp30) REVERT: A 841 VAL cc_start: 0.9842 (t) cc_final: 0.9542 (t) REVERT: A 844 MET cc_start: 0.9084 (mtm) cc_final: 0.8091 (ptt) REVERT: B 46 ASP cc_start: 0.9567 (m-30) cc_final: 0.9341 (t0) REVERT: B 411 ASP cc_start: 0.9292 (t70) cc_final: 0.8797 (t0) REVERT: B 424 PHE cc_start: 0.9389 (m-80) cc_final: 0.8985 (m-80) REVERT: B 541 ARG cc_start: 0.9125 (tpp80) cc_final: 0.8653 (tpp80) REVERT: B 563 TRP cc_start: 0.9687 (m-10) cc_final: 0.9397 (m-10) REVERT: B 619 PHE cc_start: 0.9692 (OUTLIER) cc_final: 0.9221 (t80) REVERT: B 645 MET cc_start: 0.9342 (ttm) cc_final: 0.8493 (ttm) REVERT: B 658 ASN cc_start: 0.9235 (m110) cc_final: 0.8926 (m110) REVERT: B 677 MET cc_start: 0.9472 (mtm) cc_final: 0.9263 (ptp) REVERT: B 707 TYR cc_start: 0.8984 (t80) cc_final: 0.8476 (t80) REVERT: B 717 LEU cc_start: 0.9748 (tp) cc_final: 0.9402 (pp) REVERT: B 729 CYS cc_start: 0.9549 (m) cc_final: 0.9296 (m) REVERT: B 762 HIS cc_start: 0.8150 (m-70) cc_final: 0.6606 (m-70) REVERT: B 779 LEU cc_start: 0.9861 (tp) cc_final: 0.9635 (mm) REVERT: B 784 ARG cc_start: 0.9167 (mtp85) cc_final: 0.8964 (mtp-110) REVERT: B 821 ASP cc_start: 0.8953 (m-30) cc_final: 0.8581 (p0) REVERT: C 12 ASN cc_start: 0.9498 (m110) cc_final: 0.9113 (t0) REVERT: C 411 ASP cc_start: 0.9387 (t70) cc_final: 0.8568 (t70) REVERT: C 424 PHE cc_start: 0.9343 (m-80) cc_final: 0.8945 (m-80) REVERT: C 466 ASP cc_start: 0.9325 (m-30) cc_final: 0.9121 (p0) REVERT: C 533 VAL cc_start: 0.9773 (t) cc_final: 0.9539 (p) REVERT: C 538 LYS cc_start: 0.9517 (mmtm) cc_final: 0.9210 (mmtm) REVERT: C 541 ARG cc_start: 0.9231 (tpt-90) cc_final: 0.8772 (tpt-90) REVERT: C 563 TRP cc_start: 0.9539 (m-10) cc_final: 0.9148 (m-10) REVERT: C 574 MET cc_start: 0.8032 (mtt) cc_final: 0.7769 (tpt) REVERT: C 619 PHE cc_start: 0.9685 (OUTLIER) cc_final: 0.9001 (t80) REVERT: C 647 ILE cc_start: 0.9715 (tt) cc_final: 0.9504 (tt) REVERT: C 651 MET cc_start: 0.9550 (mmm) cc_final: 0.9308 (mmm) REVERT: C 658 ASN cc_start: 0.9189 (m110) cc_final: 0.8854 (m110) REVERT: C 677 MET cc_start: 0.9717 (tpp) cc_final: 0.9433 (mmm) REVERT: C 694 ARG cc_start: 0.9610 (mtp-110) cc_final: 0.9321 (ttm110) REVERT: C 707 TYR cc_start: 0.9022 (t80) cc_final: 0.8419 (t80) REVERT: C 729 CYS cc_start: 0.9564 (m) cc_final: 0.9317 (m) REVERT: C 762 HIS cc_start: 0.8129 (m-70) cc_final: 0.7120 (m-70) REVERT: C 821 ASP cc_start: 0.8796 (m-30) cc_final: 0.8485 (p0) REVERT: C 840 GLU cc_start: 0.9658 (mt-10) cc_final: 0.9119 (tp30) REVERT: C 841 VAL cc_start: 0.9855 (t) cc_final: 0.9557 (t) REVERT: C 844 MET cc_start: 0.9395 (mtm) cc_final: 0.8206 (mtm) REVERT: D 12 ASN cc_start: 0.9548 (t0) cc_final: 0.9310 (t0) REVERT: D 424 PHE cc_start: 0.9313 (m-80) cc_final: 0.8900 (m-80) REVERT: D 533 VAL cc_start: 0.9763 (t) cc_final: 0.9501 (p) REVERT: D 538 LYS cc_start: 0.9512 (mmtm) cc_final: 0.9225 (mmtm) REVERT: D 541 ARG cc_start: 0.9218 (tpp80) cc_final: 0.8784 (tpp80) REVERT: D 563 TRP cc_start: 0.9685 (m-10) cc_final: 0.9407 (m-10) REVERT: D 574 MET cc_start: 0.8020 (mtt) cc_final: 0.7747 (tpt) REVERT: D 617 PHE cc_start: 0.9509 (t80) cc_final: 0.9071 (t80) REVERT: D 645 MET cc_start: 0.9588 (ttt) cc_final: 0.9069 (ptm) REVERT: D 647 ILE cc_start: 0.9713 (tt) cc_final: 0.9491 (tt) REVERT: D 651 MET cc_start: 0.9522 (mmm) cc_final: 0.9279 (mmm) REVERT: D 658 ASN cc_start: 0.9219 (m110) cc_final: 0.8888 (m110) REVERT: D 677 MET cc_start: 0.9660 (tpp) cc_final: 0.8902 (tmm) REVERT: D 681 ARG cc_start: 0.9624 (mtm180) cc_final: 0.8809 (mtm180) REVERT: D 729 CYS cc_start: 0.9541 (m) cc_final: 0.9272 (m) REVERT: D 840 GLU cc_start: 0.9678 (mt-10) cc_final: 0.9118 (tp30) REVERT: D 841 VAL cc_start: 0.9860 (p) cc_final: 0.9553 (m) REVERT: D 844 MET cc_start: 0.9382 (mtm) cc_final: 0.8205 (mtm) outliers start: 80 outliers final: 56 residues processed: 542 average time/residue: 0.1082 time to fit residues: 92.1667 Evaluate side-chains 526 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 468 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 421 THR 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 623 THR 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 788 GLU 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 421 THR 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 619 PHE 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 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 483 VAL Chi-restraints excluded: chain C residue 535 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 693 LEU 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 817 LYS Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 483 VAL 