Starting phenix.real_space_refine on Fri Sep 27 21:48:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/09_2024/5va2_8651.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/09_2024/5va2_8651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/09_2024/5va2_8651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/09_2024/5va2_8651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/09_2024/5va2_8651.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va2_8651/09_2024/5va2_8651.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.436 sd= 0.853 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 11456 2.51 5 N 2996 2.21 5 O 3016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17576 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4394 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 536} Chain breaks: 5 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Restraints were copied for chains: C, B, D Time building chain proxies: 9.41, per 1000 atoms: 0.54 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=0, symmetry=0 Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 2.3 seconds 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4184 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 12 sheets defined 59.5% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 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: 5.10 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 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: 1.61 - 2.27: 32 2.27 - 2.92: 6496 2.92 - 3.58: 24000 3.58 - 4.24: 36950 4.24 - 4.90: 65184 Nonbonded interactions: 132662 Sorted by model distance: nonbonded pdb=" NH1 ARG C 752 " pdb=" CD2 HIS D 771 " model vdw 1.607 3.340 nonbonded pdb=" NH1 ARG B 752 " pdb=" CD2 HIS C 771 " model vdw 1.607 3.340 nonbonded pdb=" CD2 HIS A 771 " pdb=" NH1 ARG D 752 " model vdw 1.607 3.340 nonbonded pdb=" NH1 ARG A 752 " pdb=" CD2 HIS B 771 " model vdw 1.607 3.340 nonbonded pdb=" CG HIS A 771 " pdb=" NH1 ARG D 752 " model vdw 1.799 3.340 ... (remaining 132657 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.140 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 37.220 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.220 ------------------------------------------------------------------------------- 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 0.044 18000 Z= 0.514 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 : 1.607 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 1.65 % Allowed : 7.69 % Favored : 90.66 % Rotamer: Outliers : 1.08 % Allowed : 6.49 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.14), residues: 2184 helix: -2.20 (0.11), residues: 1104 sheet: -4.06 (0.30), residues: 128 loop : -2.67 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 705 HIS 0.005 0.001 HIS A 587 PHE 0.011 0.001 PHE D 494 TYR 0.013 0.001 TYR D 652 ARG 0.003 0.000 ARG A 694 *********************** 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 fitting. rotamer outliers: 20 poor density : 896 time to evaluate : 2.140 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: 0.3176 time to fit residues: 414.5748 Evaluate side-chains 592 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 590 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain C residue 804 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 199 optimal weight: 20.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 470 ASN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 GLN A 731 HIS A 834 HIS B 12 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 GLN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS B 834 HIS C 12 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN C 762 HIS C 834 HIS D 12 ASN D 470 ASN ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 GLN D 834 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18000 Z= 0.243 Angle : 0.827 9.629 24432 Z= 0.416 Chirality : 0.047 0.197 2788 Planarity : 0.005 0.063 3064 Dihedral : 5.357 32.910 2424 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.49 % Favored : 94.78 % Rotamer: Outliers : 4.44 % Allowed : 17.21 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.17), residues: 2184 helix: -0.79 (0.14), residues: 1192 sheet: -2.21 (0.40), residues: 132 loop : -2.09 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 497 HIS 0.008 0.002 HIS D 771 PHE 0.017 0.002 PHE C 617 TYR 0.024 0.002 TYR B 700 ARG 0.008 0.001 ARG B 823 *********************** 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 694 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 612 time to evaluate : 1.988 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: A 43 TYR cc_start: 0.9474 (t80) cc_final: 0.9173 (t80) REVERT: A 533 VAL cc_start: 0.9490 (t) cc_final: 0.9091 (p) REVERT: A 574 MET cc_start: 0.8421 (mtt) cc_final: 0.7979 (ppp) REVERT: A 676 GLN cc_start: 0.9882 (mm110) cc_final: 0.9614 (pt0) REVERT: A 677 MET cc_start: 0.9836 (tpp) cc_final: 0.9441 (mmm) REVERT: A 702 GLN cc_start: 0.9649 (mt0) cc_final: 0.9425 (pp30) REVERT: A 711 ILE cc_start: 0.7015 (mt) cc_final: 0.4473 (mm) REVERT: A 741 LYS cc_start: 0.9693 (mmtt) cc_final: 0.9448 (ttpp) REVERT: A 798 ILE cc_start: 0.9832 (mp) cc_final: 0.9595 (mm) REVERT: A 840 GLU cc_start: 0.9701 (mt-10) cc_final: 0.9487 (tm-30) REVERT: A 844 MET cc_start: 0.9732 (mmp) cc_final: 0.9311 (mtm) REVERT: B 533 VAL cc_start: 0.9507 (t) cc_final: 0.9194 (p) REVERT: B 574 MET cc_start: 0.8450 (mtt) cc_final: 0.7957 (ppp) REVERT: B 677 MET cc_start: 0.9852 (tpp) cc_final: 0.9502 (mmm) REVERT: B 678 LEU cc_start: 0.9803 (mt) cc_final: 0.9503 (mt) REVERT: B 682 GLU cc_start: 0.9644 (pt0) cc_final: 0.9364 (tm-30) REVERT: B 712 ASP cc_start: 0.9514 (m-30) cc_final: 0.9237 (p0) REVERT: B 741 LYS cc_start: 0.9705 (mmtt) cc_final: 0.9468 (ttpp) REVERT: B 823 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8329 (mmp80) REVERT: C 12 ASN cc_start: 0.9179 (OUTLIER) cc_final: 0.8855 (t0) REVERT: C 59 VAL cc_start: 0.9339 (t) cc_final: 0.8854 (m) REVERT: C 424 PHE cc_start: 0.9692 (m-80) cc_final: 0.9486 (m-80) REVERT: C 533 VAL cc_start: 0.9452 (t) cc_final: 0.9192 (p) REVERT: C 574 MET cc_start: 0.8366 (mtt) cc_final: 0.7862 (ppp) REVERT: C 575 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8160 (tp30) REVERT: C 677 MET cc_start: 0.9852 (tpp) cc_final: 0.9494 (mmm) REVERT: C 711 ILE cc_start: 0.6957 (mt) cc_final: 0.4327 (mm) REVERT: C 712 ASP cc_start: 0.9441 (m-30) cc_final: 0.9169 (p0) REVERT: C 768 THR cc_start: 0.8142 (p) cc_final: 0.7730 (p) REVERT: C 821 ASP cc_start: 0.9245 (m-30) cc_final: 0.9010 (p0) REVERT: C 823 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7794 (mmp80) REVERT: C 840 GLU cc_start: 0.9688 (mt-10) cc_final: 0.9454 (tm-30) REVERT: C 844 MET cc_start: 0.9680 (mmp) cc_final: 0.9324 (mtm) REVERT: D 12 ASN cc_start: 0.9255 (OUTLIER) cc_final: 0.8938 (t0) REVERT: D 59 VAL cc_start: 0.9450 (t) cc_final: 0.9225 (p) REVERT: D 424 PHE cc_start: 0.9684 (m-80) cc_final: 0.9471 (m-80) REVERT: D 533 VAL cc_start: 0.9451 (t) cc_final: 0.9033 (p) REVERT: D 574 MET cc_start: 0.8317 (mtt) cc_final: 0.7852 (ppp) REVERT: D 575 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8215 (tp30) REVERT: D 619 PHE cc_start: 0.9813 (OUTLIER) cc_final: 0.9327 (t80) REVERT: D 677 MET cc_start: 0.9861 (tpp) cc_final: 0.9538 (tmm) REVERT: D 681 ARG cc_start: 0.9540 (mtt180) cc_final: 0.9278 (mmm160) REVERT: D 682 GLU cc_start: 0.9664 (pt0) cc_final: 0.9450 (tm-30) REVERT: D 702 GLN cc_start: 0.9650 (mt0) cc_final: 0.9407 (pp30) REVERT: D 823 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7983 (mmp80) REVERT: D 840 GLU cc_start: 0.9712 (mt-10) cc_final: 0.9482 (tm-30) REVERT: D 844 MET cc_start: 0.9712 (mmp) cc_final: 0.9363 (mtm) outliers start: 82 outliers final: 46 residues processed: 662 average time/residue: 0.2758 time to fit residues: 272.9246 Evaluate side-chains 537 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 485 time to evaluate : 1.844 ------------------------------------------------------------------------------- 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 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 36 VAL 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 736 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 823 ARG 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 36 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 823 ARG Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 36 VAL 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 736 LEU Chi-restraints excluded: chain D residue 789 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 804 ILE Chi-restraints excluded: chain D residue 823 ARG 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 111 optimal weight: 10.0000 chunk 62 optimal weight: 50.0000 chunk 166 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 55 optimal weight: 50.0000 chunk 200 optimal weight: 20.0000 chunk 216 optimal weight: 20.0000 chunk 178 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 chunk 160 optimal weight: 40.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- 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 562 HIS ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 ASN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 691 ASN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN C 70 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 70 HIS ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18000 Z= 0.272 Angle : 0.780 11.610 24432 Z= 0.394 Chirality : 0.047 0.232 2788 Planarity : 0.005 0.084 3064 Dihedral : 5.026 22.703 2420 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.17 % Favored : 95.10 % Rotamer: Outliers : 5.63 % Allowed : 20.45 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.17), residues: 2184 helix: -0.38 (0.14), residues: 1192 sheet: -1.55 (0.37), residues: 160 loop : -1.94 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 497 HIS 0.006 0.002 HIS D 771 PHE 0.025 0.002 PHE D 48 TYR 0.015 0.002 TYR D 43 ARG 0.014 0.001 ARG C 537 *********************** 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 605 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 501 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 VAL cc_start: 0.9499 (t) cc_final: 0.9181 (p) REVERT: A 538 LYS cc_start: 0.9052 (mmtm) cc_final: 0.8758 (mmtm) REVERT: A 541 ARG cc_start: 0.8998 (tpp80) cc_final: 0.8782 (tpp80) REVERT: A 642 ILE cc_start: 0.9502 (mm) cc_final: 0.9263 (mm) REVERT: A 702 GLN cc_start: 0.9653 (mt0) cc_final: 0.9435 (pp30) REVERT: A 809 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9190 (mp) REVERT: B 472 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8733 (tpt-90) REVERT: B 642 ILE cc_start: 0.9558 (mm) cc_final: 0.9338 (mm) REVERT: B 645 MET cc_start: 0.9468 (ttm) cc_final: 0.9233 (ptm) REVERT: B 712 ASP cc_start: 0.9564 (m-30) cc_final: 0.9329 (p0) REVERT: B 809 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9207 (mp) REVERT: B 840 GLU cc_start: 0.9655 (tp30) cc_final: 0.9384 (tp30) REVERT: B 844 MET cc_start: 0.9481 (mmp) cc_final: 0.9015 (mmp) REVERT: C 411 ASP cc_start: 0.9433 (t70) cc_final: 0.8740 (t70) REVERT: C 533 VAL cc_start: 0.9404 (t) cc_final: 0.8960 (p) REVERT: C 534 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8943 (mmm160) REVERT: C 541 ARG cc_start: 0.9065 (tpt-90) cc_final: 0.8687 (tpt-90) REVERT: C 574 MET cc_start: 0.8343 (mtt) cc_final: 0.8106 (tpt) REVERT: C 619 PHE cc_start: 0.9812 (OUTLIER) cc_final: 0.9392 (t80) REVERT: C 691 ASN cc_start: 0.9847 (p0) cc_final: 0.9536 (m110) REVERT: C 698 GLU cc_start: 0.9701 (pt0) cc_final: 0.9449 (pp20) REVERT: C 809 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9224 (mp) REVERT: C 821 ASP cc_start: 0.9234 (m-30) cc_final: 0.9025 (p0) REVERT: D 574 MET cc_start: 0.8302 (mtt) cc_final: 0.8053 (tpt) REVERT: D 677 MET cc_start: 0.9871 (tpp) cc_final: 0.9562 (tmm) REVERT: D 681 ARG cc_start: 0.9554 (mtt180) cc_final: 0.9262 (mmm160) REVERT: D 702 GLN cc_start: 0.9683 (mt0) cc_final: 0.9417 (pp30) REVERT: D 809 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9197 (mp) outliers start: 104 outliers final: 64 residues processed: 577 average time/residue: 0.2772 time to fit residues: 241.6895 Evaluate side-chains 522 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 451 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 809 