Starting phenix.real_space_refine on Sun Jun 15 10:58:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5va3_8652/06_2025/5va3_8652.cif Found real_map, /net/cci-nas-00/data/ceres_data/5va3_8652/06_2025/5va3_8652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5va3_8652/06_2025/5va3_8652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5va3_8652/06_2025/5va3_8652.map" model { file = "/net/cci-nas-00/data/ceres_data/5va3_8652/06_2025/5va3_8652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5va3_8652/06_2025/5va3_8652.cif" } resolution = 4.0 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= 0.459 sd= 0.788 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 11476 2.51 5 N 3000 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 48 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17600 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4400 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 22, '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: 9.69, per 1000 atoms: 0.55 Number of scatterers: 17600 At special positions: 0 Unit cell: (148.761, 148.761, 120.757, 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 3000 7.00 C 11476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.29 Conformation dependent library (CDL) restraints added in 2.3 seconds 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4192 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 16 sheets defined 58.3% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.688A pdb=" N THR A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.577A pdb=" N CYS A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 79 through 89 removed outlier: 3.796A pdb=" N ALA A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 432 removed outlier: 3.994A pdb=" N VAL A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Proline residue: A 426 - end of helix removed outlier: 3.725A pdb=" N LEU A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 473 removed outlier: 4.143A pdb=" N LEU A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG A 472 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.943A pdb=" N ILE A 489 " --> pdb=" O HIS A 485 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 removed outlier: 3.665A pdb=" N ALA A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 505' Processing helix chain 'A' and resid 521 through 531 removed outlier: 3.782A pdb=" N LEU A 524 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 527 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.889A pdb=" N ALA A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 removed outlier: 3.906A pdb=" N SER A 543 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU A 544 " --> pdb=" O ARG A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 574 removed outlier: 3.863A pdb=" N VAL A 549 " --> pdb=" O TYR A 545 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 550 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 558 " --> pdb=" O MET A 554 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 572 " --> pdb=" O TRP A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 593 Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 634 through 667 removed outlier: 3.643A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 688 removed outlier: 3.643A pdb=" N HIS A 674 " --> pdb=" O THR A 670 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 709 removed outlier: 4.209A pdb=" N ARG A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 718 removed outlier: 4.091A pdb=" N LEU A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 Processing helix chain 'A' and resid 733 through 738 removed outlier: 3.543A pdb=" N LEU A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 758 removed outlier: 3.602A pdb=" N LEU A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 843 removed outlier: 3.825A pdb=" N VAL A 841 " --> pdb=" O ASP A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 856 removed outlier: 3.572A pdb=" N ASP A 850 " --> pdb=" O PRO A 846 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 854 " --> pdb=" O ASP A 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 removed outlier: 3.688A pdb=" N THR B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.577A pdb=" N CYS B 49 " --> pdb=" O ASN B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 79 through 89 removed outlier: 3.796A pdb=" N ALA B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA B 85 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 432 removed outlier: 3.994A pdb=" N VAL B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP B 410 " --> pdb=" O PHE B 406 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Proline residue: B 426 - end of helix removed outlier: 3.725A pdb=" N LEU B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 473 removed outlier: 4.143A pdb=" N LEU B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG B 472 " --> pdb=" O LEU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.943A pdb=" N ILE B 489 " --> pdb=" O HIS B 485 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 removed outlier: 3.665A pdb=" N ALA B 504 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 500 through 505' Processing helix chain 'B' and resid 521 through 531 removed outlier: 3.782A pdb=" N LEU B 524 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 527 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.889A pdb=" N ALA B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.906A pdb=" N SER B 543 " --> pdb=" O ASP B 540 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU B 544 " --> pdb=" O ARG B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 574 removed outlier: 3.863A pdb=" N VAL B 549 " --> pdb=" O TYR B 545 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 550 " --> pdb=" O GLY B 546 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 558 " --> pdb=" O MET B 554 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 572 " --> pdb=" O TRP B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 593 Processing helix chain 'B' and resid 606 through 623 Processing helix chain 'B' and resid 634 through 667 removed outlier: 3.643A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 688 removed outlier: 3.643A pdb=" N HIS B 674 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 709 removed outlier: 4.209A pdb=" N ARG B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 718 removed outlier: 4.091A pdb=" N LEU B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 733 Processing helix chain 'B' and resid 733 through 738 removed outlier: 3.543A pdb=" N LEU B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 758 removed outlier: 3.602A pdb=" N LEU B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 843 removed outlier: 3.825A pdb=" N VAL B 841 " --> pdb=" O ASP B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 856 removed outlier: 3.572A pdb=" N ASP B 850 " --> pdb=" O PRO B 846 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 854 " --> pdb=" O ASP B 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 25 removed outlier: 3.688A pdb=" N THR C 17 " --> pdb=" O THR C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.577A pdb=" N CYS C 49 " --> pdb=" O ASN C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.796A pdb=" N ALA C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA C 85 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 432 removed outlier: 3.994A pdb=" N VAL C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP C 410 " --> pdb=" O PHE C 406 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Proline residue: C 426 - end of helix removed outlier: 3.725A pdb=" N LEU C 432 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 473 removed outlier: 4.143A pdb=" N LEU C 457 " --> pdb=" O ALA C 453 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 459 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C 471 " --> pdb=" O ILE C 467 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG C 472 " --> pdb=" O LEU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 494 removed outlier: 3.943A pdb=" N ILE C 489 " --> pdb=" O HIS C 485 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL C 491 " --> pdb=" O GLY C 487 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 505 removed outlier: 3.665A pdb=" N ALA C 504 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 500 through 505' Processing helix chain 'C' and resid 521 through 531 removed outlier: 3.782A pdb=" N LEU C 524 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 527 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 538 removed outlier: 3.889A pdb=" N ALA C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 544 removed outlier: 3.906A pdb=" N SER C 543 " --> pdb=" O ASP C 540 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU C 544 " --> pdb=" O ARG C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 574 removed outlier: 3.863A pdb=" N VAL C 549 " --> pdb=" O TYR C 545 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 550 " --> pdb=" O GLY C 546 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 558 " --> pdb=" O MET C 554 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C 572 " --> pdb=" O TRP C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 593 Processing helix chain 'C' and resid 606 through 623 Processing helix chain 'C' and resid 634 through 667 removed outlier: 3.643A pdb=" N ALA C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE C 656 " --> pdb=" O TYR C 652 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 688 removed outlier: 3.643A pdb=" N HIS C 674 " --> pdb=" O THR C 670 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 709 removed outlier: 4.209A pdb=" N ARG C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 718 removed outlier: 4.091A pdb=" N LEU C 717 " --> pdb=" O MET C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 733 Processing helix chain 'C' and resid 733 through 738 removed outlier: 3.543A pdb=" N LEU C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 758 removed outlier: 3.602A pdb=" N LEU C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 843 removed outlier: 3.825A pdb=" N VAL C 841 " --> pdb=" O ASP C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 856 removed outlier: 3.572A pdb=" N ASP C 850 " --> pdb=" O PRO C 846 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS C 851 " --> pdb=" O GLU C 847 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 854 " --> pdb=" O ASP C 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 25 removed outlier: 3.688A pdb=" N THR D 17 " --> pdb=" O THR D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 53 removed outlier: 3.577A pdb=" N CYS D 49 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 79 through 89 removed outlier: 3.796A pdb=" N ALA D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA D 85 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 432 removed outlier: 3.994A pdb=" N VAL D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP D 410 " --> pdb=" O