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 698 GLU Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 795 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 218 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 52 optimal weight: 50.0000 chunk 193 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 102 optimal weight: 40.0000 chunk 94 optimal weight: 30.0000 chunk 98 optimal weight: 20.0000 chunk 216 optimal weight: 50.0000 overall best weight: 6.9788 ------------------------------------------------------------------------------- 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 691 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 ASN ** 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** ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.066453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.053986 restraints weight = 95832.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.055522 restraints weight = 61310.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.056652 restraints weight = 44048.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.057513 restraints weight = 34146.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.058164 restraints weight = 27865.186| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 0.051 18004 Z= 0.150 Angle : 0.748 13.744 24432 Z= 0.366 Chirality : 0.046 0.283 2788 Planarity : 0.003 0.028 3064 Dihedral : 4.424 20.753 2420 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.21 % Favored : 95.42 % Rotamer: Outliers : 3.63 % Allowed : 26.62 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.17), residues: 2184 helix: -0.42 (0.14), residues: 1188 sheet: -0.49 (0.40), residues: 164 loop : -1.28 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 537 TYR 0.027 0.001 TYR B 700 PHE 0.036 0.001 PHE A 640 TRP 0.032 0.002 TRP A 410 HIS 0.012 0.001 HIS D 834 Details of bonding type rmsd covalent geometry : bond 0.00328 (18000) covalent geometry : angle 0.74849 (24432) hydrogen bonds : bond 0.04309 ( 784) hydrogen bonds : angle 5.00875 ( 2280) Misc. bond : bond 0.00017 ( 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 553 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 486 time to evaluate : 0.661 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 411 ASP cc_start: 0.9379 (t70) cc_final: 0.8708 (t0) REVERT: A 538 LYS cc_start: 0.9538 (mmtm) cc_final: 0.9266 (mmtm) REVERT: A 541 ARG cc_start: 0.9144 (tpp80) cc_final: 0.8649 (tpp80) REVERT: A 617 PHE cc_start: 0.9591 (t80) cc_final: 0.9270 (t80) REVERT: A 645 MET cc_start: 0.9682 (ptm) cc_final: 0.9359 (ptm) REVERT: A 658 ASN cc_start: 0.9252 (m110) cc_final: 0.8944 (m110) REVERT: A 677 MET cc_start: 0.9723 (tpp) cc_final: 0.8967 (tmm) REVERT: A 681 ARG cc_start: 0.9577 (mmm-85) cc_final: 0.8756 (mmm-85) REVERT: A 779 LEU cc_start: 0.9849 (tp) cc_final: 0.9620 (mm) REVERT: A 784 ARG cc_start: 0.9191 (mtp85) cc_final: 0.8893 (mtm110) REVERT: A 840 GLU cc_start: 0.9673 (mt-10) cc_final: 0.8996 (tp30) REVERT: A 841 VAL cc_start: 0.9857 (t) cc_final: 0.9515 (t) REVERT: A 844 MET cc_start: 0.9064 (mtm) cc_final: 0.8081 (ptt) REVERT: B 411 ASP cc_start: 0.9282 (t70) cc_final: 0.8800 (t0) REVERT: B 424 PHE cc_start: 0.9430 (m-80) cc_final: 0.9015 (m-80) REVERT: B 541 ARG cc_start: 0.9168 (tpp80) cc_final: 0.8722 (tpp80) REVERT: B 563 TRP cc_start: 0.9690 (m-10) cc_final: 0.9404 (m-10) REVERT: B 619 PHE cc_start: 0.9707 (OUTLIER) cc_final: 0.9261 (t80) REVERT: B 645 MET cc_start: 0.9431 (ttm) cc_final: 0.8642 (ttm) REVERT: B 658 ASN cc_start: 0.9218 (m110) cc_final: 0.8911 (m110) REVERT: B 677 MET cc_start: 0.9467 (mtm) cc_final: 0.8880 (ptp) REVERT: B 681 ARG cc_start: 0.9647 (mmm-85) cc_final: 0.9132 (mtm-85) REVERT: B 707 TYR cc_start: 0.9003 (t80) cc_final: 0.8528 (t80) REVERT: B 717 LEU cc_start: 0.9768 (tp) cc_final: 0.9443 (pp) REVERT: B 729 CYS cc_start: 0.9534 (m) cc_final: 0.9277 (m) REVERT: B 762 HIS cc_start: 0.8154 (m-70) cc_final: 0.6594 (m-70) REVERT: B 779 LEU cc_start: 0.9857 (tp) cc_final: 0.9640 (mm) REVERT: B 821 ASP cc_start: 0.8962 (m-30) cc_final: 0.8527 (p0) REVERT: C 12 ASN cc_start: 0.9558 (m110) cc_final: 0.9138 (t0) REVERT: C 411 ASP cc_start: 0.9453 (t70) cc_final: 0.8500 (t70) REVERT: C 424 PHE cc_start: 0.9368 (m-80) cc_final: 0.8938 (m-80) REVERT: C 533 VAL cc_start: 0.9768 (t) cc_final: 0.9542 (p) REVERT: C 538 LYS cc_start: 0.9547 (mmtm) cc_final: 0.9249 (mmtm) REVERT: C 541 ARG cc_start: 0.9250 (tpt-90) cc_final: 0.8802 (tpt-90) REVERT: C 563 TRP cc_start: 0.9547 (m-10) cc_final: 0.9217 (m-10) REVERT: C 574 MET cc_start: 0.8094 (mtt) cc_final: 0.7795 (tpt) REVERT: C 619 PHE cc_start: 