LEU 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 459 VAL Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 535 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 768 THR Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 817 LYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL 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 619 PHE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 823 ARG Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 472 ARG 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 789 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 804 ILE Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 103 optimal weight: 50.0000 chunk 22 optimal weight: 0.0970 chunk 95 optimal weight: 7.9990 chunk 134 optimal weight: 0.0970 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 57 optimal weight: 50.0000 overall best weight: 4.2382 ------------------------------------------------------------------------------- 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 691 ASN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 HIS B 658 ASN B 691 ASN ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 HIS C 12 ASN C 562 HIS ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 HIS D 12 ASN D 562 HIS ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 ASN D 691 ASN D 762 HIS ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18000 Z= 0.198 Angle : 0.738 13.334 24432 Z= 0.365 Chirality : 0.045 0.178 2788 Planarity : 0.004 0.036 3064 Dihedral : 4.735 22.805 2420 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.69 % Allowed : 4.17 % Favored : 95.15 % Rotamer: Outliers : 4.49 % Allowed : 21.92 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2184 helix: -0.33 (0.14), residues: 1216 sheet: -1.20 (0.38), residues: 160 loop : -1.62 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 410 HIS 0.008 0.001 HIS B 762 PHE 0.016 0.001 PHE A 640 TYR 0.015 0.001 TYR B 700 ARG 0.009 0.001 ARG B 537 *********************** 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 581 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 498 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 472 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8593 (tpp80) REVERT: A 533 VAL cc_start: 0.9441 (t) cc_final: 0.9213 (p) REVERT: A 538 LYS cc_start: 0.9174 (mmtm) cc_final: 0.8927 (mmtm) REVERT: A 677 MET cc_start: 0.9776 (tpp) cc_final: 0.9240 (tmm) REVERT: A 681 ARG cc_start: 0.9356 (mmm160) cc_final: 0.9132 (mmm-85) REVERT: A 702 GLN cc_start: 0.9642 (mt0) cc_final: 0.9420 (pp30) REVERT: A 809 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9047 (mp) REVERT: B 12 ASN cc_start: 0.9580 (t0) cc_final: 0.9315 (t0) REVERT: B 411 ASP cc_start: 0.9465 (t70) cc_final: 0.8906 (t0) REVERT: B 462 MET cc_start: 0.9548 (tpt) cc_final: 0.9342 (tpt) REVERT: B 472 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8709 (tpp80) REVERT: B 534 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.8972 (mmm160) REVERT: B 642 ILE cc_start: 0.9558 (mm) cc_final: 0.9317 (mm) REVERT: B 645 MET cc_start: 0.9493 (ttm) cc_final: 0.9289 (ptm) REVERT: B 658 ASN cc_start: 0.8996 (m110) cc_final: 0.8775 (m110) REVERT: B 712 ASP cc_start: 0.9603 (m-30) cc_final: 0.9303 (p0) REVERT: B 809 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9037 (mp) REVERT: B 843 ASP cc_start: 0.9455 (p0) cc_final: 0.9235 (p0) REVERT: C 12 ASN cc_start: 0.9434 (OUTLIER) cc_final: 0.8900 (t0) REVERT: C 411 ASP cc_start: 0.9444 (t70) cc_final: 0.8621 (t70) REVERT: C 472 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8651 (tpp80) REVERT: C 533 VAL cc_start: 0.9398 (t) cc_final: 0.8818 (p) REVERT: C 534 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8905 (mmm160) REVERT: C 541 ARG cc_start: 0.9127 (tpt-90) cc_final: 0.8770 (tpt-90) REVERT: C 619 PHE cc_start: 0.9813 (OUTLIER) cc_final: 0.9383 (t80) REVERT: C 658 ASN cc_start: 0.8936 (m110) cc_final: 0.8702 (m110) REVERT: C 809 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9121 (mp) REVERT: C 821 ASP cc_start: 0.9203 (m-30) cc_final: 0.8971 (p0) REVERT: D 12 ASN cc_start: 0.9501 (OUTLIER) cc_final: 0.9300 (t0) REVERT: D 472 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8582 (tpp80) REVERT: D 541 ARG cc_start: 0.9089 (tpp80) cc_final: 0.8843 (tpp80) REVERT: D 574 MET cc_start: 0.8252 (mtt) cc_final: 0.8028 (tpt) REVERT: D 617 PHE cc_start: 0.9688 (t80) cc_final: 0.9368 (t80) REVERT: D 658 ASN cc_start: 0.8911 (m110) cc_final: 0.8681 (m110) REVERT: D 677 MET cc_start: 0.9862 (tpp) cc_final: 0.9268 (tmm) REVERT: D 681 ARG cc_start: 0.9524 (mtt180) cc_final: 0.9063 (mmm-85) REVERT: D 702 GLN cc_start: 0.9694 (mt0) cc_final: 0.9416 (pp30) REVERT: D 809 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9027 (mp) outliers start: 83 outliers final: 54 residues processed: 552 average time/residue: 0.2750 time to fit residues: 229.1801 Evaluate side-chains 530 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 463 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 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 768 THR Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 817 LYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 534 ARG Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 714 ASN Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain C residue 823 ARG Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain D residue 12 ASN 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 472 ARG 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 698 GLU 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 782 ILE Chi-restraints excluded: chain D residue 788 GLU Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 0.0970 chunk 120 optimal weight: 50.0000 chunk 3 optimal weight: 40.0000 chunk 158 optimal weight: 50.0000 chunk 87 optimal weight: 20.0000 chunk 181 optimal weight: 20.0000 chunk 146 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 108 optimal weight: 40.0000 chunk 190 optimal weight: 7.9990 chunk 53 optimal weight: 0.3980 overall best weight: 9.