PHE D 406 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Proline residue: D 426 - end of helix removed outlier: 3.725A pdb=" N LEU D 432 " --> pdb=" O SER D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 473 removed outlier: 4.143A pdb=" N LEU D 457 " --> pdb=" O ALA D 453 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 459 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 464 " --> pdb=" O ASP D 460 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 468 " --> pdb=" O ILE D 464 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG D 472 " --> pdb=" O LEU D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 494 removed outlier: 3.943A pdb=" N ILE D 489 " --> pdb=" O HIS D 485 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA D 490 " --> pdb=" O PRO D 486 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL D 491 " --> pdb=" O GLY D 487 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D 494 " --> pdb=" O ALA D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 505 removed outlier: 3.665A pdb=" N ALA D 504 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 505 " --> pdb=" O ASP D 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 500 through 505' Processing helix chain 'D' and resid 521 through 531 removed outlier: 3.782A pdb=" N LEU D 524 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA D 527 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 538 removed outlier: 3.889A pdb=" N ALA D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 544 removed outlier: 3.906A pdb=" N SER D 543 " --> pdb=" O ASP D 540 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU D 544 " --> pdb=" O ARG D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 574 removed outlier: 3.863A pdb=" N VAL D 549 " --> pdb=" O TYR D 545 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU D 550 " --> pdb=" O GLY D 546 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA D 558 " --> pdb=" O MET D 554 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY D 572 " --> pdb=" O TRP D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 593 Processing helix chain 'D' and resid 606 through 623 Processing helix chain 'D' and resid 634 through 667 removed outlier: 3.643A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE D 656 " --> pdb=" O TYR D 652 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN D 664 " --> pdb=" O SER D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 688 removed outlier: 3.643A pdb=" N HIS D 674 " --> pdb=" O THR D 670 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 709 removed outlier: 4.209A pdb=" N ARG D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 718 removed outlier: 4.091A pdb=" N LEU D 717 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 733 Processing helix chain 'D' and resid 733 through 738 removed outlier: 3.543A pdb=" N LEU D 737 " --> pdb=" O ASN D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 758 removed outlier: 3.602A pdb=" N LEU D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 843 removed outlier: 3.825A pdb=" N VAL D 841 " --> pdb=" O ASP D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 856 removed outlier: 3.572A pdb=" N ASP D 850 " --> pdb=" O PRO D 846 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS D 851 " --> pdb=" O GLU D 847 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D 854 " --> pdb=" O ASP D 850 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.726A pdb=" N ILE A 31 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N CYS A 44 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE A 29 " --> pdb=" O CYS A 44 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET A 124 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 92 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 98 through 99 removed outlier: 4.167A pdb=" N PHE A 98 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE A 106 " --> pdb=" O PHE A 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=2 Processing sheet with id=3, first strand: chain 'A' and resid 762 through 763 removed outlier: 6.854A pdb=" N ASP A 829 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 805 " --> pdb=" O TYR A 780 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 795 through 799 Processing sheet with id=5, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.726A pdb=" N ILE B 31 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N CYS B 44 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE B 29 " --> pdb=" O CYS B 44 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET B 124 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 92 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 98 through 99 removed outlier: 4.167A pdb=" N PHE B 98 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE B 106 " --> pdb=" O PHE B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=6 Processing sheet with id=7, first strand: chain 'B' and resid 762 through 763 removed outlier: 6.854A pdb=" N ASP B 829 " --> pdb=" O SER B 783 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 805 " --> pdb=" O TYR B 780 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 795 through 799 Processing sheet with id=9, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.726A pdb=" N ILE C 31 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N CYS C 44 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE C 29 " --> pdb=" O CYS C 44 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET C 124 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C 92 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'C' and resid 98 through 99 removed outlier: 4.167A pdb=" N PHE C 98 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C 106 " --> pdb=" O PHE C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=10 Processing sheet with id=11, first strand: chain 'C' and resid 762 through 763 removed outlier: 6.854A pdb=" N ASP C 829 " --> pdb=" O SER C 783 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 805 " --> pdb=" O TYR C 780 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 795 through 799 Processing sheet with id=13, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.726A pdb=" N ILE D 31 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N CYS D 44 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE D 29 " --> pdb=" O CYS D 44 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET D 124 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 92 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'D' and resid 98 through 99 removed outlier: 4.167A pdb=" N PHE D 98 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE D 106 " --> pdb=" O PHE D 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=14 Processing sheet with id=15, first strand: chain 'D' and resid 762 through 763 removed outlier: 6.854A pdb=" N ASP D 829 " --> pdb=" O SER D 783 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 805 " --> pdb=" O TYR D 780 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 795 through 799 856 hydrogen bonds defined for protein. 2388 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: 5.20 Time building geometry restraints manager: 5.11 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: 5500 1.34 - 1.46: 2368 1.46 - 1.58: 10008 1.58 - 1.70: 0 1.70 - 1.81: 152 Bond restraints: 18028 Sorted by residual: bond pdb=" N GLY D 800 " pdb=" CA GLY D 800 " ideal model delta sigma weight residual 1.447 1.469 -0.022 7.50e-03 1.78e+04 8.54e+00 bond pdb=" N GLY A 800 " pdb=" CA GLY A 800 " ideal model delta sigma weight residual 1.447 1.469 -0.022 7.50e-03 1.78e+04 8.54e+00 bond pdb=" N GLY B 800 " pdb=" CA GLY B 800 " ideal model delta sigma weight residual 1.447 1.469 -0.022 7.50e-03 1.78e+04 8.54e+00 bond pdb=" N GLY C 800 " pdb=" CA GLY C 800 " ideal model delta sigma weight residual 1.447 1.469 -0.022 7.50e-03 1.78e+04 8.54e+00 bond pdb=" CA PRO D 764 " pdb=" C PRO D 764 " ideal model delta sigma weight residual 1.517 1.544 -0.027 9.30e-03 1.16e+04 8.14e+00 ... (remaining 18023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 20208 1.35 - 2.71: 3728 2.71 - 4.06: 444 4.06 - 5.41: 68 5.41 - 6.76: 24 Bond angle restraints: 24472 Sorted by residual: angle pdb=" N PHE A 29 " pdb=" CA PHE A 29 " pdb=" C PHE A 29 " ideal model delta sigma weight residual 108.60 115.36 -6.76 1.46e+00 4.69e-01 2.15e+01 angle pdb=" N PHE D 29 " pdb=" CA PHE D 29 " pdb=" C PHE D 29 " ideal model delta sigma weight residual 108.60 115.36 -6.76 1.46e+00 4.69e-01 2.15e+01 angle pdb=" N PHE B 29 " pdb=" CA PHE B 29 " pdb=" C PHE B 29 " ideal model delta sigma weight residual 108.60 115.36 -6.76 1.46e+00 4.69e-01 2.15e+01 angle pdb=" N PHE C 29 " pdb=" CA PHE C 29 " pdb=" C PHE C 29 " ideal model delta sigma weight residual 108.60 115.36 -6.76 1.46e+00 4.69e-01 2.15e+01 angle pdb=" N GLY D 800 " pdb=" CA GLY D 800 " pdb=" C GLY D 800 " ideal model delta sigma weight residual 110.21 114.06 -3.85 9.10e-01 1.21e+00 1.79e+01 ... (remaining 24467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.33: 9128 12.33 - 24.66: 1076 24.66 - 36.99: 236 36.99 - 49.32: 84 49.32 - 61.65: 36 Dihedral angle restraints: 10560 sinusoidal: 4064 harmonic: 6496 Sorted by residual: dihedral pdb=" CA HIS A 485 " pdb=" C HIS A 485 " pdb=" N PRO A 486 " pdb=" CA PRO A 486 " ideal model delta harmonic sigma weight residual -180.00 -155.72 -24.28 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA HIS C 485 " pdb=" C HIS C 485 " pdb=" N PRO C 486 " pdb=" CA PRO C 486 " ideal model delta harmonic sigma weight residual -180.00 -155.72 -24.28 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA HIS B 485 " pdb=" C HIS B 485 " pdb=" N PRO B 486 " pdb=" CA PRO B 486 " ideal model delta harmonic sigma weight residual -180.00 -155.72 -24.28 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 10557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1660 0.045 - 0.090: 724 0.090 - 0.135: 256 0.135 - 0.179: 108 0.179 - 0.224: 44 Chirality restraints: 2792 Sorted by residual: chirality pdb=" CA ILE A 804 " pdb=" N ILE A 804 " pdb=" C ILE A 804 " pdb=" CB ILE A 804 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE D 804 " pdb=" N ILE D 804 " pdb=" C ILE D 804 " pdb=" CB ILE D 804 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE C 804 " pdb=" N ILE C 804 " pdb=" C ILE C 804 " pdb=" CB ILE C 804 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2789 not shown) Planarity restraints: 3068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 425 " 0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO D 426 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 426 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 426 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 425 " 0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A 426 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 426 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 426 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 425 " -0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO B 426 