0.9718 (OUTLIER) cc_final: 0.9039 (t80) REVERT: C 647 ILE cc_start: 0.9706 (tt) cc_final: 0.9505 (tt) REVERT: C 651 MET cc_start: 0.9564 (mmm) cc_final: 0.9333 (mmm) REVERT: C 658 ASN cc_start: 0.9175 (m110) cc_final: 0.8848 (m110) REVERT: C 677 MET cc_start: 0.9719 (tpp) cc_final: 0.9435 (mmm) REVERT: C 707 TYR cc_start: 0.9002 (t80) cc_final: 0.8353 (t80) REVERT: C 717 LEU cc_start: 0.9762 (tp) cc_final: 0.9404 (pp) REVERT: C 729 CYS cc_start: 0.9544 (m) cc_final: 0.9302 (m) REVERT: C 762 HIS cc_start: 0.8127 (m-70) cc_final: 0.7094 (m-70) REVERT: C 840 GLU cc_start: 0.9670 (mt-10) cc_final: 0.9139 (tp30) REVERT: C 841 VAL cc_start: 0.9860 (t) cc_final: 0.9585 (t) REVERT: C 844 MET cc_start: 0.9424 (mtm) cc_final: 0.8284 (mtm) REVERT: D 12 ASN cc_start: 0.9559 (t0) cc_final: 0.9342 (t0) REVERT: D 424 PHE cc_start: 0.9351 (m-80) cc_final: 0.8943 (m-80) REVERT: D 533 VAL cc_start: 0.9755 (t) cc_final: 0.9294 (p) REVERT: D 537 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7865 (ptp90) REVERT: D 538 LYS cc_start: 0.9556 (mmtm) cc_final: 0.9279 (mmtm) REVERT: D 541 ARG cc_start: 0.9251 (tpp80) cc_final: 0.8813 (tpp80) REVERT: D 562 HIS cc_start: 0.9224 (t70) cc_final: 0.8865 (t-170) REVERT: D 574 MET cc_start: 0.8073 (mtt) cc_final: 0.7747 (tpt) REVERT: D 617 PHE cc_start: 0.9524 (t80) cc_final: 0.8975 (t80) REVERT: D 619 PHE cc_start: 0.9465 (OUTLIER) cc_final: 0.9116 (t80) REVERT: D 640 PHE cc_start: 0.9705 (t80) cc_final: 0.9473 (t80) REVERT: D 645 MET cc_start: 0.9613 (ttt) cc_final: 0.9099 (ptm) REVERT: D 647 ILE cc_start: 0.9712 (tt) cc_final: 0.9491 (tt) REVERT: D 651 MET cc_start: 0.9530 (mmm) cc_final: 0.9287 (mmm) REVERT: D 658 ASN cc_start: 0.9205 (m110) cc_final: 0.8876 (m110) REVERT: D 677 MET cc_start: 0.9672 (tpp) cc_final: 0.8942 (tmm) REVERT: D 681 ARG cc_start: 0.9626 (mtm180) cc_final: 0.8844 (mtm180) REVERT: D 729 CYS cc_start: 0.9545 (m) cc_final: 0.9279 (m) REVERT: D 840 GLU cc_start: 0.9684 (mt-10) cc_final: 0.9112 (tp30) REVERT: D 844 MET cc_start: 0.9403 (mtm) cc_final: 0.8320 (mtm) outliers start: 67 outliers final: 49 residues processed: 521 average time/residue: 0.1118 time to fit residues: 90.7173 Evaluate side-chains 532 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 479 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 623 THR 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 788 GLU 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 539 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 535 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 693 LEU Chi-restraints excluded: chain C residue 714 ASN 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 817 LYS Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 535 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 698 GLU Chi-restraints excluded: chain D residue 762 HIS Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 782 ILE 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 16 optimal weight: 9.9990 chunk 168 optimal weight: 50.0000 chunk 212 optimal weight: 30.0000 chunk 75 optimal weight: 0.0170 chunk 57 optimal weight: 20.0000 chunk 112 optimal weight: 50.0000 chunk 144 optimal weight: 8.9990 chunk 214 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 157 optimal weight: 30.0000 overall best weight: 6.2026 ------------------------------------------------------------------------------- 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 691 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 ASN ** 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** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 GLN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.066512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.054069 restraints weight = 95276.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.055606 restraints weight = 60895.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.056749 restraints weight = 43665.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.057614 restraints weight = 33779.