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 GLN A 691 ASN B 691 ASN ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18000 Z= 0.247 Angle : 0.765 13.224 24432 Z= 0.378 Chirality : 0.046 0.229 2788 Planarity : 0.004 0.030 3064 Dihedral : 4.756 23.081 2420 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.35 % Favored : 95.28 % Rotamer: Outliers : 5.03 % Allowed : 24.35 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2184 helix: -0.36 (0.14), residues: 1176 sheet: -0.96 (0.38), residues: 164 loop : -1.62 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 410 HIS 0.006 0.001 HIS B 731 PHE 0.028 0.002 PHE A 640 TYR 0.017 0.002 TYR D 43 ARG 0.014 0.001 ARG B 537 *********************** 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 569 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 476 time to evaluate : 1.948 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 411 ASP cc_start: 0.9443 (t70) cc_final: 0.9115 (t0) REVERT: A 472 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8511 (tpp80) REVERT: A 533 VAL cc_start: 0.9436 (t) cc_final: 0.9181 (p) REVERT: A 677 MET cc_start: 0.9811 (tpp) cc_final: 0.9210 (tmm) REVERT: A 681 ARG cc_start: 0.9357 (mmm160) cc_final: 0.9111 (mmm-85) REVERT: A 682 GLU cc_start: 0.9708 (pt0) cc_final: 0.9403 (tm-30) REVERT: A 702 GLN cc_start: 0.9662 (mt0) cc_final: 0.9423 (pp30) REVERT: A 809 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9006 (mp) REVERT: A 844 MET cc_start: 0.8898 (mtm) cc_final: 0.8526 (ptt) REVERT: B 12 ASN cc_start: 0.9602 (m-40) cc_final: 0.9355 (t0) REVERT: B 411 ASP cc_start: 0.9380 (t70) cc_final: 0.9008 (t0) REVERT: B 462 MET cc_start: 0.9599 (tpt) cc_final: 0.9363 (tpt) REVERT: B 472 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8680 (tpm170) REVERT: B 538 LYS cc_start: 0.8991 (mmtm) cc_final: 0.8784 (mmtm) REVERT: B 645 MET cc_start: 0.9414 (ttm) cc_final: 0.8719 (ttm) REVERT: B 677 MET cc_start: 0.9800 (tpp) cc_final: 0.9369 (tmm) REVERT: B 681 ARG cc_start: 0.9361 (mmm160) cc_final: 0.9058 (mmm-85) REVERT: B 712 ASP cc_start: 0.9593 (m-30) cc_final: 0.9322 (p0) REVERT: B 809 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9022 (mp) REVERT: C 411 ASP cc_start: 0.9325 (t70) cc_final: 0.8695 (t70) REVERT: C 472 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8528 (mmm-85) REVERT: C 541 ARG cc_start: 0.9149 (tpt-90) cc_final: 0.8767 (tpt-90) REVERT: C 619 PHE cc_start: 0.9803 (OUTLIER) cc_final: 0.9304 (t80) REVERT: C 645 MET cc_start: 0.9786 (ttt) cc_final: 0.9496 (ptm) REVERT: C 658 ASN cc_start: 0.8908 (m110) cc_final: 0.8677 (m110) REVERT: C 691 ASN cc_start: 0.9810 (p0) cc_final: 0.9533 (t0) REVERT: C 809 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.8642 (mp) REVERT: C 838 LEU cc_start: 0.9841 (tp) cc_final: 0.9629 (pp) REVERT: D 472 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8561 (tpp80) REVERT: D 541 ARG cc_start: 0.9095 (tpp80) cc_final: 0.8829 (tpp80) REVERT: D 574 MET cc_start: 0.8282 (mtt) cc_final: 0.8034 (tpt) REVERT: D 617 PHE cc_start: 0.9719 (t80) cc_final: 0.9389 (t80) REVERT: D 619 PHE cc_start: 0.9775 (OUTLIER) cc_final: 0.9447 (t80) REVERT: D 658 ASN cc_start: 0.8925 (m110) cc_final: 0.8700 (m110) REVERT: D 677 MET cc_start: 0.9886 (tpp) cc_final: 0.9577 (tmm) REVERT: D 681 ARG cc_start: 0.9535 (mtt180) cc_final: 0.9211 (mmm160) REVERT: D 702 GLN cc_start: 0.9697 (mt0) cc_final: 0.9418 (pp30) REVERT: D 713 MET cc_start: 0.8147 (mmt) cc_final: 0.7702 (mmt) REVERT: D 809 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9057 (mp) outliers start: 93 outliers final: 58 residues processed: 539 average time/residue: 0.2696 time to fit residues: 220.8491 Evaluate side-chains 527 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 459 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 589 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 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 817 LYS Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 834 HIS Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 472 ARG 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 762 HIS Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 796 VAL Chi-restraints excluded: chain C residue 809 LEU 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 82 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 472 ARG 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 741 LYS 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 804 ILE Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 858 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.0870 chunk 191 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 52 optimal weight: 30.0000 chunk 212 optimal weight: 30.0000 chunk 176 optimal weight: 50.0000 chunk 98 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 ASN ** 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** C 762 HIS ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 GLN ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18000 Z= 0.201 Angle : 0.774 13.558 24432 Z= 0.376 Chirality : 0.046 0.199 2788 Planarity : 0.004 0.035 3064 Dihedral : 4.628 21.278 2420 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.40 % Favored : 95.24 % Rotamer: Outliers : 4.11 % Allowed : 27.22 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.17), residues: 2184 helix: -0.35 (0.14), residues: 1212 sheet: -0.77 (0.40), residues: 164 loop : -1.40 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 410 HIS 0.013 0.001 HIS C 762 PHE 0.031 0.002 PHE C 424 TYR 0.015 0.001 TYR C 700 ARG 0.011 0.001 ARG C 537 *********************** 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 567 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 491 time to evaluate : 2.074 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 12 ASN cc_start: 0.9664 (t0) cc_final: 0.9432 (t0) REVERT: A 411 ASP cc_start: 0.9419 (t70) cc_final: 0.9098 (t0) REVERT: A 472 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8532 (tpp80) REVERT: A 677 MET cc_start: 0.9801 (tpp) cc_final: 0.9176 (tmm) REVERT: A 678 LEU cc_start: 0.9794 (pp) cc_final: 0.9388 (pp) REVERT: A 681 ARG cc_start: 0.9338 (mmm160) cc_final: 0.9067 (mmm-85) REVERT: A 682 GLU cc_start: 0.9709 (pt0) cc_final: 0.9401 (tm-30) REVERT: A 702 GLN cc_start: 0.9656 (mt0) cc_final: 0.9406 (pp30) REVERT: A 809 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8929 (mp) REVERT: A 821 ASP cc_start: 0.9104 (p0) cc_final: 0.8868 (m-30) REVERT: B 411 ASP cc_start: 0.9365 (t70) cc_final: 0.9004 (t0) REVERT: B 462 MET cc_start: 0.9599 (tpt) cc_final: 0.9357 (tpt) REVERT: B 472 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8641 (tpp80) REVERT: B 538 LYS cc_start: 0.9091 (mmtm) cc_final: 0.8845 (mmtm) REVERT: B 645 MET cc_start: 0.9455 (ttm) cc_final: 0.9209 (ttm) REVERT: B 712 ASP cc_start: 0.9592 (m-30) cc_final: 0.9327 (p0) REVERT: B 809 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8942 (mp) REVERT: C 411 ASP cc_start: 0.9341 (t70) cc_final: 0.8714 (t70) REVERT: C 472 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8651 (tpp80) REVERT: C 541 ARG cc_start: 0.9184 (tpt-90) cc_final: 0.8814 (tpt-90) REVERT: C 658 ASN cc_start: 0.8882 (m110) cc_final: 0.8652 (m110) REVERT: C 677 MET cc_start: 0.9587 (mmm) cc_final: 0.9302 (mmm) REVERT: C 681 ARG cc_start: 0.9518 (mmm-85) cc_final: 0.9192 (mtm-85) REVERT: C 691 ASN cc_start: 0.9818 (p0) cc_final: 0.9547 (t0) REVERT: C 809 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9049 (mp) REVERT: C 821 ASP cc_start: 0.9258 (m-30) cc_final: 0.8924 (p0) REVERT: D 472 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8533 (tpp80) REVERT: D 541 ARG cc_start: 0.9131 (tpp80) cc_final: 0.8920 (tpp80) REVERT: D 574 MET cc_start: 0.8253 (mtt) cc_final: 0.7996 (tpt) REVERT: D 617 PHE cc_start: 0.9696 (t80) cc_final: 0.9356 (t80) REVERT: D 619 PHE cc_start: 0.9713 (OUTLIER) cc_final: 0.9472 (t80) REVERT: D 658 ASN cc_start: 0.8892 (m110) cc_final: 0.8666 (m110) REVERT: D 677 MET cc_start: 0.9881 (tpp) cc_final: 0.9271 (tmm) REVERT: D 681 ARG cc_start: 0.9519 (mtt180) cc_final: 0.9051 (mmm-85) REVERT: D 702 GLN cc_start: 0.9685 (mt0) cc_final: 0.9397 (pp30) REVERT: D 713 MET cc_start: 0.8065 (mmt) cc_final: 0.7546 (mmt) REVERT: D 809 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9046 (mp) outliers start: 76 outliers final: 46 residues processed: 542 average time/residue: 0.2743 time to fit residues: 226.5031 Evaluate side-chains 520 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 465 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 483 VAL 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 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 817 LYS Chi-restraints excluded: chain B residue 834 HIS Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 809 LEU 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 413 LEU Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 472 ARG Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 537 ARG Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 676 GLN Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 741 LYS 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 804 ILE Chi-restraints excluded: chain D residue 809 LEU 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 205 optimal weight: 30.0000 chunk 23 optimal weight: 8.9990 chunk 121 optimal weight: 50.0000 chunk 155 optimal weight: 40.0000 chunk 120 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 97 optimal weight: 40.0000 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 ASN ** 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 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 HIS ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18000 Z= 0.237 Angle : 0.815 15.113 24432 Z= 0.396 Chirality : 0.047 0.267 2788 Planarity : 0.004 0.028 3064 Dihedral : 4.662 21.643 2420 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.30 % Favored : 95.33 % Rotamer: Outliers : 4.33 % Allowed : 29.33 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.17), residues: 2184 helix: -0.37 (0.14), residues: 1212 sheet: -1.09 (0.34), residues: 212 loop : -1.32 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 410 HIS 0.006 0.001 HIS C 731 PHE 0.034 0.002 PHE A 640 TYR 0.019 0.002 TYR B 43 ARG 0.009 0.001 ARG C 537 *********************** 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 562 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 482 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9673 (t0) cc_final: 0.9436 (t0) REVERT: A 411 ASP cc_start: 0.9409 (t70) cc_final: 0.9096 (t0) REVERT: A 472 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8501 (tpp80) REVERT: A 619 PHE cc_start: 0.9828 (OUTLIER) cc_final: 0.9484 (t80) REVERT: A 677 MET cc_start: 0.9800 (tpp) cc_final: 0.9173 (tmm) REVERT: A 678 LEU cc_start: 0.9792 (pp) cc_final: 0.9353 (pp) REVERT: A 681 ARG cc_start: 0.9333 (mmm160) cc_final: 0.9069 (mmm-85) REVERT: A 682 GLU cc_start: 0.9717 (pt0) cc_final: 0.9408 (tm-30) REVERT: A 702 GLN cc_start: 0.9661 (mt0) cc_final: 0.9412 (pp30) REVERT: A 809 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8932 (mp) REVERT: A 821 ASP cc_start: 0.9114 (p0) cc_final: 0.8875 (m-30) REVERT: B 12 ASN cc_start: 0.9626 (t0) cc_final: 0.9306 (t0) REVERT: B 410 TRP cc_start: 0.9568 (t-100) cc_final: 0.9185 (t-100) REVERT: B 411 ASP cc_start: 0.9353 (t70) cc_final: 0.9072 (t0) REVERT: B 462 MET cc_start: 0.9656 (tpt) cc_final: 0.9369 (tpt) REVERT: B 472 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8601 (tpp80) REVERT: B 538 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8877 (mmtm) REVERT: B 619 PHE cc_start: 0.9823 (OUTLIER) cc_final: 0.9481 (t80) REVERT: B 645 MET cc_start: 0.9412 (ttm) cc_final: 0.8602 (ttm) REVERT: B 712 ASP cc_start: 0.9600 (m-30) cc_final: 0.9350 (p0) REVERT: B 809 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8885 (mp) REVERT: C 411 ASP cc_start: 0.9314 (t70) cc_final: 0.8724 (t70) REVERT: C 472 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8600 (tpp80) REVERT: C 541 ARG cc_start: 0.9174 (tpt-90) cc_final: 0.8802 (tpt-90) REVERT: C 619 PHE cc_start: 0.9809 (OUTLIER) cc_final: 0.9340 (t80) REVERT: C 658 ASN cc_start: 0.8876 (m110) cc_final: 0.8648 (m110) REVERT: C 677 MET cc_start: 0.9644 (mmm) cc_final: 0.9360 (mmm) REVERT: C 681 ARG cc_start: 0.9540 (mmm-85) cc_final: 0.9155 (mtm-85) REVERT: C 809 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9144 (mp) REVERT: C 821 ASP cc_start: 0.9257 (m-30) cc_final: 0.8880 (p0) REVERT: D 411 ASP cc_start: 0.9390 (t70) cc_final: 0.8957 (t0) REVERT: D 472 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8515 (tpp80) REVERT: D 541 ARG cc_start: 0.9164 (tpp80) cc_final: 0.8885 (tpp80) REVERT: D 574 MET cc_start: 0.8283 (mtt) cc_final: 0.8007 (tpt) REVERT: D 617 PHE cc_start: 0.9707 (t80) cc_final: 0.9417 (t80) REVERT: D 658 ASN cc_start: 0.8884 (m110) cc_final: 0.8659 (m110) REVERT: D 677 MET cc_start: 0.9874 (tpp) cc_final: 0.9524 (tmm) REVERT: D 681 ARG cc_start: 0.9522 (mtt180) cc_final: 0.9160 (mmm160) REVERT: D 702 GLN cc_start: 0.9685 (mt0) cc_final: 0.9399 (pp30) REVERT: D 713 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7638 (mmt) REVERT: D 809 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9054 (mp) REVERT: D 821 ASP cc_start: 0.9078 (p0) cc_final: 0.8849 (m-30) outliers start: 80 outliers final: 55 residues processed: 529 average time/residue: 0.2677 time to fit residues: 216.1377 Evaluate side-chains 534 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 467 time to evaluate : 1.935 ------------------------------------------------------------------------------- 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 472 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 VAL 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 768 THR Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 817 LYS Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 645 MET Chi-restraints excluded: chain C residue 762 HIS Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 809 LEU 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 82 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 472 ARG 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 641 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 713 MET Chi-restraints excluded: chain D residue 741 LYS Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 787 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 809 LEU 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 131 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 126 optimal weight: 0.0770 chunk 63 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 104 optimal weight: 50.0000 chunk 19 optimal weight: 0.0870 chunk 166 optimal weight: 5.9990 chunk 192 optimal weight: 30.0000 overall best weight: 4.0322 ------------------------------------------------------------------------------- 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** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS ** 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 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.6624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18000 Z= 0.195 Angle : 0.836 14.224 24432 Z= 0.400 Chirality : 0.047 0.272 2788 Planarity : 0.004 0.035 3064 Dihedral : 4.581 21.644 2420 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.12 % Favored : 95.51 % Rotamer: Outliers : 3.73 % Allowed : 31.01 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.17), residues: 2184 helix: -0.38 (0.14), residues: 1212 sheet: -0.97 (0.34), residues: 212 loop : -1.24 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 410 HIS 0.012 0.001 HIS B 834 PHE 0.032 0.002 PHE C 48 TYR 0.052 0.001 TYR B 700 ARG 0.006 0.000 ARG C 537 *********************** 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 560 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 491 time to evaluate : 1.894 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 12 ASN cc_start: 0.9654 (m-40) cc_final: 0.9438 (t0) REVERT: A 109 LEU cc_start: 0.9517 (tp) cc_final: 0.9077 (pp) REVERT: A 411 ASP cc_start: 0.9422 (t70) cc_final: 0.9172 (t0) REVERT: A 472 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8463 (tpp80) REVERT: A 538 LYS cc_start: 0.8986 (mmtm) cc_final: 0.8771 (mmtm) REVERT: A 619 PHE cc_start: 0.9822 (OUTLIER) cc_final: 0.9461 (t80) REVERT: A 677 MET cc_start: 0.9793 (tpp) cc_final: 0.9175 (tmm) REVERT: A 678 LEU cc_start: 0.9776 (pp) cc_final: 0.9359 (pp) REVERT: A 681 ARG cc_start: 0.9313 (mmm160) cc_final: 0.9035 (mmm-85) REVERT: A 682 GLU cc_start: 0.9726 (pt0) cc_final: 0.9430 (tm-30) REVERT: A 702 GLN cc_start: 0.9657 (mt0) cc_final: 0.9403 (pp30) REVERT: A 809 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8936 (mp) REVERT: B 12 ASN cc_start: 0.9594 (t0) cc_final: 0.9274 (t0) REVERT: B 109 LEU cc_start: 0.9504 (tp) cc_final: 0.9064 (pp) REVERT: B 410 TRP cc_start: 0.9569 (t-100) cc_final: 0.9313 (t-100) REVERT: B 411 ASP cc_start: 0.9306 (t70) cc_final: 0.9051 (t0) REVERT: B 462 MET cc_start: 0.9659 (tpt) cc_final: 0.9389 (tpt) REVERT: B 538 LYS cc_start: 0.9204 (mmtm) cc_final: 0.8964 (mmtm) REVERT: B 645 MET cc_start: 0.9429 (ttm) cc_final: 0.8654 (ttm) REVERT: B 658 ASN cc_start: 0.8892 (m110) cc_final: 0.8670 (m110) REVERT: B 677 MET cc_start: 0.9687 (tmm) cc_final: 0.9337 (mtm) REVERT: B 712 ASP cc_start: 0.9637 (m-30) cc_final: 0.9351 (p0) REVERT: B 809 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8880 (mp) REVERT: C 411 ASP cc_start: 0.9325 (t70) cc_final: 0.8698 (t70) REVERT: C 472 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8392 (mmm160) REVERT: C 541 ARG cc_start: 0.9222 (tpt-90) cc_final: 0.8877 (tpt-90) REVERT: C 619 PHE cc_start: 0.9804 (OUTLIER) cc_final: 0.9322 (t80) REVERT: C 658 ASN cc_start: 0.8831 (m110) cc_final: 0.8605 (m110) REVERT: C 677 MET cc_start: 0.9634 (mmm) cc_final: 0.9314 (mmm) REVERT: C 681 ARG cc_start: 0.9530 (mmm-85) cc_final: 0.9169 (mtm-85) REVERT: C 691 ASN cc_start: 0.9803 (p0) cc_final: 0.9561 (t0) REVERT: C 809 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9114 (mp) REVERT: C 821 ASP cc_start: 0.9241 (m-30) cc_final: 0.8856 (p0) REVERT: D 411 ASP cc_start: 0.9378 (t70) cc_final: 0.8965 (t0) REVERT: D 472 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8291 (mmm160) REVERT: D 541 ARG cc_start: 0.9186 (tpp80) cc_final: 0.8932 (tpp80) REVERT: D 574 MET cc_start: 0.8254 (mtt) cc_final: 0.7973 (tpt) REVERT: D 617 PHE cc_start: 0.9691 (t80) cc_final: 0.9413 (t80) REVERT: D 658 ASN cc_start: 0.8839 (m110) cc_final: 0.8613 (m110) REVERT: D 677 MET cc_start: 0.9871 (tpp) cc_final: 0.9177 (tmm) REVERT: D 681 ARG