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 426 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 426 " -0.043 5.00e-02 4.00e+02 ... (remaining 3065 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 44 2.56 - 3.15: 12280 3.15 - 3.73: 25114 3.73 - 4.32: 34422 4.32 - 4.90: 56576 Nonbonded interactions: 128436 Sorted by model distance: nonbonded pdb=" NH1 ARG B 56 " pdb=" OD2 ASP C 803 " model vdw 1.977 3.120 nonbonded pdb=" NH1 ARG A 56 " pdb=" OD2 ASP B 803 " model vdw 1.977 3.120 nonbonded pdb=" OD2 ASP A 803 " pdb=" NH1 ARG D 56 " model vdw 1.977 3.120 nonbonded pdb=" NH1 ARG C 56 " pdb=" OD2 ASP D 803 " model vdw 1.977 3.120 nonbonded pdb=" OD1 ASP A 803 " pdb=" NH1 ARG D 56 " model vdw 2.239 3.120 ... (remaining 128431 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.710 Find NCS groups from input model: 0.340 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 : 0.009 0.297 18032 Z= 0.730 Angle : 1.066 6.765 24472 Z= 0.730 Chirality : 0.064 0.224 2792 Planarity : 0.005 0.077 3068 Dihedral : 12.271 61.651 6368 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 1.10 % Allowed : 4.75 % Favored : 94.15 % Rotamer: Outliers : 1.30 % Allowed : 3.46 % Favored : 95.24 % 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: -3.78 (0.14), residues: 2188 helix: -2.33 (0.11), residues: 1092 sheet: -3.72 (0.35), residues: 112 loop : -2.44 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 412 HIS 0.003 0.001 HIS A 402 PHE 0.013 0.002 PHE A 494 TYR 0.017 0.002 TYR B 427 ARG 0.003 0.000 ARG C 541 Details of bonding type rmsd hydrogen bonds : bond 0.29578 ( 856) hydrogen bonds : angle 9.64811 ( 2388) covalent geometry : bond 0.00825 (18028) covalent geometry : angle 1.06574 (24472) Misc. bond : bond 0.29690 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 770 time to evaluate : 1.868 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.9615 (mt0) cc_final: 0.9373 (mm110) REVERT: A 75 GLN cc_start: 0.6506 (mp10) cc_final: 0.6017 (mp10) REVERT: A 92 ARG cc_start: 0.5517 (OUTLIER) cc_final: 0.5238 (mtp-110) REVERT: A 95 GLU cc_start: 0.8933 (tt0) cc_final: 0.8163 (pp20) REVERT: A 411 ASP cc_start: 0.9641 (m-30) cc_final: 0.9414 (m-30) REVERT: A 424 PHE cc_start: 0.9435 (m-80) cc_final: 0.9141 (m-80) REVERT: A 459 VAL cc_start: 0.9565 (t) cc_final: 0.9152 (p) REVERT: A 462 MET cc_start: 0.9592 (mmm) cc_final: 0.9311 (tpt) REVERT: A 463 PHE cc_start: 0.9733 (m-80) cc_final: 0.9148 (m-80) REVERT: A 501 ASP cc_start: 0.9233 (m-30) cc_final: 0.9032 (p0) REVERT: A 574 MET cc_start: 0.7798 (mtt) cc_final: 0.7598 (mmt) REVERT: A 588 ASN cc_start: 0.9175 (t0) cc_final: 0.8725 (t0) REVERT: A 638 LYS cc_start: 0.9817 (mttt) cc_final: 0.9481 (mmtt) REVERT: A 641 SER cc_start: 0.9740 (t) cc_final: 0.9327 (p) REVERT: A 645 MET cc_start: 0.9697 (mtp) cc_final: 0.9277 (mtp) REVERT: A 656 PHE cc_start: 0.9635 (m-80) cc_final: 0.9349 (m-10) REVERT: A 676 GLN cc_start: 0.9666 (mt0) cc_final: 0.9417 (pt0) REVERT: A 681 ARG cc_start: 0.9699 (mtt180) cc_final: 0.9228 (tpp-160) REVERT: A 691 ASN cc_start: 0.9755 (m-40) cc_final: 0.9489 (t0) REVERT: A 697 LEU cc_start: 0.9955 (mt) cc_final: 0.9709 (pp) REVERT: A 698 GLU cc_start: 0.9708 (mt-10) cc_final: 0.9431 (pt0) REVERT: A 705 TRP cc_start: 0.9424 (t60) cc_final: 0.9195 (t60) REVERT: A 723 CYS cc_start: 0.9609 (m) cc_final: 0.9303 (p) REVERT: A 757 LYS cc_start: 0.9312 (mttt) cc_final: 0.9068 (mtpt) REVERT: A 768 THR cc_start: 0.9321 (p) cc_final: 0.9084 (t) REVERT: A 781 PHE cc_start: 0.9902 (m-80) cc_final: 0.9651 (m-80) REVERT: A 782 ILE cc_start: 0.9849 (mt) cc_final: 0.9566 (tp) REVERT: A 801 LYS cc_start: 0.9122 (mttt) cc_final: 0.8910 (mptt) REVERT: A 817 LYS cc_start: 0.9583 (mttt) cc_final: 0.9366 (mmmt) REVERT: A 827 TYR cc_start: 0.8780 (m-80) cc_final: 0.8560 (m-80) REVERT: A 832 LYS cc_start: 0.9624 (tttt) cc_final: 0.9289 (mtpp) REVERT: A 861 ASN cc_start: 0.9364 (t0) cc_final: 0.9032 (t0) REVERT: B 61 GLN cc_start: 0.9647 (mt0) cc_final: 0.9383 (mm110) REVERT: B 92 ARG cc_start: 0.5735 (OUTLIER) cc_final: 0.5523 (mtp-110) REVERT: B 95 GLU cc_start: 0.8895 (tt0) cc_final: 0.8244 (pp20) REVERT: B 424 PHE cc_start: 0.9385 (m-80) cc_final: 0.9090 (m-80) REVERT: B 459 VAL cc_start: 0.9592 (t) cc_final: 0.9201 (p) REVERT: B 462 MET cc_start: 0.9592 (mmm) cc_final: 0.9318 (tpt) REVERT: B 463 PHE cc_start: 0.9740 (m-80) cc_final: 0.9169 (m-80) REVERT: B 501 ASP cc_start: 0.9199 (m-30) cc_final: 0.8983 (p0) REVERT: B 588 ASN cc_start: 0.9197 (t0) cc_final: 0.8763 (t0) REVERT: B 629 ASN cc_start: 0.7614 (m110) cc_final: 0.6976 (m110) REVERT: B 638 LYS cc_start: 0.9804 (mttt) cc_final: 0.9501 (mmtt) REVERT: B 641 SER cc_start: 0.9744 (t) cc_final: 0.9346 (p) REVERT: B 645 MET cc_start: 0.9696 (mtp) cc_final: 0.9311 (mtp) REVERT: B 656 PHE cc_start: 0.9638 (m-80) cc_final: 0.9367 (m-80) REVERT: B 676 GLN cc_start: 0.9662 (mt0) cc_final: 0.9420 (pt0) REVERT: B 681 ARG cc_start: 0.9710 (mtt180) cc_final: 0.9235 (tpp-160) REVERT: B 691 ASN cc_start: 0.9738 (m-40) cc_final: 0.9458 (t0) REVERT: B 697 LEU cc_start: 0.9950 (mt) cc_final: 0.9699 (pp) REVERT: B 698 GLU cc_start: 0.9687 (mt-10) cc_final: 0.9419 (pt0) REVERT: B 705 TRP cc_start: 0.9407 (t60) cc_final: 0.9156 (t60) REVERT: B 723 CYS cc_start: 0.9588 (m) cc_final: 0.9242 (p) REVERT: B 758 PHE cc_start: 0.9633 (m-80) cc_final: 0.9168 (m-80) REVERT: B 768 THR cc_start: 0.9329 (p) cc_final: 0.9061 (t) REVERT: B 776 LEU cc_start: 0.9620 (mt) cc_final: 0.9401 (tt) REVERT: B 781 PHE cc_start: 0.9906 (m-80) cc_final: 0.9631 (m-80) REVERT: B 782 ILE cc_start: 0.9834 (mt) cc_final: 0.9617 (tp) REVERT: B 827 TYR cc_start: 0.8698 (m-80) cc_final: 0.8477 (m-80) REVERT: B 832 LYS cc_start: 0.9637 (tttt) cc_final: 0.9412 (tttm) REVERT: B 861 ASN cc_start: 0.9373 (t0) cc_final: 0.9037 (t0) REVERT: C 8 VAL cc_start: 0.9636 (m) cc_final: 0.9369 (p) REVERT: C 61 GLN cc_start: 0.9637 (mt0) cc_final: 0.9364 (mm110) REVERT: C 95 GLU cc_start: 0.8860 (tt0) cc_final: 0.8168 (tm-30) REVERT: C 420 TYR cc_start: 0.9471 (t80) cc_final: 0.9221 (t80) REVERT: C 424 PHE cc_start: 0.9355 (m-80) cc_final: 0.9062 (m-80) REVERT: C 459 VAL cc_start: 0.9607 (t) cc_final: 0.9295 (p) REVERT: C 463 PHE cc_start: 0.9733 (m-80) cc_final: 0.8857 (m-80) REVERT: C 588 ASN cc_start: 0.9146 (t0) cc_final: 0.8672 (t0) REVERT: C 629 ASN cc_start: 0.7589 (m110) cc_final: 0.6896 (m110) REVERT: C 643 CYS cc_start: 0.9630 (t) cc_final: 0.9417 (t) REVERT: C 645 MET cc_start: 0.9734 (mtp) cc_final: 0.9253 (mtp) REVERT: C 656 PHE cc_start: 0.9620 (m-80) cc_final: 0.9387 (m-10) REVERT: C 676 GLN cc_start: 0.9660 (mt0) cc_final: 0.9430 (pt0) REVERT: C 681 ARG cc_start: 0.9701 (mtt180) cc_final: 0.9208 (tpp-160) REVERT: C 682 GLU cc_start: 0.9618 (mt-10) cc_final: 0.9410 (mt-10) REVERT: C 691 ASN cc_start: 0.9745 (m-40) cc_final: 0.9478 (t0) REVERT: C 697 LEU cc_start: 0.9953 (mt) cc_final: 0.9710 (pp) REVERT: C 698 GLU cc_start: 0.9684 (mt-10) cc_final: 0.9413 (pt0) REVERT: C 705 TRP cc_start: 0.9434 (t60) cc_final: 0.9200 (t60) REVERT: C 723 CYS cc_start: 0.9542 (m) cc_final: 0.9284 (p) REVERT: C 757 LYS cc_start: 0.9289 (mttt) cc_final: 0.9053 (mtpt) REVERT: C 768 THR cc_start: 0.9302 (p) cc_final: 0.8911 (t) REVERT: C 781 PHE cc_start: 0.9884 (m-80) cc_final: 0.9662 (m-80) REVERT: C 832 LYS cc_start: 0.9602 (tttt) cc_final: 0.9260 (mtpp) REVERT: C 861 ASN cc_start: 0.9387 (t0) cc_final: 0.9060 (t0) REVERT: D 8 VAL cc_start: 0.9613 (m) cc_final: 0.9309 (p) REVERT: D 61 GLN cc_start: 0.9607 (mt0) cc_final: 0.9356 (mm110) REVERT: D 75 GLN cc_start: 0.6441 (mp10) cc_final: 0.5952 (mp10) REVERT: D 92 ARG cc_start: 0.5493 (OUTLIER) cc_final: 0.5287 (mtp-110) REVERT: D 95 GLU cc_start: 0.8890 (tt0) cc_final: 0.8108 (pp20) REVERT: D 424 PHE cc_start: 0.9396 (m-80) cc_final: 0.9088 (m-80) REVERT: D 459 VAL cc_start: 0.9576 (t) cc_final: 0.9052 (p) REVERT: D 462 MET cc_start: 0.9564 (mmm) cc_final: 0.9222 (tpt) REVERT: D 463 PHE cc_start: 0.9728 (m-80) cc_final: 0.8956 (m-80) REVERT: D 574 MET cc_start: 0.7918 (mtt) cc_final: 0.7502 (mmt) REVERT: D 588 ASN cc_start: 0.9128 (t0) cc_final: 0.8684 (t0) REVERT: D 638 LYS cc_start: 0.9790 (mttt) cc_final: 0.9548 (mmmm) REVERT: D 651 MET cc_start: 0.9540 (tpp) cc_final: 0.9289 (tpp) REVERT: D 656 PHE cc_start: 0.9618 (m-80) cc_final: 0.9197 (m-80) REVERT: D 676 GLN cc_start: 0.9668 (mt0) cc_final: 0.9429 (pt0) REVERT: D 678 LEU cc_start: 0.9644 (mt) cc_final: 0.9440 (pp) REVERT: D 681 ARG cc_start: 0.9690 (mtt180) cc_final: 0.9222 (tpp-160) REVERT: D 691 ASN cc_start: 0.9760 (m-40) cc_final: 0.9490 (t0) REVERT: D 697 LEU cc_start: 0.9956 (mt) cc_final: 0.9706 (pp) REVERT: D 698 GLU cc_start: 0.9699 (mt-10) cc_final: 0.9393 (pt0) REVERT: D 705 TRP cc_start: 0.9450 (t60) cc_final: 0.9226 (t60) REVERT: D 723 CYS cc_start: 0.9562 (m) cc_final: 0.9288 (p) REVERT: D 741 LYS cc_start: 0.9745 (mttt) cc_final: 0.9524 (pttp) REVERT: D 757 LYS cc_start: 0.9303 (mttt) cc_final: 0.9070 (mtpt) REVERT: D 768 THR cc_start: 0.9303 (p) cc_final: 0.8961 (t) REVERT: D 782 ILE cc_start: 0.9818 (mt) cc_final: 0.9613 (tp) REVERT: D 817 LYS cc_start: 0.9611 (mttt) cc_final: 0.9403 (mmmt) REVERT: D 832 LYS cc_start: 0.9593 (tttt) cc_final: 0.9202 (mtpp) REVERT: D 861 ASN cc_start: 0.9366 (t0) cc_final: 0.9005 (t0) outliers start: 24 outliers final: 8 residues processed: 786 average time/residue: 0.3653 time to fit residues: 414.7658 Evaluate side-chains 522 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 511 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 597 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 199 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 HIS ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 HIS C 470 ASN C 739 HIS ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 834 HIS D 470 ASN D 739 HIS ** D 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.083819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.063453 restraints weight = 72857.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.065538 restraints weight = 48061.