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.058256 restraints weight = 27528.530| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.6521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18004 Z= 0.145 Angle : 0.776 13.307 24432 Z= 0.376 Chirality : 0.046 0.310 2788 Planarity : 0.003 0.029 3064 Dihedral : 4.420 20.549 2420 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.12 % Favored : 95.51 % Rotamer: Outliers : 3.25 % Allowed : 28.35 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.17), residues: 2184 helix: -0.43 (0.14), residues: 1188 sheet: -0.48 (0.39), residues: 164 loop : -1.22 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 537 TYR 0.022 0.001 TYR B 700 PHE 0.028 0.001 PHE D 48 TRP 0.025 0.002 TRP B 410 HIS 0.011 0.001 HIS D 762 Details of bonding type rmsd covalent geometry : bond 0.00318 (18000) covalent geometry : angle 0.77610 (24432) hydrogen bonds : bond 0.04338 ( 784) hydrogen bonds : angle 5.03850 ( 2280) Misc. bond : bond 0.00048 ( 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 543 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 483 time to evaluate : 0.686 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: 0.9399 (t70) cc_final: 0.8857 (t0) REVERT: A 538 LYS cc_start: 0.9548 (mmtm) cc_final: 0.9263 (mmtm) REVERT: A 541 ARG cc_start: 0.9161 (tpp80) cc_final: 0.8693 (tpp80) REVERT: A 617 PHE cc_start: 0.9578 (t80) cc_final: 0.9265 (t80) REVERT: A 645 MET cc_start: 0.9679 (ptm) cc_final: 0.9348 (ptm) REVERT: A 658 ASN cc_start: 0.9233 (m110) cc_final: 0.8926 (m110) REVERT: A 677 MET cc_start: 0.9709 (tpp) cc_final: 0.8996 (tmm) REVERT: A 681 ARG cc_start: 0.9579 (mmm-85) cc_final: 0.8948 (mtm180) REVERT: A 779 LEU cc_start: 0.9842 (tp) cc_final: 0.9628 (mm) REVERT: A 784 ARG cc_start: 0.9200 (mtp85) cc_final: 0.8907 (mtm110) REVERT: A 821 ASP cc_start: 0.9000 (m-30) cc_final: 0.8607 (p0) REVERT: A 840 GLU cc_start: 0.9682 (mt-10) cc_final: 0.9177 (tp30) REVERT: B 411 ASP cc_start: 0.9275 (t70) cc_final: 0.8807 (t0) REVERT: B 424 PHE cc_start: 0.9438 (m-80) cc_final: 0.9035 (m-80) REVERT: B 541 ARG cc_start: 0.9177 (tpp80) cc_final: 0.8730 (tpp80) REVERT: B 563 TRP cc_start: 0.9697 (m-10) cc_final: 0.9412 (m-10) REVERT: B 619 PHE cc_start: 0.9712 (OUTLIER) cc_final: 0.9229 (t80) REVERT: B 645 MET cc_start: 0.9414 (ttm) cc_final: 0.8597 (ttm) REVERT: B 658 ASN cc_start: 0.9217 (m110) cc_final: 0.8906 (m110) REVERT: B 677 MET cc_start: 0.9455 (mtm) cc_final: 0.8801 (ptp) REVERT: B 681 ARG cc_start: 0.9643 (mmm-85) cc_final: 0.9135 (mtm-85) REVERT: B 707 TYR cc_start: 0.9050 (t80) cc_final: 0.8574 (t80) REVERT: B 729 CYS cc_start: 0.9550 (m) cc_final: 0.9312 (m) REVERT: B 762 HIS cc_start: 0.8231 (m-70) cc_final: 0.6678 (m-70) REVERT: B 779 LEU cc_start: 0.9851 (tp) cc_final: 0.9639 (mm) REVERT: B 821 ASP cc_start: 0.8996 (m-30) cc_final: 0.8434 (p0) REVERT: C 12 ASN cc_start: 0.9575 (m110) cc_final: 0.9165 (t0) REVERT: C 411 ASP cc_start: 0.9466 (t70) cc_final: 0.8507 (t70) REVERT: C 424 PHE cc_start: 0.9396 (m-80) cc_final: 0.8972 (m-80) REVERT: C 533 VAL cc_start: 0.9760 (t) cc_final: 0.9503 (p) REVERT: C 537 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8713 (ptp-170) REVERT: C 538 LYS cc_start: 0.9550 (mmtm) cc_final: 0.9266 (mmtm) REVERT: C 541 ARG cc_start: 0.9255 (tpt-90) cc_final: 0.8806 (tpt-90) REVERT: C 574 MET cc_start: 0.8110 (mtt) cc_final: 0.7782 (tpt) REVERT: C 619 PHE cc_start: 0.9719 (OUTLIER) cc_final: 0.9054 (t80) REVERT: C 647 ILE cc_start: 0.9703 (tt) cc_final: 0.9496 (tt) REVERT: C 651 MET cc_start: 0.9550 (mmm) cc_final: 0.9320 (mmm) REVERT: C 658 ASN cc_start: 0.9165 (m110) cc_final: 0.8840 (m110) REVERT: C 677 MET cc_start: 0.9713 (tpp) cc_final: 0.9066 (mmm) REVERT: C 681 ARG cc_start: 0.9633 (mmm-85) cc_final: 0.9097 (mtm-85) REVERT: C 707 TYR cc_start: 0.9001 (t80) cc_final: 0.8417 (t80) REVERT: C 729 CYS cc_start: 0.9544 (m) cc_final: 0.9317 (m) REVERT: C 762 HIS cc_start: 0.8184 (m-70) cc_final: 0.6790 (m-70) REVERT: C 821 ASP cc_start: 0.8932 (m-30) cc_final: 0.8548 (p0) REVERT: C 840 GLU cc_start: 0.9679 (mt-10) cc_final: 0.9155 (tp30) REVERT: C 841 VAL cc_start: 0.9856 (t) cc_final: 0.9596 (t) REVERT: C 844 MET cc_start: 0.9419 (mtm) cc_final: 0.8263 (mtm) REVERT: D 12 ASN cc_start: 0.9558 (t0) cc_final: 0.9353 (t0) REVERT: D 109 LEU cc_start: 0.9278 (tp) cc_final: 0.8614 (pp) REVERT: D 411 ASP cc_start: 0.9336 (t70) cc_final: 0.8755 (t0) REVERT: D 533 VAL cc_start: 0.9754 (t) cc_final: 0.9500 (p) REVERT: D 538 LYS cc_start: 0.9556 (mmtm) cc_final: 0.9273 (mmtm) REVERT: D 541 ARG cc_start: 0.9241 (tpp80) cc_final: 0.8746 (tpp80) REVERT: D 562 HIS cc_start: 0.9206 (t70) cc_final: 0.8853 (t-170) REVERT: D 563 TRP cc_start: 0.9638 (m-10) cc_final: 0.9395 (m-10) REVERT: D 574 MET cc_start: 0.8050 (mtt) cc_final: 0.7729 (tpt) REVERT: D 617 PHE cc_start: 0.9526 (t80) cc_final: 0.9066 (t80) REVERT: D 619 PHE cc_start: 0.9487 (OUTLIER) cc_final: 0.9229 (t80) REVERT: D 645 MET cc_start: 0.9619 (ttt) cc_final: 0.9116 (ptm) REVERT: D 647 ILE cc_start: 0.9701 (tt) cc_final: 0.9486 (tt) REVERT: D 651 MET cc_start: 0.9527 (mmm) cc_final: 0.9295 (mmm) REVERT: D 658 ASN cc_start: 0.9201 (m110) cc_final: 0.8876 (m110) REVERT: D 677 MET cc_start: 