cc_start: 0.9500 (mtt180) cc_final: 0.8986 (mmm-85) REVERT: D 702 GLN cc_start: 0.9682 (mt0) cc_final: 0.9378 (pp30) REVERT: D 713 MET cc_start: 0.8189 (mmt) cc_final: 0.7738 (mmt) REVERT: D 809 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9047 (mp) outliers start: 69 outliers final: 42 residues processed: 534 average time/residue: 0.2672 time to fit residues: 217.8584 Evaluate side-chains 528 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 477 time to evaluate : 1.828 ------------------------------------------------------------------------------- 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 472 ARG Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 809 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 472 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 VAL 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 768 THR Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 817 LYS Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 535 VAL 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 782 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 809 LEU 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 421 THR Chi-restraints excluded: chain D residue 472 ARG Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 535 VAL 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 809 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 0.0970 chunk 185 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 155 optimal weight: 40.0000 chunk 60 optimal weight: 20.0000 chunk 178 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 chunk 196 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- 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** ** 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18000 Z= 0.197 Angle : 0.879 19.209 24432 Z= 0.417 Chirality : 0.048 0.353 2788 Planarity : 0.003 0.026 3064 Dihedral : 4.539 21.170 2420 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.03 % Favored : 95.60 % Rotamer: Outliers : 3.19 % Allowed : 32.03 % Favored : 64.77 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.17), residues: 2184 helix: -0.45 (0.14), residues: 1204 sheet: -0.97 (0.34), residues: 212 loop : -1.21 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 410 HIS 0.006 0.001 HIS C 731 PHE 0.035 0.002 PHE B 617 TYR 0.038 0.001 TYR B 700 ARG 0.006 0.001 ARG C 537 *********************** 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 544 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 485 time to evaluate : 2.023 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: A 12 ASN cc_start: 0.9668 (m-40) cc_final: 0.9449 (t0) REVERT: A 109 LEU cc_start: 0.9525 (tp) cc_final: 0.9091 (pp) REVERT: A 411 ASP cc_start: 0.9420 (t70) cc_final: 0.9015 (t0) REVERT: A 472 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8255 (mmm160) REVERT: A 619 PHE cc_start: 0.9829 (OUTLIER) cc_final: 0.9542 (t80) REVERT: A 677 MET cc_start: 0.9787 (tpp) cc_final: 0.9232 (tmm) REVERT: A 678 LEU cc_start: 0.9770 (pp) cc_final: 0.9355 (pp) REVERT: A 681 ARG cc_start: 0.9310 (mmm160) cc_final: 0.9019 (mmm-85) REVERT: A 682 GLU cc_start: 0.9732 (pt0) cc_final: 0.9454 (tm-30) REVERT: A 809 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8937 (mp) REVERT: B 12 ASN cc_start: 0.9597 (t0) cc_final: 0.9285 (t0) REVERT: B 109 LEU cc_start: 0.9510 (tp) cc_final: 0.9075 (pp) REVERT: B 410 TRP cc_start: 0.9625 (t-100) cc_final: 0.9340 (t-100) REVERT: B 462 MET cc_start: 0.9684 (tpt) cc_final: 0.9340 (tpt) REVERT: B 619 PHE cc_start: 0.9823 (OUTLIER) cc_final: 0.9517 (t80) REVERT: B 645 MET cc_start: 0.9393 (ttm) cc_final: 0.8580 (ttm) REVERT: B 658 ASN cc_start: 0.8859 (m110) cc_final: 0.8637 (m110) REVERT: B 712 ASP cc_start: 0.9643 (m-30) cc_final: 0.9385 (p0) REVERT: B 809 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8934 (mp) REVERT: B 821 ASP cc_start: 0.9309 (m-30) cc_final: 0.8988 (p0) REVERT: C 109 LEU cc_start: 0.9490 (tp) cc_final: 0.9056 (pp) REVERT: C 411 ASP cc_start: 0.9322 (t70) cc_final: 0.8672 (t70) REVERT: C 541 ARG cc_start: 0.9230 (tpt-90) cc_final: 0.8939 (tpt-90) REVERT: C 562 HIS cc_start: 0.9130 (t70) cc_final: 0.8664 (t-90) REVERT: C 619 PHE cc_start: 0.9796 (OUTLIER) cc_final: 0.9281 (t80) REVERT: C 658 ASN cc_start: 0.8819 (m110) cc_final: 0.8590 (m110) REVERT: C 677 MET cc_start: 0.9643 (mmm) cc_final: 0.9313 (mmm) REVERT: C 681 ARG cc_start: 0.9518 (mmm-85) cc_final: 0.9152 (mtm-85) REVERT: C 691 ASN cc_start: 0.9800 (p0) cc_final: 0.9544 (t0) REVERT: C 804 ILE cc_start: 0.9567 (OUTLIER) cc_final: 0.9290 (tp) REVERT: C 809 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9119 (mp) REVERT: C 821 ASP cc_start: 0.9231 (m-30) cc_final: 0.8827 (p0) REVERT: D 411 ASP cc_start: 0.9356 (t70) cc_final: 0.9000 (t0) REVERT: D 541 ARG cc_start: 0.9197 (tpp80) cc_final: 0.8949 (tpp80) REVERT: D 562 HIS cc_start: 0.9111 (t70) cc_final: 0.8805 (t70) REVERT: D 574 MET cc_start: 0.8244 (mtt) cc_final: 0.7968 (tpt) REVERT: D 617 PHE cc_start: 0.9676 (t80) cc_final: 0.9340 (t80) REVERT: D 658 ASN cc_start: 0.8814 (m110) cc_final: 0.8587 (m110) REVERT: D 677 MET cc_start: 0.9864 (tpp) cc_final: 0.9157 (tmm) REVERT: D 681 ARG cc_start: 0.9494 (mtt180) cc_final: 0.8965 (mmm-85) REVERT: D 702 GLN cc_start: 0.9677 (mt0) cc_final: 0.9365 (pp30) REVERT: D 713 MET cc_start: 0.8205 (mmt) cc_final: 0.7791 (mmt) REVERT: D 809 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9026 (mp) outliers start: 59 outliers final: 41 residues processed: 523 average time/residue: 0.2854 time to fit residues: 228.0194 Evaluate side-chains 518 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 468 time to evaluate : 2.006 ------------------------------------------------------------------------------- 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 472 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 817 LYS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 804 ILE Chi-restraints excluded: chain C residue 809 LEU 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 421 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 741 LYS 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 809 LEU Chi-restraints excluded: chain D residue 842 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 174 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 676 GLN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18000 Z= 0.214 Angle : 0.873 13.582 24432 Z= 0.417 Chirality : 0.048 0.334 2788 Planarity : 0.004 0.044 3064 Dihedral : 4.592 21.790 2420 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.49 % Favored : 95.15 % Rotamer: Outliers : 2.81 % Allowed : 33.12 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2184 helix: -0.49 (0.14), residues: 1212 sheet: -1.02 (0.34), residues: 212 loop : -1.15 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 410 HIS 0.006 0.001 HIS D 587 PHE 0.035 0.002 PHE A 617 TYR 0.034 0.001 TYR B 700 ARG 0.008 0.001 ARG B 681 ********************** 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 521 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 469 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.9678 (m-40) cc_final: 0.9442 (t0) REVERT: A 109 LEU cc_start: 0.9532 (tp) cc_final: 0.9096 (pp) REVERT: A 411 ASP cc_start: 0.9414 (t70) cc_final: 0.9056 (t0) REVERT: A 619 PHE cc_start: 0.9837 (OUTLIER) cc_final: 0.9543 (t80) REVERT: A 677 MET cc_start: 0.9787 (tpp) cc_final: 0.9224 (tmm) REVERT: A 681 ARG cc_start: 0.9306 (mmm160) cc_final: 0.9021 (mmm-85) REVERT: A 682 GLU cc_start: 0.9739 (pt0) cc_final: 0.9494 (tm-30) REVERT: A 757 LYS cc_start: 0.8950 (mtpt) cc_final: 0.8746 (ptmt) REVERT: A 809 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8892 (mp) REVERT: B 12 ASN cc_start: 0.9610 (t0) cc_final: 0.9320 (t0) REVERT: B 109 LEU cc_start: 0.9520 (tp) cc_final: 0.9085 (pp) REVERT: B 462 MET cc_start: 0.9690 (tpt) cc_final: 0.9376 (tpt) REVERT: B 619 PHE cc_start: 0.9833 (OUTLIER) cc_final: 0.9514 (t80) REVERT: B 645 MET cc_start: 0.9327 (ttm) cc_final: 0.8628 (ttm) REVERT: B 658 ASN cc_start: 0.8858 (m110) cc_final: 0.8635 (m110) REVERT: B 677 MET cc_start: 0.9707 (tmm) cc_final: 0.9217 (tmm) REVERT: B 681 ARG cc_start: 0.9340 (mmm160) cc_final: 0.9099 (mmm-85) REVERT: B 712 ASP cc_start: 0.9676 (m-30) cc_final: 0.9432 (p0) REVERT: B 821 ASP cc_start: 0.9309 (m-30) cc_final: 0.8978 (p0) REVERT: C 109 LEU cc_start: 0.9506 (tp) cc_final: 0.9073 (pp) REVERT: C 411 ASP cc_start: 0.9308 (t70) cc_final: 0.8818 (t70) REVERT: C 541 ARG cc_start: 0.9214 (tpt-90) cc_final: 0.8899 (tpt-90) REVERT: C 562 HIS cc_start: 0.9160 (t70) cc_final: 0.8757 (t-90) REVERT: C 619 PHE cc_start: 0.9797 (OUTLIER) cc_final: 0.9269 (t80) REVERT: C 645 MET cc_start: 0.9408 (ptt) cc_final: 0.8708 (ppp) REVERT: C 658 ASN cc_start: 0.8818 (m110) cc_final: 0.8588 (m110) REVERT: C 677 MET cc_start: 0.9616 (mmm) cc_final: 0.9302 (mmm) REVERT: C 681 ARG cc_start: 0.9515 (mmm-85) cc_final: 0.9144 (mtm-85) REVERT: C 691 ASN cc_start: 0.9796 (p0) cc_final: 0.9534 (t0) REVERT: C 784 ARG cc_start: 0.9511 (mtp-110) cc_final: 0.9135 (ptm160) REVERT: C 804 ILE cc_start: 0.9593 (OUTLIER) cc_final: 0.9315 (tp) REVERT: C 809 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9099 (mp) REVERT: C 821 ASP cc_start: 0.9261 (m-30) cc_final: 0.8861 (p0) REVERT: D 411 ASP cc_start: 0.9396 (t70) cc_final: 0.9057 (t0) REVERT: D 541 ARG cc_start: 0.9197 (tpp80) cc_final: 0.8941 (tpp80) REVERT: D 562 HIS cc_start: 0.9107 (t70) cc_final: 0.8721 (t-90) REVERT: D 574 MET cc_start: 0.8262 (mtt) cc_final: 0.7982 (tpt) REVERT: D 617 PHE cc_start: 0.9687 (t80) cc_final: 0.9424 (t80) REVERT: D 658 ASN cc_start: 0.8817 (m110) cc_final: 0.8591 (m110) REVERT: D 677 MET cc_start: 0.9868 (tpp) cc_final: 0.9175 (tmm) REVERT: D 681 ARG cc_start: 0.9508 (mtt180) cc_final: 0.8981 (mmm-85) REVERT: D 702 GLN cc_start: 0.9672 (mt0) cc_final: 0.9354 (pp30) REVERT: D 713 MET cc_start: 0.8299 (mmt) cc_final: 0.7872 (mmt) REVERT: D 809 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8999 (mp) outliers start: 52 outliers final: 42 residues processed: 503 average time/residue: 0.2622 time to fit residues: 203.3810 Evaluate side-chains 510 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 461 time to evaluate : 1.926 ------------------------------------------------------------------------------- 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 472 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 817 LYS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 804 ILE Chi-restraints excluded: chain C residue 809 LEU 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 421 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 698 GLU Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain D residue 741 LYS 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 809 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 174 optimal weight: 30.0000 chunk 73 optimal weight: 0.7980 chunk 179 optimal weight: 0.0270 chunk 22 optimal weight: 20.0000 chunk 32 optimal weight: 0.3980 chunk 153 optimal weight: 0.0980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 GLN ** B 702 GLN ** 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 834 HIS ** 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 = 0.3341 r_free = 0.3341 target = 0.068150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.055611 restraints weight = 92269.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.057216 restraints weight = 59181.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.058390 restraints weight = 42406.023| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.7006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18000 Z= 0.196 Angle : 0.910 13.941 24432 Z= 0.429 Chirality : 0.050 0.361 2788 Planarity : 0.004 0.038 3064 Dihedral : 4.538 20.989 2420 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.30 % Favored : 95.28 % Rotamer: Outliers : 2.44 % Allowed : 33.66 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2184 helix: -0.56 (0.14), residues: 1172 sheet: -0.89 (0.34), residues: 212 loop : -1.24 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP C 410 HIS 0.005 0.001 HIS C 731 PHE 0.038 0.002 PHE C 617 TYR 0.031 0.001 TYR B 700 ARG 0.009 0.001 ARG B 681 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5737.90 seconds wall clock time: 101 minutes 50.70 seconds (6110.70 seconds total)