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067107 restraints weight = 35865.549| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18032 Z= 0.166 Angle : 0.797 11.749 24472 Z= 0.396 Chirality : 0.047 0.177 2792 Planarity : 0.005 0.044 3068 Dihedral : 6.085 59.128 2448 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.47 % Favored : 96.34 % Rotamer: Outliers : 3.03 % Allowed : 13.74 % Favored : 83.23 % 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: -1.91 (0.17), residues: 2188 helix: -0.57 (0.15), residues: 1116 sheet: -2.83 (0.28), residues: 180 loop : -1.70 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 563 HIS 0.007 0.001 HIS B 834 PHE 0.018 0.002 PHE C 686 TYR 0.014 0.002 TYR D 700 ARG 0.008 0.001 ARG A 734 Details of bonding type rmsd hydrogen bonds : bond 0.05518 ( 856) hydrogen bonds : angle 5.58075 ( 2388) covalent geometry : bond 0.00355 (18028) covalent geometry : angle 0.79719 (24472) Misc. bond : bond 0.00140 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 553 time to evaluate : 2.664 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: A 92 ARG cc_start: 0.4876 (OUTLIER) cc_final: 0.4569 (mtp85) REVERT: A 424 PHE cc_start: 0.9288 (m-80) cc_final: 0.8881 (m-80) REVERT: A 459 VAL cc_start: 0.9912 (t) cc_final: 0.9508 (t) REVERT: A 462 MET cc_start: 0.9796 (mmm) cc_final: 0.9586 (tpt) REVERT: A 463 PHE cc_start: 0.9641 (m-80) cc_final: 0.9220 (m-80) REVERT: A 544 GLU cc_start: 0.8325 (pm20) cc_final: 0.7891 (pm20) REVERT: A 574 MET cc_start: 0.7825 (mtt) cc_final: 0.7586 (mmt) REVERT: A 586 LEU cc_start: 0.9596 (mt) cc_final: 0.9370 (pt) REVERT: A 638 LYS cc_start: 0.9856 (mttt) cc_final: 0.9496 (mmtm) REVERT: A 640 PHE cc_start: 0.9427 (t80) cc_final: 0.8992 (t80) REVERT: A 641 SER cc_start: 0.9807 (t) cc_final: 0.9485 (p) REVERT: A 645 MET cc_start: 0.9551 (mtp) cc_final: 0.9088 (ttm) REVERT: A 651 MET cc_start: 0.9589 (tpp) cc_final: 0.9385 (tpp) REVERT: A 656 PHE cc_start: 0.9675 (m-80) cc_final: 0.9380 (m-10) REVERT: A 681 ARG cc_start: 0.9567 (mtt180) cc_final: 0.9324 (tpp-160) REVERT: A 691 ASN cc_start: 0.9797 (m-40) cc_final: 0.9512 (t0) REVERT: A 698 GLU cc_start: 0.9682 (mt-10) cc_final: 0.9339 (pt0) REVERT: A 705 TRP cc_start: 0.9280 (t60) cc_final: 0.9015 (t60) REVERT: A 748 LYS cc_start: 0.9900 (mttt) cc_final: 0.9641 (tptp) REVERT: A 757 LYS cc_start: 0.9605 (mttt) cc_final: 0.9198 (mtmt) REVERT: A 758 PHE cc_start: 0.9453 (m-80) cc_final: 0.9201 (m-80) REVERT: A 781 PHE cc_start: 0.9779 (m-80) cc_final: 0.9301 (m-80) REVERT: A 801 LYS cc_start: 0.9166 (mttt) cc_final: 0.8883 (mptt) REVERT: A 827 TYR cc_start: 0.8605 (m-80) cc_final: 0.8378 (m-80) REVERT: B 60 MET cc_start: 0.8496 (ppp) cc_final: 0.7871 (ppp) REVERT: B 92 ARG cc_start: 0.5163 (OUTLIER) cc_final: 0.4902 (mtp85) REVERT: B 424 PHE cc_start: 0.9266 (m-80) cc_final: 0.8853 (m-80) REVERT: B 459 VAL cc_start: 0.9927 (t) cc_final: 0.9553 (t) REVERT: B 462 MET cc_start: 0.9777 (mmm) cc_final: 0.9577 (tpt) REVERT: B 463 PHE cc_start: 0.9601 (m-80) cc_final: 0.8705 (m-80) REVERT: B 533 VAL cc_start: 0.9285 (m) cc_final: 0.9034 (p) REVERT: B 544 GLU cc_start: 0.8242 (pm20) cc_final: 0.7794 (pm20) REVERT: B 638 LYS cc_start: 0.9858 (mttt) cc_final: 0.9334 (mmtm) REVERT: B 640 PHE cc_start: 0.9427 (t80) cc_final: 0.8932 (t80) REVERT: B 641 SER cc_start: 0.9804 (t) cc_final: 0.9452 (p) REVERT: B 642 ILE cc_start: 0.9526 (mm) cc_final: 0.8950 (mm) REVERT: B 645 MET cc_start: 0.9539 (mtp) cc_final: 0.9306 (mtp) REVERT: B 681 ARG cc_start: 0.9580 (mtt180) cc_final: 0.9330 (tpp-160) REVERT: B 691 ASN cc_start: 0.9793 (m-40) cc_final: 0.9490 (t0) REVERT: B 696 ARG cc_start: 0.9780 (mtt180) cc_final: 0.9548 (mtp85) REVERT: B 698 GLU cc_start: 0.9661 (mt-10) cc_final: 0.9390 (pt0) REVERT: B 705 TRP cc_start: 0.9232 (t60) cc_final: 0.8971 (t60) REVERT: B 758 PHE cc_start: 0.9390 (m-80) cc_final: 0.9178 (m-80) REVERT: B 759 LYS cc_start: 0.8862 (ptpt) cc_final: 0.8652 (pttm) REVERT: B 781 PHE cc_start: 0.9788 (m-80) cc_final: 0.9333 (m-80) REVERT: C 424 PHE cc_start: 0.9217 (m-80) cc_final: 0.8797 (m-80) REVERT: C 459 VAL cc_start: 0.9917 (t) cc_final: 0.9606 (p) REVERT: C 463 PHE cc_start: 0.9438 (m-80) cc_final: 0.9055 (m-80) REVERT: C 544 GLU cc_start: 0.8440 (pm20) cc_final: 0.8028 (pm20) REVERT: C 638 LYS cc_start: 0.9789 (mmtt) cc_final: 0.9320 (mmtm) REVERT: C 640 PHE cc_start: 0.9377 (t80) cc_final: 0.8880 (t80) REVERT: C 641 SER cc_start: 0.9773 (t) cc_final: 0.9362 (p) REVERT: C 642 ILE cc_start: 0.9599 (mm) cc_final: 0.9068 (mm) REVERT: C 645 MET cc_start: 0.9533 (mtp) cc_final: 0.9232 (mtp) REVERT: C 682 GLU cc_start: 0.9568 (mt-10) cc_final: 0.9339 (pt0) REVERT: C 691 ASN cc_start: 0.9794 (m-40) cc_final: 0.9506 (t0) REVERT: C 698 GLU cc_start: 0.9658 (mt-10) cc_final: 0.9323 (pt0) REVERT: C 705 TRP cc_start: 0.9261 (t60) cc_final: 0.8996 (t60) REVERT: C 757 LYS cc_start: 0.9604 (mttt) cc_final: 0.9189 (mtmt) REVERT: C 781 PHE cc_start: 0.9720 (m-80) cc_final: 0.9427 (m-80) REVERT: C 827 TYR cc_start: 0.8349 (m-80) cc_final: 0.7884 (m-80) REVERT: C 830 LEU cc_start: 0.9894 (pt) cc_final: 0.9360 (tt) REVERT: C 840 GLU cc_start: 0.9672 (mt-10) cc_final: 0.9470 (mt-10) REVERT: D 92 ARG cc_start: 0.4916 (OUTLIER) cc_final: 0.4610 (mtp85) REVERT: D 424 PHE cc_start: 0.9235 (m-80) cc_final: 0.8822 (m-80) REVERT: D 459 VAL cc_start: 0.9903 (t) cc_final: 0.9477 (t) REVERT: D 462 MET cc_start: 0.9784 (mmm) cc_final: 0.9331 (tpt) REVERT: D 463 PHE cc_start: 0.9452 (m-80) cc_final: 0.9098 (m-80) REVERT: D 533 VAL cc_start: 0.9418 (m) cc_final: 0.9216 (p) REVERT: D 574 MET cc_start: 0.7800 (mtt) cc_final: 0.7575 (mmt) REVERT: D 617 PHE cc_start: 0.9754 (t80) cc_final: 0.9409 (t80) REVERT: D 638 LYS cc_start: 0.9870 (mttt) cc_final: 0.9433 (mmtm) REVERT: D 640 PHE cc_start: 0.9454 (t80) cc_final: 0.8895 (t80) REVERT: D 641 SER cc_start: 0.9872 (t) cc_final: 0.9617 (p) REVERT: D 656 PHE cc_start: 0.9660 (m-80) cc_final: 0.9440 (m-10) REVERT: D 681 ARG cc_start: 0.9554 (mtt180) cc_final: 0.9303 (tpp-160) REVERT: D 691 ASN cc_start: 0.9804 (m-40) cc_final: 0.9554 (t0) REVERT: D 696 ARG cc_start: 0.9838 (mtt180) cc_final: 0.9621 (mtp85) REVERT: D 698 GLU cc_start: 0.9668 (mt-10) cc_final: 0.9431 (pt0) REVERT: D 699 GLU cc_start: 0.9642 (pt0) cc_final: 0.9360 (pp20) REVERT: D 705 TRP cc_start: 0.9297 (t60) cc_final: 0.9040 (t60) REVERT: D 744 ARG cc_start: 0.9483 (ptp-110) cc_final: 0.9219 (mmp80) REVERT: D 757 LYS cc_start: 0.9610 (mttt) cc_final: 0.8966 (mtmt) REVERT: D 781 PHE cc_start: 0.9475 (m-80) cc_final: 0.9257 (m-80) REVERT: D 827 TYR cc_start: 0.8451 (m-80) cc_final: 0.7986 (m-80) REVERT: D 830 LEU cc_start: 0.9910 (pt) cc_final: 0.9491 (tt) outliers start: 56 outliers final: 35 residues processed: 580 average time/residue: 0.3682 time to fit residues: 307.5544 Evaluate side-chains 518 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 480 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 53 optimal weight: 50.0000 chunk 179 optimal weight: 30.0000 chunk 152 optimal weight: 50.0000 chunk 80 optimal weight: 30.0000 chunk 186 optimal weight: 0.5980 chunk 79 optimal weight: 50.0000 chunk 74 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 176 optimal weight: 30.0000 chunk 3 optimal weight: 30.0000 overall best weight: 9.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.073783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.055303 restraints weight = 79316.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.057364 restraints weight = 50538.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.058884 restraints weight = 36560.050| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18032 Z= 0.169 Angle : 0.738 11.938 24472 Z= 0.366 Chirality : 0.046 0.247 2792 Planarity : 0.005 0.043 3068 Dihedral : 5.864 57.564 2440 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.52 % Favored : 96.30 % Rotamer: Outliers : 2.81 % Allowed : 16.88 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 2188 helix: -0.06 (0.15), residues: 1116 sheet: -2.18 (0.30), residues: 204 loop : -1.32 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 705 HIS 0.017 0.001 HIS A 70 PHE 0.023 0.002 PHE C 860 TYR 0.013 0.001 TYR C 427 ARG 0.006 0.001 ARG A 534 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 856) hydrogen bonds : angle 5.38566 ( 2388) covalent geometry : bond 0.00360 (18028) covalent geometry : angle 0.73756 (24472) Misc. bond : bond 0.00152 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 494 time to evaluate : 1.970 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: A 46 ASP cc_start: 0.9635 (p0) cc_final: 0.9391 (p0) REVERT: A 92 ARG cc_start: 0.5069 (OUTLIER) cc_final: 0.4588 (mtp85) REVERT: A 424 PHE cc_start: 0.9236 (m-80) cc_final: 0.8779 (m-80) REVERT: A 463 PHE cc_start: 0.9462 (m-80) cc_final: 0.9044 (m-80) REVERT: A 544 GLU cc_start: 0.8343 (pm20) cc_final: 0.8026 (pm20) REVERT: A 638 LYS cc_start: 0.9836 (mttt) cc_final: 0.9474 (mtpp) REVERT: A 640 PHE cc_start: 0.9519 (t80) cc_final: 0.8961 (t80) REVERT: A 641 SER cc_start: 0.9802 (t) cc_final: 0.9597 (p) REVERT: A 651 MET cc_start: 0.9618 (tpp) cc_final: 0.9380 (tpp) REVERT: A 656 PHE cc_start: 0.9591 (m-80) cc_final: 0.9302 (m-10) REVERT: A 677 MET cc_start: 0.9639 (tpp) cc_final: 0.9404 (tpp) REVERT: A 691 ASN cc_start: 0.9793 (m-40) cc_final: 0.9562 (t0) REVERT: A 748 LYS cc_start: 0.9867 (mttt) cc_final: 0.9549 (tptp) REVERT: A 757 LYS cc_start: 0.9615 (mttt) cc_final: 0.8950 (mtmt) REVERT: A 758 PHE cc_start: 0.9514 (m-80) cc_final: 0.9225 (m-80) REVERT: A 781 PHE cc_start: 0.9742 (m-80) cc_final: 0.9235 (m-80) REVERT: A 788 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8086 (pm20) REVERT: A 840 GLU cc_start: 0.9574 (mt-10) cc_final: 0.9350 (tm-30) REVERT: B 61 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8425 (mp10) REVERT: B 66 CYS cc_start: 0.8473 (m) cc_final: 0.8256 (m) REVERT: B 92 ARG cc_start: 0.5314 (OUTLIER) cc_final: 0.4892 (mtp85) REVERT: B 424 PHE cc_start: 0.9212 (m-80) cc_final: 0.8739 (m-80) REVERT: B 459 VAL cc_start: 0.9921 (t) cc_final: 0.9482 (p) REVERT: B 463 PHE cc_start: 0.9159 (m-80) cc_final: 0.8646 (m-80) REVERT: B 551 PHE cc_start: 0.9555 (t80) cc_final: 0.9337 (t80) REVERT: B 619 PHE cc_start: 0.9677 (m-80) cc_final: 0.9470 (m-80) REVERT: B 638 LYS cc_start: 0.9803 (mttt) cc_final: 0.9470 (mmtm) REVERT: B 640 PHE cc_start: 0.9465 (t80) cc_final: 0.8876 (t80) REVERT: B 677 MET cc_start: 0.9630 (tpp) cc_final: 0.9377 (tpp) REVERT: B 691 ASN cc_start: 0.9791 (m-40) cc_final: 0.9337 (t0) REVERT: B 695 GLN cc_start: 0.9758 (mt0) cc_final: 0.9439 (mm-40) REVERT: B 698 GLU cc_start: 0.9615 (mt-10) cc_final: 0.9296 (pt0) REVERT: B 758 PHE cc_start: 0.9435 (m-80) cc_final: 0.9166 (m-80) REVERT: B 781 PHE cc_start: 0.9763 (m-80) cc_final: 0.9245 (m-80) REVERT: C 60 MET cc_start: 0.8644 (ppp) cc_final: 0.7596 (ppp) REVERT: C 424 PHE cc_start: 0.9168 (m-80) cc_final: 0.8678 (m-80) REVERT: C 681 ARG cc_start: 0.9562 (mmm160) cc_final: 0.9086 (tpp-160) REVERT: C 682 GLU cc_start: 0.9555 (mt-10) cc_final: 0.9297 (pt0) REVERT: C 691 ASN cc_start: 0.9782 (m-40) cc_final: 0.9537 (t0) REVERT: C 698 GLU cc_start: 0.9608 (mt-10) cc_final: 0.9337 (pt0) REVERT: C 757 LYS cc_start: 0.9610 (mttt) cc_final: 0.9027 (mtmt) REVERT: C 781 PHE cc_start: 0.9688 (m-80) cc_final: 0.9396 (m-80) REVERT: C 830 LEU cc_start: 0.9851 (pt) cc_final: 0.9369 (tt) REVERT: D 46 ASP cc_start: 0.9624 (p0) cc_final: 0.9380 (p0) REVERT: D 424 PHE cc_start: 0.9186 (m-80) cc_final: 0.8717 (m-80) REVERT: D 459 VAL cc_start: 0.9903 (t) cc_final: 0.9551 (p) REVERT: D 463 PHE cc_start: 0.9472 (m-80) cc_final: 0.9197 (m-80) REVERT: D 586 LEU cc_start: 0.9536 (mt) cc_final: 0.9305 (pt) REVERT: D 638 LYS cc_start: 0.9832 (mttt) cc_final: 0.9450 (mmtm) REVERT: D 640 PHE cc_start: 0.9520 (t80) cc_final: 0.8965 (t80) REVERT: D 651 MET cc_start: 0.9545 (mmm) cc_final: 0.9327 (mmm) REVERT: D 656 PHE cc_start: 0.9492 (m-80) cc_final: 0.9259 (m-10) REVERT: D 691 ASN cc_start: 0.9804 (m-40) cc_final: 0.9485 (t0) REVERT: D 744 ARG cc_start: 0.9476 (ptp-110) cc_final: 0.9119 (mmp80) REVERT: D 757 LYS cc_start: 0.9563 (mttt) cc_final: 0.9281 (mtmt) REVERT: D 830 LEU cc_start: 0.9854 (pt) cc_final: 0.9391 (tt) outliers start: 52 outliers final: 36 residues processed: 521 average time/residue: 0.3018 time to fit residues: 232.2000 Evaluate side-chains 487 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 447 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 171 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 36 optimal weight: 50.0000 chunk 74 optimal weight: 50.0000 chunk 172 optimal weight: 0.3980 chunk 103 optimal weight: 50.0000 chunk 201 optimal weight: 40.0000 chunk 64 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 overall best weight: 6.