0.9665 (tpp) cc_final: 0.8901 (tmm) REVERT: D 681 ARG cc_start: 0.9619 (mtm180) cc_final: 0.8829 (mtm180) REVERT: D 729 CYS cc_start: 0.9539 (m) cc_final: 0.9309 (m) REVERT: D 821 ASP cc_start: 0.8943 (m-30) cc_final: 0.8597 (p0) REVERT: D 840 GLU cc_start: 0.9680 (mt-10) cc_final: 0.9095 (tp30) REVERT: D 844 MET cc_start: 0.9381 (mtm) cc_final: 0.8290 (mtm) outliers start: 60 outliers final: 44 residues processed: 513 average time/residue: 0.1064 time to fit residues: 85.1456 Evaluate side-chains 522 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 474 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 623 THR 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 788 GLU 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 539 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 537 ARG 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 718 LYS 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 817 LYS Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 535 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 698 GLU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 782 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 213 optimal weight: 40.0000 chunk 72 optimal weight: 30.0000 chunk 139 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 18 optimal weight: 50.0000 chunk 121 optimal weight: 40.0000 chunk 204 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 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 470 ASN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 GLN ** D 702 GLN ** 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 = 0.3292 r_free = 0.3292 target = 0.065874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.053658 restraints weight = 95596.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.055162 restraints weight = 61114.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.056278 restraints weight = 43863.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.057106 restraints weight = 33894.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.057744 restraints weight = 27692.149| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.6663 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= 0.154 Angle : 0.800 14.490 24432 Z= 0.386 Chirality : 0.047 0.321 2788 Planarity : 0.003 0.028 3064 Dihedral : 4.435 20.936 2420 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.17 % Favored : 95.47 % Rotamer: Outliers : 3.41 % Allowed : 29.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.17), residues: 2184 helix: -0.44 (0.15), residues: 1188 sheet: -0.48 (0.39), residues: 164 loop : -1.23 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 537 TYR 0.023 0.002 TYR B 700 PHE 0.024 0.001 PHE B 640 TRP 0.050 0.002 TRP B 410 HIS 0.007 0.001 HIS D 834 Details of bonding type rmsd covalent geometry : bond 0.00339 (18000) covalent geometry : angle 0.79979 (24432) hydrogen bonds : bond 0.04396 ( 784) hydrogen bonds : angle 5.15682 ( 2280) Misc. bond : bond 0.00049 ( 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 547 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 484 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9660 (t0) cc_final: 0.9366 (t0) REVERT: A 109 LEU cc_start: 0.9286 (tp) cc_final: 0.8593 (pp) REVERT: A 411 ASP cc_start: 0.9370 (t70) cc_final: 0.8770 (t0) REVERT: A 538 LYS cc_start: 0.9569 (mmtm) cc_final: 0.9314 (mmtm) REVERT: A 541 ARG cc_start: 0.9183 (tpp80) cc_final: 0.8705 (tpp80) REVERT: A 617 PHE cc_start: 0.9587 (t80) cc_final: 0.9263 (t80) REVERT: A 658 ASN cc_start: 0.9233 (m110) cc_final: 0.8928 (m110) REVERT: A 677 MET cc_start: 0.9716 (tpp) cc_final: 0.9000 (tmm) REVERT: A 681 ARG cc_start: 0.9576 (mmm-85) cc_final: 0.8942 (mtm180) REVERT: A 779 LEU cc_start: 0.9838 (tp) cc_final: 0.9628 (mm) REVERT: A 821 ASP cc_start: 0.8994 (m-30) cc_final: 0.8593 (p0) REVERT: A 840 GLU cc_start: 0.9698 (mt-10) cc_final: 0.9203 (tp30) REVERT: B 46 ASP cc_start: 0.9561 (m-30) cc_final: 0.9236 (t0) REVERT: B 411 ASP cc_start: 0.9276 (t70) cc_final: 0.8786 (t0) REVERT: B 424 PHE cc_start: 0.9454 (m-80) cc_final: 0.9050 (m-80) REVERT: B 541 ARG cc_start: 0.9195 (tpp80) cc_final: 0.8747 (tpp80) REVERT: B 617 PHE cc_start: 0.9634 (t80) cc_final: 0.9404 (t80) REVERT: B 645 MET cc_start: 0.9401 (ttm) cc_final: 0.8872 (ttt) REVERT: B 658 ASN cc_start: 0.9200 (m110) cc_final: 0.8892 (m110) REVERT: B 677 MET cc_start: 0.9453 (mtm) cc_final: 0.8773 (ptp) REVERT: B 681 ARG cc_start: 0.9644 (mmm-85) cc_final: 0.9137 (mtm-85) REVERT: B 717 LEU cc_start: 0.9785 (tp) cc_final: 0.9445 (pp) REVERT: B 729 CYS cc_start: 0.9556 (m) cc_final: 0.9305 (m) REVERT: B 821 ASP cc_start: 0.8995 (m-30) cc_final: 0.8457 (p0) REVERT: C 109 LEU cc_start: 0.9272 (tp) cc_final: 0.8604 (pp) REVERT: C 411 ASP cc_start: 0.9469 (t70) cc_final: 0.8503 (t70) REVERT: C 424 PHE cc_start: 0.9403 (m-80) cc_final: 0.8993 (m-80) REVERT: C 533 VAL cc_start: 0.9746 (t) cc_final: 0.9482 (p) REVERT: C 537 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8744 (ptp-170) REVERT: C 538 LYS cc_start: 0.9551 (mmtm) cc_final: 0.9272 (mmtm) REVERT: C 541 ARG cc_start: 0.9245 (tpt-90) cc_final: 0.8771 (tpt-90) REVERT: C 562 HIS cc_start: 0.9268 (t70) cc_final: 0.8930 (t-90) REVERT: C 574 MET cc_start: 0.8087 (mtt) cc_final: 0.7750 (tpt) REVERT: C 617 PHE cc_start: 0.9634 (t80) cc_final: 0.9311 (t80) REVERT: C 619 PHE cc_start: 0.9701 (OUTLIER) cc_final: 0.9162 (t80) REVERT: C 640 PHE cc_start: 0.9684 (t80) cc_final: 0.9469 (t80) REVERT: C 647 ILE cc_start: 0.9701 (tt) cc_final: 0.9499 (tt) REVERT: C 651 MET cc_start: 0.9557 (mmm) cc_final: 0.9334 (mmm) REVERT: C 658 ASN cc_start: 0.9158 (m110) cc_final: 0.8840 (m110) REVERT: C 677 MET cc_start: 0.9720 (tpp) cc_final: 0.9055 (mmm) REVERT: C 681 ARG cc_start: 0.9629 (mmm-85) cc_final: 0.9082 (mtm-85) REVERT: C 707 TYR cc_start: 0.9014 (t80) cc_final: 0.8436 (t80) REVERT: C 729 CYS cc_start: 0.9542 (m) cc_final: 0.9293 (m) REVERT: C 762 HIS cc_start: 0.8173 (m-70) cc_final: 0.6801 (m-70) REVERT: C 821 ASP cc_start: 0.8968 (m-30) cc_final: 0.8541 (p0) REVERT: C 840 GLU cc_start: 0.9687 (mt-10) cc_final: 0.9167 (tp30) REVERT: C 841 VAL cc_start: 0.9851 (t) cc_final: 0.9602 (t) REVERT: C 844 MET cc_start: 0.9432 (mtm) cc_final: 0.8271 (mtm) REVERT: D 109 LEU cc_start: 0.9298 (tp) cc_final: 0.8649 (pp) REVERT: D 411 ASP cc_start: 0.9379 (t70) cc_final: 0.8839 (t0) REVERT: D 414 ILE cc_start: 0.9715 (tt) cc_final: 0.9488 (pt) REVERT: D 424 PHE cc_start: 0.9443 (m-80) cc_final: 0.9065 (m-80) REVERT: D 533 VAL cc_start: 0.9738 (t) cc_final: 0.9470 (p) REVERT: D 538 LYS cc_start: 0.9564 (mmtm) cc_final: 0.9297 (mmtm) REVERT: D 541 ARG cc_start: 0.9264 (tpp80) cc_final: 0.8776 (tpp80) REVERT: D 562 HIS cc_start: 0.9250 (t70) cc_final: 0.8943 (t-170) REVERT: D 563 TRP cc_start: 0.9649 (m-10) cc_final: 0.9421 (m-10) REVERT: D 574 MET cc_start: 0.8086 (mtt) cc_final: 0.7755 (tpt) REVERT: D 619 PHE cc_start: 0.9510 (OUTLIER) cc_final: 0.9305 (t80) REVERT: D 645 MET cc_start: 0.9636 (ttt) cc_final: 0.9118 (ptm) REVERT: D 647 ILE cc_start: 0.9704 (tt) cc_final: 0.9488 (tt) REVERT: D 651 MET cc_start: 0.9535 (mmm) cc_final: 0.9298 (mmm) REVERT: D 658 ASN cc_start: 0.9194 (m110) cc_final: 0.8869 (m110) REVERT: D 677 MET cc_start: 0.9669 (tpp) cc_final: 0.8933 (tmm) REVERT: D 681 ARG cc_start: 0.9624 (mtm180) cc_final: 0.8856 (mtm180) REVERT: D 729 CYS cc_start: 0.9548 (m) cc_final: 0.9292 (m) REVERT: D 821 ASP cc_start: 0.8957 (m-30) cc_final: 0.8608 (p0) REVERT: D 827 TYR cc_start: 0.8688 (m-80) cc_final: 0.8387 (m-10) REVERT: D 840 GLU cc_start: 0.9689 (mt-10) cc_final: 0.9075 (tp30) REVERT: D 844 MET cc_start: 0.9395 (mtm) cc_final: 0.8311 (mtm) outliers start: 63 outliers final: 51 residues processed: 515 average time/residue: 0.1065 time to fit residues: 85.7823 Evaluate side-chains 530 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 476 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 415 LEU 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 623 THR 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 788 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 842 LEU 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 539 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 761 THR 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 C residue 17 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 537 ARG 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 645 MET Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 718 LYS 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 36 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 842 LEU 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 18 optimal weight: 50.0000 chunk 76 optimal weight: 20.0000 chunk 101 optimal weight: 0.5980 chunk 182 optimal weight: 10.0000 chunk 126 optimal weight: 30.0000 chunk 146 optimal weight: 30.0000 chunk 63 optimal weight: 8.9990 chunk 2 optimal weight: 50.0000 chunk 25 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- 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 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 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 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 676 GLN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.066225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.053924 restraints weight = 95033.