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 834 HIS ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 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 = 0.3418 r_free = 0.3418 target = 0.080443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.058987 restraints weight = 73107.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.060904 restraints weight = 49149.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.062314 restraints weight = 37220.897| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18032 Z= 0.148 Angle : 0.727 12.197 24472 Z= 0.355 Chirality : 0.045 0.178 2792 Planarity : 0.004 0.039 3068 Dihedral : 5.517 57.093 2436 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.93 % Favored : 95.89 % Rotamer: Outliers : 3.08 % Allowed : 20.94 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2188 helix: -0.07 (0.15), residues: 1128 sheet: -1.82 (0.32), residues: 204 loop : -0.97 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 705 HIS 0.015 0.001 HIS D 70 PHE 0.032 0.002 PHE C 557 TYR 0.015 0.001 TYR B 707 ARG 0.007 0.001 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 856) hydrogen bonds : angle 5.21080 ( 2388) covalent geometry : bond 0.00325 (18028) covalent geometry : angle 0.72737 (24472) Misc. bond : bond 0.00131 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 473 time to evaluate : 1.921 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: A 92 ARG cc_start: 0.4794 (OUTLIER) cc_final: 0.4332 (mtp85) REVERT: A 424 PHE cc_start: 0.9231 (m-80) cc_final: 0.8754 (m-80) REVERT: A 459 VAL cc_start: 0.9877 (t) cc_final: 0.9471 (p) REVERT: A 463 PHE cc_start: 0.9593 (m-80) cc_final: 0.8978 (m-80) REVERT: A 638 LYS cc_start: 0.9866 (mttt) cc_final: 0.9550 (mmtm) REVERT: A 641 SER cc_start: 0.9825 (t) cc_final: 0.9572 (p) REVERT: A 645 MET cc_start: 0.9155 (ttm) cc_final: 0.8912 (ttt) REVERT: A 656 PHE cc_start: 0.9569 (m-80) cc_final: 0.9220 (m-10) REVERT: A 681 ARG cc_start: 0.9574 (mmm160) cc_final: 0.9120 (tpp-160) REVERT: A 691 ASN cc_start: 0.9786 (m-40) cc_final: 0.9555 (t0) REVERT: A 705 TRP cc_start: 0.9268 (t60) cc_final: 0.8997 (t60) REVERT: A 757 LYS cc_start: 0.9561 (mttt) cc_final: 0.9239 (mtmt) REVERT: A 781 PHE cc_start: 0.9703 (m-80) cc_final: 0.9161 (m-80) REVERT: B 66 CYS cc_start: 0.8502 (m) cc_final: 0.8210 (m) REVERT: B 92 ARG cc_start: 0.5048 (OUTLIER) cc_final: 0.4631 (mtp85) REVERT: B 424 PHE cc_start: 0.9207 (m-80) cc_final: 0.8724 (m-80) REVERT: B 638 LYS cc_start: 0.9820 (mttt) cc_final: 0.9604 (mmtm) REVERT: B 640 PHE cc_start: 0.9532 (t80) cc_final: 0.8955 (t80) REVERT: B 645 MET cc_start: 0.9233 (ttm) cc_final: 0.8904 (ttt) REVERT: B 681 ARG cc_start: 0.9560 (mmm160) cc_final: 0.9098 (tpp-160) REVERT: B 691 ASN cc_start: 0.9781 (m-40) cc_final: 0.9536 (t0) REVERT: B 698 GLU cc_start: 0.9610 (mt-10) cc_final: 0.9403 (pt0) REVERT: B 705 TRP cc_start: 0.9235 (t60) cc_final: 0.8979 (t60) REVERT: B 781 PHE cc_start: 0.9725 (m-80) cc_final: 0.9265 (m-80) REVERT: B 830 LEU cc_start: 0.9851 (pt) cc_final: 0.9343 (tt) REVERT: C 424 PHE cc_start: 0.9150 (m-80) cc_final: 0.8653 (m-80) REVERT: C 551 PHE cc_start: 0.9555 (t80) cc_final: 0.9306 (t80) REVERT: C 645 MET cc_start: 0.9194 (ttm) cc_final: 0.8887 (ttt) REVERT: C 681 ARG cc_start: 0.9515 (mmm160) cc_final: 0.9065 (tpp-160) REVERT: C 682 GLU cc_start: 0.9574 (mt-10) cc_final: 0.9324 (pt0) REVERT: C 691 ASN cc_start: 0.9778 (m-40) cc_final: 0.9546 (t0) REVERT: C 705 TRP cc_start: 0.9296 (t60) cc_final: 0.9053 (t60) REVERT: C 757 LYS cc_start: 0.9503 (mttt) cc_final: 0.9167 (mtmt) REVERT: C 781 PHE cc_start: 0.9667 (m-80) cc_final: 0.9385 (m-80) REVERT: C 830 LEU cc_start: 0.9847 (pt) cc_final: 0.9377 (tt) REVERT: C 832 LYS cc_start: 0.9570 (tttt) cc_final: 0.9327 (tttm) REVERT: D 424 PHE cc_start: 0.9180 (m-80) cc_final: 0.8699 (m-80) REVERT: D 459 VAL cc_start: 0.9908 (t) cc_final: 0.9604 (p) REVERT: D 463 PHE cc_start: 0.9700 (m-80) cc_final: 0.9119 (m-80) REVERT: D 638 LYS cc_start: 0.9844 (mttt) cc_final: 0.9580 (mmtm) REVERT: D 651 MET cc_start: 0.9638 (mmm) cc_final: 0.9392 (mmm) REVERT: D 681 ARG cc_start: 0.9590 (mmm160) cc_final: 0.9069 (tpp-160) REVERT: D 691 ASN cc_start: 0.9819 (m-40) cc_final: 0.9448 (t0) REVERT: D 695 GLN cc_start: 0.9756 (pt0) cc_final: 0.9481 (mm-40) REVERT: D 705 TRP cc_start: 0.9288 (t60) cc_final: 0.9031 (t60) REVERT: D 744 ARG cc_start: 0.9552 (ptp-110) cc_final: 0.9198 (mmp80) REVERT: D 757 LYS cc_start: 0.9538 (mttt) cc_final: 0.9240 (mtmt) REVERT: D 804 ILE cc_start: 0.9844 (mt) cc_final: 0.9585 (tp) REVERT: D 830 LEU cc_start: 0.9811 (pt) cc_final: 0.9414 (tt) outliers start: 57 outliers final: 46 residues processed: 497 average time/residue: 0.2976 time to fit residues: 219.7462 Evaluate side-chains 500 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 452 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 850 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 758 PHE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 822 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 96 optimal weight: 40.0000 chunk 99 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 106 optimal weight: 50.0000 chunk 75 optimal weight: 30.0000 chunk 145 optimal weight: 50.0000 chunk 36 optimal weight: 50.0000 chunk 202 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 5 optimal weight: 30.0000 chunk 104 optimal weight: 0.8980 overall best weight: 12.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.070268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.052268 restraints weight = 81723.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.054248 restraints weight = 50849.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.055689 restraints weight = 36491.714| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18032 Z= 0.205 Angle : 0.748 11.939 24472 Z= 0.375 Chirality : 0.046 0.180 2792 Planarity : 0.004 0.039 3068 Dihedral : 5.577 49.305 2436 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.30 % Favored : 95.52 % Rotamer: Outliers : 4.17 % Allowed : 22.13 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.18), residues: 2188 helix: 0.07 (0.15), residues: 1108 sheet: -2.33 (0.27), residues: 308 loop : -0.63 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 568 HIS 0.005 0.001 HIS A 687 PHE 0.027 0.002 PHE C 551 TYR 0.016 0.002 TYR A 427 ARG 0.005 0.001 ARG A 681 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 856) hydrogen bonds : angle 5.36850 ( 2388) covalent geometry : bond 0.00425 (18028) covalent geometry : angle 0.74784 (24472) Misc. bond : bond 0.00092 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 467 time to evaluate : 1.835 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: A 92 ARG cc_start: 0.5253 (OUTLIER) cc_final: 0.4665 (mtp85) REVERT: A 424 PHE cc_start: 0.9304 (m-80) cc_final: 0.8836 (m-80) REVERT: A 459 VAL cc_start: 0.9883 (t) cc_final: 0.9486 (p) REVERT: A 463 PHE cc_start: 0.9571 (m-80) cc_final: 0.9030 (m-80) REVERT: A 619 PHE cc_start: 0.9700 (OUTLIER) cc_final: 0.9349 (t80) REVERT: A 638 LYS cc_start: 0.9840 (mttt) cc_final: 0.9506 (mmtm) REVERT: A 640 PHE cc_start: 0.9494 (t80) cc_final: 0.8981 (t80) REVERT: A 641 SER cc_start: 0.9818 (t) cc_final: 0.9547 (p) REVERT: A 645 MET cc_start: 0.9155 (ttm) cc_final: 0.8809 (ttt) REVERT: A 651 MET cc_start: 0.9519 (mmm) cc_final: 0.9284 (mmm) REVERT: A 656 PHE cc_start: 0.9504 (m-80) cc_final: 0.9200 (m-10) REVERT: A 681 ARG cc_start: 0.9554 (mmm160) cc_final: 0.9088 (tpp-160) REVERT: A 691 ASN cc_start: 0.9807 (m-40) cc_final: 0.9419 (t0) REVERT: A 695 GLN cc_start: 0.9800 (mt0) cc_final: 0.9534 (mm110) REVERT: A 698 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9212 (pt0) REVERT: A 757 LYS cc_start: 0.9589 (mttt) cc_final: 0.9282 (mtmt) REVERT: A 781 PHE cc_start: 0.9699 (m-80) cc_final: 0.9410 (m-80) REVERT: B 92 ARG cc_start: 0.5466 (OUTLIER) cc_final: 0.4733 (mtp85) REVERT: B 127 LEU cc_start: 0.9254 (tp) cc_final: 0.8703 (tp) REVERT: B 424 PHE cc_start: 0.9250 (m-80) cc_final: 0.8777 (m-80) REVERT: B 638 LYS cc_start: 0.9823 (mttt) cc_final: 0.9600 (mmtm) REVERT: B 640 PHE cc_start: 0.9505 (t80) cc_final: 0.8878 (t80) REVERT: B 645 MET cc_start: 0.9280 (ttm) cc_final: 0.8888 (ttt) REVERT: B 677 MET cc_start: 0.9685 (tpp) cc_final: 0.9463 (tpp) REVERT: B 681 ARG cc_start: 0.9535 (mmm160) cc_final: 0.9226 (mmm160) REVERT: B 691 ASN cc_start: 0.9795 (m-40) cc_final: 0.9399 (t0) REVERT: B 695 GLN cc_start: 0.9772 (mt0) cc_final: 0.9471 (mm110) REVERT: B 698 GLU cc_start: 0.9583 (mt-10) cc_final: 0.9371 (mt-10) REVERT: B 705 TRP cc_start: 0.9225 (t60) cc_final: 0.8938 (t60) REVERT: B 780 TYR cc_start: 0.9695 (m-80) cc_final: 0.9424 (m-80) REVERT: B 781 PHE cc_start: 0.9722 (m-80) cc_final: 0.9270 (m-80) REVERT: C 424 PHE cc_start: 0.9236 (m-80) cc_final: 0.8758 (m-80) REVERT: C 640 PHE cc_start: 0.9495 (t80) cc_final: 0.8845 (t80) REVERT: C 645 MET cc_start: 0.9309 (ttm) cc_final: 0.9003 (ttm) REVERT: C 656 PHE cc_start: 0.9324 (m-10) cc_final: 0.9113 (m-80) REVERT: C 681 ARG cc_start: 0.9524 (mmm160) cc_final: 0.9025 (tpp-160) REVERT: C 682 GLU cc_start: 0.9565 (mt-10) cc_final: 0.9300 (mt-10) REVERT: C 691 ASN cc_start: 0.9804 (m-40) cc_final: 0.9436 (t0) REVERT: C 695 GLN cc_start: 0.9759 (mt0) cc_final: 0.9520 (mm-40) REVERT: C 705 TRP cc_start: 0.9271 (t60) cc_final: 0.9010 (t60) REVERT: C 757 LYS cc_start: 0.9546 (mttt) cc_final: 0.9152 (mtmt) REVERT: C 781 PHE cc_start: 0.9673 (m-80) cc_final: 0.9435 (m-80) REVERT: C 830 LEU cc_start: 0.9861 (pt) cc_final: 0.9384 (tt) REVERT: C 832 LYS cc_start: 0.9620 (tttt) cc_final: 0.9361 (tttm) REVERT: D 60 MET cc_start: 0.8892 (ppp) cc_final: 0.8607 (pmm) REVERT: D 424 PHE cc_start: 0.9251 (m-80) cc_final: 0.8764 (m-80) REVERT: D 638 LYS cc_start: 0.9836 (mttt) cc_final: 0.9562 (mmtm) REVERT: D 640 PHE cc_start: 0.9506 (t80) cc_final: 0.8993 (t80) REVERT: D 681 ARG cc_start: 0.9555 (mmm160) cc_final: 0.9274 (mmm160) REVERT: D 691 ASN cc_start: 0.9827 (m-40) cc_final: 0.9612 (t0) REVERT: D 705 TRP cc_start: 0.9281 (t60) cc_final: 0.9004 (t60) REVERT: D 712 ASP cc_start: 0.9617 (t0) cc_final: 0.9370 (t0) REVERT: D 757 LYS cc_start: 0.9555 (mttt) cc_final: 0.9198 (mtmt) outliers start: 77 outliers final: 67 residues processed: 507 average time/residue: 0.2920 time to fit residues: 219.4600 Evaluate side-chains 509 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 439 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 850 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain D residue 758 PHE 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 822 VAL Chi-restraints excluded: chain D residue 844 MET Chi-restraints excluded: chain D residue 850 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 199 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 38 optimal weight: 30.0000 chunk 125 optimal weight: 40.0000 chunk 47 optimal weight: 30.0000 chunk 168 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.071597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.053360 restraints weight = 80833.