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.055470 restraints weight = 60635.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.056605 restraints weight = 43330.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.057457 restraints weight = 33466.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.058075 restraints weight = 27294.265| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.6804 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= 0.144 Angle : 0.831 14.730 24432 Z= 0.394 Chirality : 0.047 0.336 2788 Planarity : 0.003 0.028 3064 Dihedral : 4.432 20.639 2420 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.21 % Favored : 95.42 % Rotamer: Outliers : 2.87 % Allowed : 30.14 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.17), residues: 2184 helix: -0.42 (0.15), residues: 1172 sheet: -0.57 (0.46), residues: 124 loop : -1.12 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 537 TYR 0.021 0.001 TYR B 700 PHE 0.031 0.001 PHE D 48 TRP 0.048 0.002 TRP B 410 HIS 0.008 0.001 HIS D 834 Details of bonding type rmsd covalent geometry : bond 0.00319 (18000) covalent geometry : angle 0.83074 (24432) hydrogen bonds : bond 0.04412 ( 784) hydrogen bonds : angle 5.18266 ( 2280) Misc. bond : bond 0.00045 ( 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 540 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 487 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9650 (t0) cc_final: 0.9348 (t0) REVERT: A 109 LEU cc_start: 0.9281 (tp) cc_final: 0.8612 (pp) REVERT: A 411 ASP cc_start: 0.9379 (t70) cc_final: 0.8794 (t0) REVERT: A 424 PHE cc_start: 0.9402 (m-80) cc_final: 0.9028 (m-80) REVERT: A 538 LYS cc_start: 0.9569 (mmtm) cc_final: 0.9323 (mmtm) REVERT: A 541 ARG cc_start: 0.9190 (tpp80) cc_final: 0.8741 (tpp80) REVERT: A 617 PHE cc_start: 0.9567 (t80) cc_final: 0.9246 (t80) REVERT: A 658 ASN cc_start: 0.9223 (m110) cc_final: 0.8913 (m110) REVERT: A 677 MET cc_start: 0.9714 (tpp) cc_final: 0.9023 (tmm) REVERT: A 681 ARG cc_start: 0.9574 (mmm-85) cc_final: 0.8941 (mtm180) REVERT: A 779 LEU cc_start: 0.9837 (tp) cc_final: 0.9629 (mm) REVERT: A 821 ASP cc_start: 0.9013 (m-30) cc_final: 0.8609 (p0) REVERT: A 840 GLU cc_start: 0.9686 (mt-10) cc_final: 0.9158 (tp30) REVERT: A 841 VAL cc_start: 0.9858 (p) cc_final: 0.9654 (m) REVERT: B 46 ASP cc_start: 0.9550 (m-30) cc_final: 0.9252 (t0) REVERT: B 411 ASP cc_start: 0.9281 (t70) cc_final: 0.8802 (t0) REVERT: B 424 PHE cc_start: 0.9457 (m-80) cc_final: 0.9046 (m-80) REVERT: B 541 ARG cc_start: 0.9206 (tpp80) cc_final: 0.8786 (tpp80) REVERT: B 563 TRP cc_start: 0.9680 (m-10) cc_final: 0.9447 (m-10) REVERT: B 617 PHE cc_start: 0.9613 (t80) cc_final: 0.9376 (t80) REVERT: B 619 PHE cc_start: 0.9694 (OUTLIER) cc_final: 0.9298 (t80) REVERT: B 658 ASN cc_start: 0.9176 (m110) cc_final: 0.8866 (m110) REVERT: B 677 MET cc_start: 0.9459 (mtm) cc_final: 0.8765 (ptp) REVERT: B 681 ARG cc_start: 0.9648 (mmm-85) cc_final: 0.9132 (mtm-85) REVERT: B 717 LEU cc_start: 0.9774 (tp) cc_final: 0.9447 (pp) REVERT: B 729 CYS cc_start: 0.9554 (m) cc_final: 0.9292 (m) REVERT: B 821 ASP cc_start: 0.8990 (m-30) cc_final: 0.8449 (p0) REVERT: C 109 LEU cc_start: 0.9272 (tp) cc_final: 0.8625 (pp) REVERT: C 411 ASP cc_start: 0.9458 (t70) cc_final: 0.8487 (t70) REVERT: C 424 PHE cc_start: 0.9395 (m-80) cc_final: 0.8980 (m-80) REVERT: C 533 VAL cc_start: 0.9744 (t) cc_final: 0.9477 (p) REVERT: C 537 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8757 (ptp-170) REVERT: C 538 LYS cc_start: 0.9549 (mmtm) cc_final: 0.9272 (mmtm) REVERT: C 541 ARG cc_start: 0.9228 (tpt-90) cc_final: 0.8771 (tpt-90) REVERT: C 562 HIS cc_start: 0.9244 (t70) cc_final: 0.8889 (t-90) REVERT: C 574 MET cc_start: 0.8042 (mtt) cc_final: 0.7711 (tpt) REVERT: C 617 PHE cc_start: 0.9617 (t80) cc_final: 0.9313 (t80) REVERT: C 645 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.8595 (tmm) REVERT: C 647 ILE cc_start: 0.9694 (tt) cc_final: 0.9481 (tt) REVERT: C 651 MET cc_start: 0.9551 (mmm) cc_final: 0.9331 (mmm) REVERT: C 658 ASN cc_start: 0.9146 (m110) cc_final: 0.8830 (m110) REVERT: C 677 MET cc_start: 0.9716 (tpp) cc_final: 0.9052 (mmm) REVERT: C 681 ARG cc_start: 0.9628 (mmm-85) cc_final: 0.9085 (mtm-85) REVERT: C 707 TYR cc_start: 0.9036 (t80) cc_final: 0.8479 (t80) REVERT: C 729 CYS cc_start: 0.9544 (m) cc_final: 0.9282 (m) REVERT: C 762 HIS cc_start: 0.8224 (m-70) cc_final: 0.6809 (m-70) REVERT: C 821 ASP cc_start: 0.8999 (m-30) cc_final: 0.8595 (p0) REVERT: C 840 GLU cc_start: 0.9683 (mt-10) cc_final: 