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.055422 restraints weight = 50052.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.056965 restraints weight = 35889.851| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18032 Z= 0.138 Angle : 0.761 13.154 24472 Z= 0.362 Chirality : 0.046 0.207 2792 Planarity : 0.004 0.036 3068 Dihedral : 5.365 48.582 2436 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.56 % Favored : 96.25 % Rotamer: Outliers : 4.27 % Allowed : 23.54 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.18), residues: 2188 helix: 0.05 (0.15), residues: 1140 sheet: -1.83 (0.33), residues: 224 loop : -0.74 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 705 HIS 0.004 0.001 HIS D 587 PHE 0.023 0.002 PHE B 852 TYR 0.023 0.001 TYR D 652 ARG 0.005 0.000 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 856) hydrogen bonds : angle 5.15761 ( 2388) covalent geometry : bond 0.00307 (18028) covalent geometry : angle 0.76067 (24472) Misc. bond : bond 0.00112 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 459 time to evaluate : 1.843 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: A 92 ARG cc_start: 0.5187 (OUTLIER) cc_final: 0.4608 (mmm-85) REVERT: A 127 LEU cc_start: 0.9284 (tp) cc_final: 0.9012 (tp) REVERT: A 424 PHE cc_start: 0.9309 (m-80) cc_final: 0.8852 (m-80) REVERT: A 459 VAL cc_start: 0.9885 (t) cc_final: 0.9461 (p) REVERT: A 463 PHE cc_start: 0.9589 (m-80) cc_final: 0.9033 (m-80) REVERT: A 554 MET cc_start: 0.9220 (ptt) cc_final: 0.8991 (ptt) REVERT: A 619 PHE cc_start: 0.9668 (OUTLIER) cc_final: 0.9290 (t80) REVERT: A 638 LYS cc_start: 0.9834 (mttt) cc_final: 0.9512 (mmtm) REVERT: A 640 PHE cc_start: 0.9476 (t80) cc_final: 0.8927 (t80) REVERT: A 641 SER cc_start: 0.9773 (t) cc_final: 0.9512 (p) REVERT: A 645 MET cc_start: 0.9111 (ttm) cc_final: 0.8804 (ttt) REVERT: A 651 MET cc_start: 0.9567 (mmm) cc_final: 0.9244 (mmm) REVERT: A 656 PHE cc_start: 0.9468 (m-80) cc_final: 0.9105 (m-80) REVERT: A 681 ARG cc_start: 0.9532 (mmm160) cc_final: 0.9052 (tpp-160) REVERT: A 691 ASN cc_start: 0.9803 (m-40) cc_final: 0.9420 (t0) REVERT: A 695 GLN cc_start: 0.9794 (mt0) cc_final: 0.9478 (mm-40) REVERT: A 698 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9203 (pt0) REVERT: A 757 LYS cc_start: 0.9569 (mttt) cc_final: 0.9303 (mtmt) REVERT: A 781 PHE cc_start: 0.9712 (m-80) cc_final: 0.9370 (m-80) REVERT: B 92 ARG cc_start: 0.5338 (OUTLIER) cc_final: 0.4730 (mmm-85) REVERT: B 127 LEU cc_start: 0.9246 (tp) cc_final: 0.8641 (tp) REVERT: B 424 PHE cc_start: 0.9262 (m-80) cc_final: 0.8786 (m-80) REVERT: B 462 MET cc_start: 0.9719 (tpt) cc_final: 0.9451 (tpt) REVERT: B 638 LYS cc_start: 0.9827 (mttt) cc_final: 0.9613 (mmtm) REVERT: B 640 PHE cc_start: 0.9486 (t80) cc_final: 0.8788 (t80) REVERT: B 645 MET cc_start: 0.9312 (ttm) cc_final: 0.8881 (ttt) REVERT: B 681 ARG cc_start: 0.9517 (mmm160) cc_final: 0.9046 (tpp-160) REVERT: B 691 ASN cc_start: 0.9787 (m-40) cc_final: 0.9560 (t0) REVERT: B 780 TYR cc_start: 0.9697 (m-80) cc_final: 0.9469 (m-80) REVERT: B 781 PHE cc_start: 0.9729 (m-80) cc_final: 0.9229 (m-80) REVERT: B 782 ILE cc_start: 0.9780 (mp) cc_final: 0.9529 (tp) REVERT: B 830 LEU cc_start: 0.9864 (pt) cc_final: 0.9421 (tt) REVERT: C 127 LEU cc_start: 0.9210 (tp) cc_final: 0.8735 (tp) REVERT: C 424 PHE cc_start: 0.9233 (m-80) cc_final: 0.8750 (m-80) REVERT: C 640 PHE cc_start: 0.9489 (t80) cc_final: 0.8754 (t80) REVERT: C 645 MET cc_start: 0.9378 (ttm) cc_final: 0.9029 (ttm) REVERT: C 681 ARG cc_start: 0.9504 (mmm160) cc_final: 0.8995 (tpp-160) REVERT: C 682 GLU cc_start: 0.9569 (mt-10) cc_final: 0.9290 (mt-10) REVERT: C 691 ASN cc_start: 0.9792 (m-40) cc_final: 0.9436 (t0) REVERT: C 695 GLN cc_start: 0.9777 (mt0) cc_final: 0.9524 (mm-40) REVERT: C 698 GLU cc_start: 0.9455 (pt0) cc_final: 0.9241 (pt0) REVERT: C 705 TRP cc_start: 0.9286 (t60) cc_final: 0.9006 (t60) REVERT: C 757 LYS cc_start: 0.9511 (mttt) cc_final: 0.9209 (mtmt) REVERT: C 781 PHE cc_start: 0.9679 (m-80) cc_final: 0.9434 (m-80) REVERT: C 830 LEU cc_start: 0.9869 (pt) cc_final: 0.9413 (tt) REVERT: C 832 LYS cc_start: 0.9637 (tttt) cc_final: 0.9374 (tttm) REVERT: D 127 LEU cc_start: 0.9284 (tp) cc_final: 0.8965 (tp) REVERT: D 424 PHE cc_start: 0.9252 (m-80) cc_final: 0.8778 (m-80) REVERT: D 638 LYS cc_start: 0.9827 (mttt) cc_final: 0.9555 (mmtm) REVERT: D 640 PHE cc_start: 0.9477 (t80) cc_final: 0.8961 (t80) REVERT: D 656 PHE cc_start: 0.9325 (m-10) cc_final: 0.9090 (m-10) REVERT: D 681 ARG cc_start: 0.9540 (mmm160) cc_final: 0.9031 (tpp-160) REVERT: D 691 ASN cc_start: 0.9825 (m-40) cc_final: 0.9609 (t0) REVERT: D 705 TRP cc_start: 0.9262 (t60) cc_final: 0.8968 (t60) REVERT: D 757 LYS cc_start: 0.9512 (mttt) cc_final: 0.9206 (mtmt) REVERT: D 821 ASP cc_start: 0.9429 (p0) cc_final: 0.9143 (t0) outliers start: 79 outliers final: 64 residues processed: 507 average time/residue: 0.2904 time to fit residues: 219.0120 Evaluate side-chains 504 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 437 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 597 TYR Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 758 PHE 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 822 VAL Chi-restraints excluded: chain D residue 844 MET Chi-restraints excluded: chain D residue 850 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 52 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 40.0000 chunk 10 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 157 optimal weight: 50.0000 chunk 207 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.071598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.053342 restraints weight = 79885.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.055368 restraints weight = 49879.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.056890 restraints weight = 35887.227| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18032 Z= 0.140 Angle : 0.755 12.312 24472 Z= 0.360 Chirality : 0.045 0.209 2792 Planarity : 0.004 0.036 3068 Dihedral : 5.244 44.692 2436 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.88 % Favored : 95.93 % Rotamer: Outliers : 4.38 % Allowed : 25.97 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2188 helix: 0.10 (0.15), residues: 1128 sheet: -1.65 (0.34), residues: 224 loop : -0.66 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 705 HIS 0.005 0.001 HIS D 70 PHE 0.025 0.002 PHE A 551 TYR 0.027 0.001 TYR B 707 ARG 0.004 0.000 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 856) hydrogen bonds : angle 5.15143 ( 2388) covalent geometry : bond 0.00309 (18028) covalent geometry : angle 0.75502 (24472) Misc. bond : bond 0.00079 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 450 time to evaluate : 1.859 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: A 92 ARG cc_start: 0.5400 (OUTLIER) cc_final: 0.4828 (mmm-85) REVERT: A 424 PHE cc_start: 0.9337 (m-80) cc_final: 0.8893 (m-80) REVERT: A 459 VAL cc_start: 0.9888 (t) cc_final: 0.9641 (p) REVERT: A 463 PHE cc_start: 0.9600 (m-80) cc_final: 0.8929 (m-80) REVERT: A 619 PHE cc_start: 0.9688 (OUTLIER) cc_final: 0.9342 (t80) REVERT: A 638 LYS cc_start: 0.9843 (mttt) cc_final: 0.9558 (mmtm) REVERT: A 640 PHE cc_start: 0.9477 (t80) cc_final: 0.8970 (t80) REVERT: A 641 SER cc_start: 0.9779 (t) cc_final: 0.9531 (p) REVERT: A 651 MET cc_start: 0.9591 (mmm) cc_final: 0.9294 (mmm) REVERT: A 656 PHE cc_start: 0.9466 (m-80) cc_final: 0.9072 (m-80) REVERT: A 677 MET cc_start: 0.9707 (tpp) cc_final: 0.9504 (tpp) REVERT: A 681 ARG cc_start: 0.9527 (mmm160) cc_final: 0.9235 (mmm160) REVERT: A 691 ASN cc_start: 0.9803 (m-40) cc_final: 0.9430 (t0) REVERT: A 695 GLN cc_start: 0.9791 (mt0) cc_final: 0.9467 (mm-40) REVERT: A 698 GLU cc_start: 0.9454 (mt-10) cc_final: 0.9210 (pt0) REVERT: A 757 LYS cc_start: 0.9552 (mttt) cc_final: 0.9272 (mtmt) REVERT: A 781 PHE cc_start: 0.9701 (m-80) cc_final: 0.9249 (m-80) REVERT: A 782 ILE cc_start: 0.9764 (mp) cc_final: 0.9443 (tp) REVERT: B 92 ARG cc_start: 0.5449 (OUTLIER) cc_final: 0.4809 (mmm-85) REVERT: B 127 LEU cc_start: 0.9228 (tp) cc_final: 0.8735 (tp) REVERT: B 424 PHE cc_start: 0.9292 (m-80) cc_final: 0.8828 (m-80) REVERT: B 462 MET cc_start: 0.9729 (tpt) cc_final: 0.9472 (tpt) REVERT: B 638 LYS cc_start: 0.9835 (mttt) cc_final: 0.9627 (mmtm) REVERT: B 640 PHE cc_start: 0.9496 (t80) cc_final: 0.8930 (t80) REVERT: B 645 MET cc_start: 0.9342 (ttm) cc_final: 0.8918 (ttt) REVERT: B 677 MET cc_start: 0.9659 (tpp) cc_final: 0.9441 (tpp) REVERT: B 681 ARG cc_start: 0.9519 (mmm160) cc_final: 0.9205 (mmm160) REVERT: B 691 ASN cc_start: 0.9794 (m-40) cc_final: 0.9410 (t0) REVERT: B 695 GLN cc_start: 0.9790 (mt0) cc_final: 0.9524 (mm110) REVERT: B 780 TYR cc_start: 0.9698 (m-80) cc_final: 0.9451 (m-80) REVERT: B 781 PHE cc_start: 0.9734 (m-80) cc_final: 0.9219 (m-80) REVERT: B 782 ILE cc_start: 0.9788 (mp) cc_final: 0.9543 (tp) REVERT: B 830 LEU cc_start: 0.9866 (pt) cc_final: 0.9436 (tt) REVERT: C 127 LEU cc_start: 0.9225 (tp) cc_final: 0.8778 (tp) REVERT: C 420 TYR cc_start: 0.9592 (t80) cc_final: 0.9157 (t80) REVERT: C 424 PHE cc_start: 0.9242 (m-80) cc_final: 0.8861 (m-80) REVERT: C 640 PHE cc_start: 0.9497 (t80) cc_final: 0.8901 (t80) REVERT: C 645 MET cc_start: 0.9438 (ttm) cc_final: 0.8761 (ttm) REVERT: C 656 PHE cc_start: 0.9345 (m-10) cc_final: 0.9050 (m-80) REVERT: C 681 ARG cc_start: 0.9487 (mmm160) cc_final: 0.9233 (mmm160) REVERT: C 682 GLU cc_start: 0.9563 (mt-10) cc_final: 0.9303 (mt-10) REVERT: C 691 ASN cc_start: 0.9793 (m-40) cc_final: 0.9440 (t0) REVERT: C 695 GLN cc_start: 0.9768 (mt0) cc_final: 0.9518 (mm-40) REVERT: C 698 GLU cc_start: 0.9442 (pt0) cc_final: 0.9170 (pt0) REVERT: C 757 LYS cc_start: 0.9514 (mttt) cc_final: 0.9215 (mtmt) REVERT: C 781 PHE cc_start: 0.9688 (m-80) cc_final: 0.9437 (m-80) REVERT: C 830 LEU cc_start: 0.9868 (pt) cc_final: 0.9420 (tt) REVERT: C 832 LYS cc_start: 0.9629 (tttt) cc_final: 0.9377 (tttm) REVERT: D 424 PHE cc_start: 0.9274 (m-80) cc_final: 0.8804 (m-80) REVERT: D 619 PHE cc_start: 0.9649 (OUTLIER) cc_final: 0.9045 (t80) REVERT: D 638 LYS cc_start: 0.9836 (mttt) cc_final: 0.9575 (mmtm) REVERT: D 640 PHE cc_start: 0.9483 (t80) cc_final: 0.9011 (t80) REVERT: D 649 SER cc_start: 0.9777 (p) cc_final: 0.9391 (p) REVERT: D 664 GLN cc_start: 0.9585 (mt0) cc_final: 0.9302 (mm-40) REVERT: D 681 ARG cc_start: 0.9542 (mmm160) cc_final: 0.9282 (mmm160) REVERT: D 691 ASN cc_start: 0.9823 (m-40) cc_final: 0.9606 (t0) REVERT: D 705 TRP cc_start: 0.9265 (t60) cc_final: 0.8962 (t60) REVERT: D 744 ARG cc_start: 0.9535 (ptp-110) cc_final: 0.8974 (mpt90) REVERT: D 757 LYS cc_start: 0.9486 (mttt) cc_final: 0.9189 (mtmt) REVERT: D 821 ASP cc_start: 0.9318 (p0) cc_final: 0.9108 (t0) outliers start: 81 outliers final: 69 residues processed: 496 average time/residue: 0.2919 time to fit residues: 216.0617 Evaluate side-chains 514 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 441 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 720 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 597 TYR Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 713 MET Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 758 PHE 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 822 VAL Chi-restraints excluded: chain D residue 844 MET Chi-restraints excluded: chain D residue 850 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 20.0000 chunk 156 optimal weight: 30.0000 chunk 126 optimal weight: 50.0000 chunk 3 optimal weight: 50.0000 chunk 145 optimal weight: 40.0000 chunk 64 optimal weight: 9.9990 chunk 190 optimal weight: 50.0000 chunk 37 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.069585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.051645 restraints weight = 81022.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.053652 restraints weight = 50316.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.055109 restraints weight = 36076.052| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18032 Z= 0.165 Angle : 0.784 14.246 24472 Z= 0.377 Chirality : 0.046 0.231 2792 Planarity : 0.004 0.036 3068 Dihedral : 5.272 42.717 2436 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.93 % Favored : 95.89 % Rotamer: Outliers : 4.55 % Allowed : 26.68 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.18), residues: 2188 helix: 0.16 (0.15), residues: 1116 sheet: -1.71 (0.31), residues: 268 loop : -0.72 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 705 HIS 0.005 0.001 HIS D 687 PHE 0.031 0.002 PHE D 551 TYR 0.025 0.002 TYR B 707 ARG 0.003 0.000 ARG D 696 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 856) hydrogen bonds : angle 5.29634 ( 2388) covalent geometry : bond 0.00355 (18028) covalent geometry : angle 0.78405 (24472) Misc. bond : bond 0.00068 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 454 time to evaluate : 1.833 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: A 92 ARG cc_start: 0.5534 (OUTLIER) cc_final: 0.5219 (mmm-85) REVERT: A 127 LEU cc_start: 0.9151 (tp) cc_final: 0.8653 (tp) REVERT: A 424 PHE cc_start: 0.9380 (m-80) cc_final: 0.8954 (m-80) REVERT: A 459 VAL cc_start: 0.9842 (t) cc_final: 0.9420 (p) REVERT: A 463 PHE cc_start: 0.9581 (m-80) cc_final: 0.9120 (m-80) REVERT: A 619 PHE cc_start: 0.9720 (OUTLIER) cc_final: 0.9404 (t80) REVERT: A 638 LYS cc_start: 0.9854 (mttt) cc_final: 0.9560 (mmtm) REVERT: A 640 PHE cc_start: 0.9484 (t80) cc_final: 0.9016 (t80) REVERT: A 641 SER cc_start: 0.9809 (t) cc_final: 0.9554 (p) REVERT: A 651 MET cc_start: 0.9584 (mmm) cc_final: 0.9297 (mmm) REVERT: A 656 PHE cc_start: 0.9497 (m-80) cc_final: 0.9082 (m-80) REVERT: A 677 MET cc_start: 0.9703 (tpp) cc_final: 0.9471 (tpp) REVERT: A 681 ARG cc_start: 0.9530 (mmm160) cc_final: 0.9224 (mmm160) REVERT: A 691 ASN cc_start: 0.9813 (m-40) cc_final: 0.9428 (t0) REVERT: A 695 GLN cc_start: 0.9798 (mt0) cc_final: 0.9507 (mm110) REVERT: A 698 GLU cc_start: 0.9458 (mt-10) cc_final: 0.9145 (pt0) REVERT: A 757 LYS cc_start: 0.9530 (mttt) cc_final: 0.9261 (mtmt) REVERT: A 781 PHE cc_start: 0.9709 (m-80) cc_final: 0.9240 (m-80) REVERT: B 92 ARG cc_start: 0.5609 (OUTLIER) cc_final: 0.5181 (mmm-85) REVERT: B 127 LEU cc_start: 0.9253 (tp) cc_final: 0.8729 (tp) REVERT: B 424 PHE cc_start: 0.9349 (m-80) cc_final: 0.8917 (m-80) REVERT: B 462 MET cc_start: 0.9735 (tpt) cc_final: 0.9469 (tpt) REVERT: B 638 LYS cc_start: 0.9853 (mttt) cc_final: 0.9638 (mmtm) REVERT: B 640 PHE cc_start: 0.9518 (t80) cc_final: 0.8988 (t80) REVERT: B 645 MET cc_start: 0.9399 (ttm) cc_final: 0.8572 (ttt) REVERT: B 656 PHE cc_start: 0.9438 (m-10) cc_final: 0.9201 (m-10) REVERT: B 677 MET cc_start: 0.9661 (tpp) cc_final: 0.9441 (tpp) REVERT: B 681 ARG cc_start: 0.9537 (mmm160) cc_final: 0.9217 (mmm160) REVERT: B 691 ASN cc_start: 0.9808 (m-40) cc_final: 0.9591 (t0) REVERT: B 781 PHE cc_start: 0.9760 (m-80) cc_final: 0.9236 (m-80) REVERT: B 782 ILE cc_start: 0.9813 (mp) cc_final: 0.9460 (tp) REVERT: C 127 LEU cc_start: 0.9252 (tp) cc_final: 0.8813 (tp) REVERT: C 410 TRP cc_start: 0.9220 (t60) cc_final: 0.8910 (t60) REVERT: C 424 PHE cc_start: 0.9280 (m-80) cc_final: 0.8807 (m-80) REVERT: C 619 PHE cc_start: 0.9684 (OUTLIER) cc_final: 0.9041 (t80) REVERT: C 640 PHE cc_start: 0.9535 (t80) cc_final: 0.8976 (t80) REVERT: C 645 MET cc_start: 0.9460 (ttm) cc_final: 0.8738 (ttm) REVERT: C 681 ARG cc_start: 0.9476 (mmm160) cc_final: 0.9243 (mmm160) REVERT: C 682 GLU cc_start: 0.9561 (mt-10) cc_final: 0.9324 (mt-10) REVERT: C 691 ASN cc_start: 0.9816 (m-40) cc_final: 0.9459 (t0) REVERT: C 695 GLN cc_start: 0.9776 (mt0) cc_final: 0.9478 (mm-40) REVERT: C 698 GLU cc_start: 0.9453 (pt0) cc_final: 0.9181 (pt0) REVERT: C 757 LYS cc_start: 0.9506 (mttt) cc_final: 0.8981 (mtpt) REVERT: C 781 PHE cc_start: 0.9697 (m-80) cc_final: 0.9354 (m-80) REVERT: C 821 ASP cc_start: 0.9375 (p0) cc_final: 0.9081 (m-30) REVERT: C 830 LEU cc_start: 0.9874 (pt) cc_final: 0.9428 (tt) REVERT: C 832 LYS cc_start: 0.9643 (tttt) cc_final: 0.9429 (tttm) REVERT: D 127 LEU cc_start: 0.9212 (tp) cc_final: 0.8708 (tp) REVERT: D 424 PHE cc_start: 0.9295 (m-80) cc_final: 0.8821 (m-80) REVERT: D 619 PHE cc_start: 0.9679 (OUTLIER) cc_final: 0.9095 (t80) REVERT: D 638 LYS cc_start: 0.9854 (mttt) cc_final: 0.9597 (mmtm) REVERT: D 640 PHE cc_start: 0.9488 (t80) cc_final: 0.9039 (t80) REVERT: D 649 SER cc_start: 0.9776 (p) cc_final: 0.9389 (p) REVERT: D 656 PHE cc_start: 0.9340 (m-10) cc_final: 0.9085 (m-10) REVERT: D 664 GLN cc_start: 0.9583 (mt0) cc_final: 0.9317 (mm-40) REVERT: D 681 ARG cc_start: 0.9546 (mmm160) cc_final: 0.9325 (mmm160) REVERT: D 691 ASN cc_start: 0.9830 (m-40) cc_final: 0.9626 (t0) REVERT: D 705 TRP cc_start: 0.9261 (t60) cc_final: 0.8928 (t60) REVERT: D 744 ARG cc_start: 0.9544 (ptp-110) cc_final: 0.8999 (mpt90) REVERT: D 757 LYS cc_start: 0.9459 (mttt) cc_final: 0.9162 (mtmt) REVERT: D 821 ASP cc_start: 0.9371 (p0) cc_final: 0.9135 (t0) outliers start: 84 outliers final: 73 residues processed: 502 average time/residue: 0.3083 time to fit residues: 232.6362 Evaluate side-chains 516 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 438 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 720 PHE Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 720 PHE Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 597 TYR Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 713 MET Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 758 PHE 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 822 VAL Chi-restraints excluded: chain D residue 840 GLU Chi-restraints excluded: chain D residue 844 MET Chi-restraints excluded: chain D residue 850 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 77 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 45 optimal weight: 0.0970 chunk 5 optimal weight: 40.0000 chunk 214 optimal weight: 5.9990 chunk 181 optimal weight: 40.0000 chunk 104 optimal weight: 40.0000 chunk 8 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 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 = 0.3343 r_free = 0.3343 target = 0.070534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.052249 restraints weight = 80229.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.054344 restraints weight = 49841.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.055900 restraints weight = 35761.299| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.6721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18032 Z= 0.136 Angle : 0.818 13.382 24472 Z= 0.386 Chirality : 0.046 0.296 2792 Planarity : 0.004 0.036 3068 Dihedral : 5.107 41.702 2436 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.52 % Favored : 96.30 % Rotamer: Outliers : 4.06 % Allowed : 28.41 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.18), residues: 2188 helix: 0.21 (0.15), residues: 1128 sheet: -1.38 (0.33), residues: 248 loop : -0.79 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 705 HIS 0.005 0.001 HIS B 70 PHE 0.032 0.002 PHE C 656 TYR 0.029 0.001 TYR D 707 ARG 0.011 0.001 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 856) hydrogen bonds : angle 5.24138 ( 2388) covalent geometry : bond 0.00304 (18028) covalent geometry : angle 0.81788 (24472) Misc. bond : bond 0.00129 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 454 time to evaluate : 2.318 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: A 31 ILE cc_start: 0.9694 (pt) cc_final: 0.9396 (tp) REVERT: A 92 ARG cc_start: 0.5670 (OUTLIER) cc_final: 0.5141 (mmm-85) REVERT: A 127 LEU cc_start: 0.9137 (tp) cc_final: 0.8669 (tp) REVERT: A 459 VAL cc_start: 0.9879 (t) cc_final: 0.9489 (p) REVERT: A 463 PHE cc_start: 0.9630 (m-80) cc_final: 0.9106 (m-80) REVERT: A 619 PHE cc_start: 0.9699 (OUTLIER) cc_final: 0.9391 (t80) REVERT: A 638 LYS cc_start: 0.9842 (mttt) cc_final: 0.9543 (mmtm) REVERT: A 640 PHE cc_start: 0.9476 (t80) cc_final: 0.9034 (t80) REVERT: A 651 MET cc_start: 0.9569 (mmm) cc_final: 0.9288 (mmm) REVERT: A 656 PHE cc_start: 0.9500 (m-80) cc_final: 0.9074 (m-80) REVERT: A 677 MET cc_start: 0.9697 (tpp) cc_final: 0.9492 (tpp) REVERT: A 681 ARG cc_start: 0.9506 (mmm160) cc_final: 0.9237 (mmm160) REVERT: A 691 ASN cc_start: 0.9807 (m-40) cc_final: 0.9586 (t0) REVERT: A 757 LYS cc_start: 0.9508 (mttt) cc_final: 0.9300 (mtmt) REVERT: A 781 PHE cc_start: 0.9732 (m-80) cc_final: 0.9224 (m-80) REVERT: A 782 ILE cc_start: 0.9791 (mp) cc_final: 0.9496 (tp) REVERT: B 60 MET cc_start: 0.8651 (ppp) cc_final: 0.8187 (ppp) REVERT: B 424 PHE cc_start: 0.9341 (m-80) cc_final: 0.8914 (m-80) REVERT: B 462 MET cc_start: 0.9727 (tpt) cc_final: 0.9467 (tpt) REVERT: B 619 PHE cc_start: 0.9702 (OUTLIER) cc_final: 0.9276 (t80) REVERT: B 638 LYS cc_start: 0.9838 (mttt) cc_final: 0.9631 (mmtm) REVERT: B 640 PHE cc_start: 0.9501 (t80) cc_final: 0.8974 (t80) REVERT: B 645 MET cc_start: 0.9427 (ttm) cc_final: 0.8995 (ttt) REVERT: B 656 PHE cc_start: 0.9424 (m-10) cc_final: 0.9159 (m-80) REVERT: B 677 MET cc_start: 0.9654 (tpp) cc_final: 0.9367 (tpp) REVERT: B 681 ARG cc_start: 0.9519 (mmm160) cc_final: 0.9162 (mmm160) REVERT: B 691 ASN cc_start: 0.9801 (m-40) cc_final: 0.9583 (t0) REVERT: B 780 TYR cc_start: 0.9720 (m-80) cc_final: 0.9409 (m-80) REVERT: B 781 PHE cc_start: 0.9765 (m-80) cc_final: 0.9310 (m-80) REVERT: B 782 ILE cc_start: 0.9816 (mp) cc_final: 0.9498 (tp) REVERT: C 112 VAL cc_start: 0.8606 (t) cc_final: 