0.9172 (tp30) REVERT: C 841 VAL cc_start: 0.9847 (t) cc_final: 0.9607 (t) REVERT: C 844 MET cc_start: 0.9411 (mtm) cc_final: 0.8265 (mtm) REVERT: D 12 ASN cc_start: 0.9460 (t0) cc_final: 0.9206 (t0) REVERT: D 109 LEU cc_start: 0.9285 (tp) cc_final: 0.8649 (pp) REVERT: D 411 ASP cc_start: 0.9387 (t70) cc_final: 0.8849 (t0) REVERT: D 414 ILE cc_start: 0.9708 (tt) cc_final: 0.9485 (pt) REVERT: D 424 PHE cc_start: 0.9436 (m-80) cc_final: 0.9077 (m-80) REVERT: D 533 VAL cc_start: 0.9734 (t) cc_final: 0.9467 (p) REVERT: D 538 LYS cc_start: 0.9565 (mmtm) cc_final: 0.9311 (mmtm) REVERT: D 541 ARG cc_start: 0.9269 (tpp80) cc_final: 0.8801 (tpp80) REVERT: D 562 HIS cc_start: 0.9216 (t70) cc_final: 0.8925 (t-170) REVERT: D 563 TRP cc_start: 0.9641 (m-10) cc_final: 0.9435 (m-10) REVERT: D 574 MET cc_start: 0.8055 (mtt) cc_final: 0.7713 (tpt) REVERT: D 619 PHE cc_start: 0.9500 (OUTLIER) cc_final: 0.8931 (t80) REVERT: D 645 MET cc_start: 0.9622 (ttt) cc_final: 0.9107 (ptm) REVERT: D 647 ILE cc_start: 0.9696 (tt) cc_final: 0.9479 (tt) REVERT: D 651 MET cc_start: 0.9526 (mmm) cc_final: 0.9293 (mmm) REVERT: D 658 ASN cc_start: 0.9174 (m110) cc_final: 0.8851 (m110) REVERT: D 677 MET cc_start: 0.9662 (tpp) cc_final: 0.8923 (tmm) REVERT: D 681 ARG cc_start: 0.9621 (mtm180) cc_final: 0.8935 (mtm180) REVERT: D 729 CYS cc_start: 0.9566 (m) cc_final: 0.9316 (m) REVERT: D 784 ARG cc_start: 0.9541 (mtp-110) cc_final: 0.9296 (ptm160) REVERT: D 821 ASP cc_start: 0.8937 (m-30) cc_final: 0.8525 (p0) REVERT: D 827 TYR cc_start: 0.8657 (m-80) cc_final: 0.8442 (m-10) REVERT: D 840 GLU cc_start: 0.9689 (mt-10) cc_final: 0.9131 (tp30) REVERT: D 841 VAL cc_start: 0.9835 (p) cc_final: 0.9477 (m) REVERT: D 844 MET cc_start: 0.9390 (mtm) cc_final: 0.8266 (mtm) outliers start: 53 outliers final: 45 residues processed: 515 average time/residue: 0.1079 time to fit residues: 86.6825 Evaluate side-chains 526 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 477 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 623 THR Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 842 LEU 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 539 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 761 THR 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 C residue 17 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 537 ARG 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 645 MET Chi-restraints excluded: chain C residue 718 LYS 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 36 VAL 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 646 LEU Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 782 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 188 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 66 optimal weight: 40.0000 chunk 10 optimal weight: 0.0270 chunk 24 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 209 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- 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 12 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 676 GLN ** D 702 GLN ** 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 = 0.3319 r_free = 0.3319 target = 0.066963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.054505 restraints weight = 94720.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.056073 restraints weight = 60638.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.057239 restraints weight = 43433.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058094 restraints weight = 33540.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.058744 restraints weight = 27333.171| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.6905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18004 Z= 0.136 Angle : 0.840 14.854 24432 Z= 0.397 Chirality : 0.048 0.355 2788 Planarity : 0.003 0.027 3064 Dihedral : 4.394 19.819 2420 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.26 % Favored : 95.38 % Rotamer: Outliers : 3.08 % Allowed : 30.36 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.17), residues: 2184 helix: -0.47 (0.15), residues: 1188 sheet: -0.53 (0.46), residues: 124 loop : -1.11 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 694 TYR 0.020 0.001 TYR B 700 PHE 0.018 0.001 PHE B 640 TRP 0.047 0.002 TRP A 410 HIS 0.006 0.001 HIS D 834 Details of bonding type rmsd covalent geometry : bond 0.00303 (18000) covalent geometry : angle 0.83955 (24432) hydrogen bonds : bond 0.04384 ( 784) hydrogen bonds : angle 5.14289 ( 2280) Misc. bond : bond 0.00044 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3778.83 seconds wall clock time: 65 minutes 42.15 seconds (3942.15 seconds total)