0.8358 (p) REVERT: C 127 LEU cc_start: 0.9283 (tp) cc_final: 0.8865 (tp) REVERT: C 410 TRP cc_start: 0.9188 (t60) cc_final: 0.8849 (t60) REVERT: C 420 TYR cc_start: 0.9584 (t80) cc_final: 0.9155 (t80) REVERT: C 424 PHE cc_start: 0.9322 (m-80) cc_final: 0.8938 (m-80) REVERT: C 640 PHE cc_start: 0.9513 (t80) cc_final: 0.8943 (t80) REVERT: C 645 MET cc_start: 0.9487 (ttm) cc_final: 0.8803 (ttm) REVERT: C 681 ARG cc_start: 0.9453 (mmm160) cc_final: 0.9203 (mmm160) REVERT: C 682 GLU cc_start: 0.9552 (mt-10) cc_final: 0.9311 (mt-10) REVERT: C 691 ASN cc_start: 0.9808 (m-40) cc_final: 0.9461 (t0) REVERT: C 695 GLN cc_start: 0.9766 (mt0) cc_final: 0.9477 (mm-40) REVERT: C 698 GLU cc_start: 0.9444 (pt0) cc_final: 0.9214 (pt0) REVERT: C 757 LYS cc_start: 0.9491 (mttt) cc_final: 0.9070 (mtmm) REVERT: C 781 PHE cc_start: 0.9690 (m-80) cc_final: 0.9412 (m-80) REVERT: C 821 ASP cc_start: 0.9359 (p0) cc_final: 0.9095 (t0) REVERT: C 830 LEU cc_start: 0.9872 (pt) cc_final: 0.9429 (tt) REVERT: C 832 LYS cc_start: 0.9647 (tttt) cc_final: 0.9369 (tttm) REVERT: D 127 LEU cc_start: 0.9207 (tp) cc_final: 0.8728 (tp) REVERT: D 410 TRP cc_start: 0.9271 (t60) cc_final: 0.8882 (t60) REVERT: D 424 PHE cc_start: 0.9340 (m-80) cc_final: 0.8875 (m-80) REVERT: D 619 PHE cc_start: 0.9667 (OUTLIER) cc_final: 0.9096 (t80) REVERT: D 638 LYS cc_start: 0.9838 (mttt) cc_final: 0.9612 (mmtm) REVERT: D 640 PHE cc_start: 0.9467 (t80) cc_final: 0.9010 (t80) REVERT: D 664 GLN cc_start: 0.9567 (mt0) cc_final: 0.9320 (mm-40) REVERT: D 681 ARG cc_start: 0.9522 (mmm160) cc_final: 0.9302 (mmm160) REVERT: D 691 ASN cc_start: 0.9825 (m-40) cc_final: 0.9465 (t0) REVERT: D 695 GLN cc_start: 0.9767 (pt0) cc_final: 0.9498 (mm-40) REVERT: D 705 TRP cc_start: 0.9265 (t60) cc_final: 0.8933 (t60) REVERT: D 744 ARG cc_start: 0.9546 (ptp-110) cc_final: 0.8977 (mpt90) REVERT: D 757 LYS cc_start: 0.9460 (mttt) cc_final: 0.9153 (mtmt) REVERT: D 821 ASP cc_start: 0.9367 (p0) cc_final: 0.9148 (t0) outliers start: 75 outliers final: 63 residues processed: 498 average time/residue: 0.3844 time to fit residues: 294.4105 Evaluate side-chains 508 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 441 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 693 LEU 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 822 VAL Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 720 PHE Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 597 TYR Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 713 MET Chi-restraints excluded: chain D residue 758 PHE 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 822 VAL Chi-restraints excluded: chain D residue 844 MET Chi-restraints excluded: chain D residue 850 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 92 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 171 optimal weight: 40.0000 chunk 173 optimal weight: 2.9990 chunk 112 optimal weight: 40.0000 chunk 207 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 71 optimal weight: 0.0970 chunk 25 optimal weight: 20.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN B 664 GLN ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 861 ASN ** D 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.071706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053381 restraints weight = 79178.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.055499 restraints weight = 48954.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.057091 restraints weight = 34931.882| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.6835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18032 Z= 0.137 Angle : 0.850 14.309 24472 Z= 0.406 Chirality : 0.047 0.320 2792 Planarity : 0.004 0.034 3068 Dihedral : 5.077 41.214 2436 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.66 % Favored : 96.16 % Rotamer: Outliers : 3.57 % Allowed : 29.82 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2188 helix: 0.28 (0.16), residues: 1128 sheet: -1.36 (0.33), residues: 248 loop : -0.83 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 705 HIS 0.009 0.001 HIS A 70 PHE 0.029 0.002 PHE C 551 TYR 0.031 0.001 TYR C 707 ARG 0.004 0.000 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 856) hydrogen bonds : angle 5.25677 ( 2388) covalent geometry : bond 0.00304 (18028) covalent geometry : angle 0.84963 (24472) Misc. bond : bond 0.00074 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 457 time to evaluate : 2.069 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 31 ILE cc_start: 0.9694 (pt) cc_final: 0.9396 (tp) REVERT: A 92 ARG cc_start: 0.5731 (OUTLIER) cc_final: 0.5224 (mmm-85) REVERT: A 127 LEU cc_start: 0.9136 (tp) cc_final: 0.8658 (tp) REVERT: A 463 PHE cc_start: 0.9656 (m-80) cc_final: 0.9161 (m-80) REVERT: A 619 PHE cc_start: 0.9703 (OUTLIER) cc_final: 0.9386 (t80) REVERT: A 633 ASN cc_start: 0.9200 (m-40) cc_final: 0.8924 (p0) REVERT: A 638 LYS cc_start: 0.9850 (mttt) cc_final: 0.9506 (mtpp) REVERT: A 651 MET cc_start: 0.9562 (mmm) cc_final: 0.9277 (mmm) REVERT: A 656 PHE cc_start: 0.9514 (m-80) cc_final: 0.9273 (m-10) REVERT: A 664 GLN cc_start: 0.9585 (mt0) cc_final: 0.9332 (mm-40) REVERT: A 677 MET cc_start: 0.9688 (tpp) cc_final: 0.9470 (tpp) REVERT: A 681 ARG cc_start: 0.9521 (mmm160) cc_final: 0.9234 (mmm160) REVERT: A 691 ASN cc_start: 0.9806 (m-40) cc_final: 0.9423 (t0) REVERT: A 695 GLN cc_start: 0.9764 (mt0) cc_final: 0.9473 (mm-40) REVERT: A 757 LYS cc_start: 0.9540 (mttt) cc_final: 0.9172 (mtmt) REVERT: A 781 PHE cc_start: 0.9743 (m-80) cc_final: 0.9248 (m-80) REVERT: A 782 ILE cc_start: 0.9794 (mp) cc_final: 0.9524 (tp) REVERT: B 127 LEU cc_start: 0.9257 (tp) cc_final: 0.8860 (tp) REVERT: B 410 TRP cc_start: 0.8906 (t60) cc_final: 0.8569 (t60) REVERT: B 424 PHE cc_start: 0.9350 (m-80) cc_final: 0.8915 (m-80) REVERT: B 462 MET cc_start: 0.9734 (tpt) cc_final: 0.9468 (tpt) REVERT: B 559 LEU cc_start: 0.9816 (tp) cc_final: 0.9487 (tp) REVERT: B 563 TRP cc_start: 0.9482 (m-10) cc_final: 0.9280 (m-10) REVERT: B 638 LYS cc_start: 0.9844 (mttt) cc_final: 0.9639 (mmtm) REVERT: B 640 PHE cc_start: 0.9489 (t80) cc_final: 0.8982 (t80) REVERT: B 645 MET cc_start: 0.9436 (ttm) cc_final: 0.9002 (ttt) REVERT: B 656 PHE cc_start: 0.9438 (m-10) cc_final: 0.9179 (m-80) REVERT: B 677 MET cc_start: 0.9660 (tpp) cc_final: 0.9378 (tpp) REVERT: B 681 ARG cc_start: 0.9525 (mmm160) cc_final: 0.9211 (mmm160) REVERT: B 691 ASN cc_start: 0.9792 (m-40) cc_final: 0.9571 (t0) REVERT: B 781 PHE cc_start: 0.9719 (m-80) cc_final: 0.9322 (m-80) REVERT: B 782 ILE cc_start: 0.9801 (mp) cc_final: 0.9569 (tp) REVERT: B 830 LEU cc_start: 0.9814 (pp) cc_final: 0.9318 (tt) REVERT: C 60 MET cc_start: 0.8633 (ppp) cc_final: 0.8256 (ptm) REVERT: C 112 VAL cc_start: 0.8569 (t) cc_final: 0.8329 (p) REVERT: C 127 LEU cc_start: 0.9282 (tp) cc_final: 0.8779 (tp) REVERT: C 410 TRP cc_start: 0.9186 (t60) cc_final: 0.8825 (t60) REVERT: C 420 TYR cc_start: 0.9576 (t80) cc_final: 0.9144 (t80) REVERT: C 424 PHE cc_start: 0.9336 (m-80) cc_final: 0.8958 (m-80) REVERT: C 640 PHE cc_start: 0.9514 (t80) cc_final: 0.8954 (t80) REVERT: C 645 MET cc_start: 0.9480 (ttm) cc_final: 0.8747 (ttm) REVERT: C 652 TYR cc_start: 0.8723 (t80) cc_final: 0.8415 (t80) REVERT: C 681 ARG cc_start: 0.9451 (mmm160) cc_final: 0.9194 (mmm160) REVERT: C 682 GLU cc_start: 0.9546 (mt-10) cc_final: 0.9307 (mt-10) REVERT: C 691 ASN cc_start: 0.9806 (m-40) cc_final: 0.9465 (t0) REVERT: C 695 GLN cc_start: 0.9768 (mt0) cc_final: 0.9480 (mm-40) REVERT: C 698 GLU cc_start: 0.9474 (pt0) cc_final: 0.9200 (pt0) REVERT: C 780 TYR cc_start: 0.9766 (m-10) cc_final: 0.9504 (m-10) REVERT: C 781 PHE cc_start: 0.9716 (m-80) cc_final: 0.9244 (m-80) REVERT: C 821 ASP cc_start: 0.9356 (p0) cc_final: 0.9102 (m-30) REVERT: C 830 LEU cc_start: 0.9865 (pt) cc_final: 0.9383 (tt) REVERT: D 127 LEU cc_start: 0.9196 (tp) cc_final: 0.8717 (tp) REVERT: D 410 TRP cc_start: 0.9228 (t60) cc_final: 0.8768 (t60) REVERT: D 424 PHE cc_start: 0.9361 (m-80) cc_final: 0.8904 (m-80) REVERT: D 619 PHE cc_start: 0.9671 (OUTLIER) cc_final: 0.9082 (t80) REVERT: D 638 LYS cc_start: 0.9844 (mttt) cc_final: 0.9609 (mmtm) REVERT: D 640 PHE cc_start: 0.9449 (t80) cc_final: 0.9000 (t80) REVERT: D 664 GLN cc_start: 0.9567 (mt0) cc_final: 0.9329 (mm-40) REVERT: D 681 ARG cc_start: 0.9525 (mmm160) cc_final: 0.9305 (mmm160) REVERT: D 691 ASN cc_start: 0.9823 (m-40) cc_final: 0.9612 (t0) REVERT: D 705 TRP cc_start: 0.9264 (t60) cc_final: 0.8953 (t60) REVERT: D 744 ARG cc_start: 0.9540 (ptp-110) cc_final: 0.9002 (mpt90) REVERT: D 757 LYS cc_start: 0.9442 (mttt) cc_final: 0.8900 (mtpt) REVERT: D 821 ASP cc_start: 0.9352 (p0) cc_final: 0.9143 (t0) outliers start: 66 outliers final: 59 residues processed: 492 average time/residue: 0.3252 time to fit residues: 239.8652 Evaluate side-chains 499 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 437 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 714 ASN Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 597 TYR Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 713 MET Chi-restraints excluded: chain D residue 758 PHE 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 822 VAL Chi-restraints excluded: chain D residue 844 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 195 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 214 optimal weight: 0.0060 chunk 201 optimal weight: 50.0000 chunk 58 optimal weight: 20.0000 chunk 61 optimal weight: 0.3980 chunk 52 optimal weight: 50.0000 chunk 208 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 213 optimal weight: 10.0000 overall best weight: 4.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 861 ASN ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 861 ASN ** D 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.071261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.052984 restraints weight = 80027.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.055100 restraints weight = 49734.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.056650 restraints weight = 35722.394| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.6991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18032 Z= 0.142 Angle : 0.860 13.670 24472 Z= 0.411 Chirality : 0.047 0.345 2792 Planarity : 0.004 0.073 3068 Dihedral : 5.061 40.924 2436 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.47 % Favored : 96.34 % Rotamer: Outliers : 3.79 % Allowed : 30.41 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2188 helix: 0.26 (0.16), residues: 1124 sheet: -1.30 (0.33), residues: 248 loop : -0.84 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 705 HIS 0.020 0.001 HIS A 70 PHE 0.030 0.002 PHE B 551 TYR 0.028 0.001 TYR D 707 ARG 0.014 0.001 ARG C 814 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 856) hydrogen bonds : angle 5.23029 ( 2388) covalent geometry : bond 0.00322 (18028) covalent geometry : angle 0.86046 (24472) Misc. bond : bond 0.00080 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9767.33 seconds wall clock time: 171 minutes 23.28 seconds (10283.28 seconds total)