Starting phenix.real_space_refine on Sun Aug 24 05:17:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5va3_8652/08_2025/5va3_8652.cif Found real_map, /net/cci-nas-00/data/ceres_data/5va3_8652/08_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_8652/08_2025/5va3_8652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5va3_8652/08_2025/5va3_8652.map" model { file = "/net/cci-nas-00/data/ceres_data/5va3_8652/08_2025/5va3_8652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5va3_8652/08_2025/5va3_8652.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.459 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'ASP:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 63 Restraints were copied for chains: B, C, D Time building chain proxies: 3.54, per 1000 atoms: 0.20 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: 1.08 Conformation dependent library (CDL) restraints added in 630.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.65 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: 2.09 Time building geometry restraints manager: 1.50 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.170 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.78 (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 ARG 0.003 0.000 ARG C 541 TYR 0.017 0.002 TYR B 427 PHE 0.013 0.002 PHE A 494 TRP 0.009 0.001 TRP C 412 HIS 0.003 0.001 HIS A 402 Details of bonding type rmsd covalent geometry : bond 0.00825 (18028) covalent geometry : angle 1.06574 (24472) hydrogen bonds : bond 0.29578 ( 856) hydrogen bonds : angle 9.64811 ( 2388) 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 : 0.527 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: 0.1331 time to fit residues: 151.9549 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 : 0.666 ------------------------------------------------------------------------------- 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 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 10.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.078881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.057585 restraints weight = 78252.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.059811 restraints weight = 50681.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061468 restraints weight = 37114.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.062720 restraints weight = 29365.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.063693 restraints weight = 24449.254| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18032 Z= 0.163 Angle : 0.796 12.093 24472 Z= 0.395 Chirality : 0.047 0.163 2792 Planarity : 0.005 0.042 3068 Dihedral : 6.063 58.835 2448 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.38 % Favored : 96.44 % Rotamer: Outliers : 3.14 % Allowed : 13.58 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.17), residues: 2188 helix: -0.54 (0.15), residues: 1108 sheet: -2.76 (0.29), residues: 180 loop : -1.74 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 679 TYR 0.014 0.002 TYR D 700 PHE 0.020 0.002 PHE C 686 TRP 0.017 0.002 TRP B 563 HIS 0.008 0.002 HIS B 739 Details of bonding type rmsd covalent geometry : bond 0.00341 (18028) covalent geometry : angle 0.79576 (24472) hydrogen bonds : bond 0.05344 ( 856) hydrogen bonds : angle 5.53853 ( 2388) Misc. bond : bond 0.00261 ( 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 616 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 558 time to evaluate : 0.489 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: 0.4843 (OUTLIER) cc_final: 0.4511 (mtp85) REVERT: A 424 PHE cc_start: 0.9283 (m-80) cc_final: 0.8863 (m-80) REVERT: A 459 VAL cc_start: 0.9902 (t) cc_final: 0.9472 (t) REVERT: A 462 MET cc_start: 0.9786 (mmm) cc_final: 0.9578 (tpt) REVERT: A 463 PHE cc_start: 0.9615 (m-80) cc_final: 0.9207 (m-80) REVERT: A 544 GLU cc_start: 0.8252 (pm20) cc_final: 0.7846 (pm20) REVERT: A 574 MET cc_start: 0.7809 (mtt) cc_final: 0.7542 (mmt) REVERT: A 586 LEU cc_start: 0.9588 (mt) cc_final: 0.9352 (pt) REVERT: A 638 LYS cc_start: 0.9854 (mttt) cc_final: 0.9492 (mmtm) REVERT: A 640 PHE cc_start: 0.9431 (t80) cc_final: 0.8936 (t80) REVERT: A 641 SER cc_start: 0.9825 (t) cc_final: 0.9499 (p) REVERT: A 645 MET cc_start: 0.9558 (mtp) cc_final: 0.9099 (ttm) REVERT: A 651 MET cc_start: 0.9592 (tpp) cc_final: 0.9381 (tpp) REVERT: A 656 PHE cc_start: 0.9638 (m-80) cc_final: 0.9346 (m-10) REVERT: A 681 ARG cc_start: 0.9547 (mtt180) cc_final: 0.9325 (tpp-160) REVERT: A 691 ASN cc_start: 0.9791 (m-40) cc_final: 0.9501 (t0) REVERT: A 698 GLU cc_start: 0.9670 (mt-10) cc_final: 0.9325 (pt0) REVERT: A 705 TRP cc_start: 0.9281 (t60) cc_final: 0.9016 (t60) REVERT: A 748 LYS cc_start: 0.9897 (mttt) cc_final: 0.9638 (tptp) REVERT: A 757 LYS cc_start: 0.9620 (mttt) cc_final: 0.9282 (mtmt) REVERT: A 758 PHE cc_start: 0.9446 (m-80) cc_final: 0.9025 (m-80) REVERT: A 781 PHE cc_start: 0.9809 (m-80) cc_final: 0.9297 (m-80) REVERT: A 801 LYS cc_start: 0.9134 (mttt) cc_final: 0.8857 (mptt) REVERT: A 827 TYR cc_start: 0.8627 (m-80) cc_final: 0.8401 (m-80) REVERT: B 60 MET cc_start: 0.8495 (ppp) cc_final: 0.7946 (ppp) REVERT: B 92 ARG cc_start: 0.5162 (OUTLIER) cc_final: 0.4910 (mtp85) REVERT: B 424 PHE cc_start: 0.9260 (m-80) cc_final: 0.8842 (m-80) REVERT: B 459 VAL cc_start: 0.9919 (t) cc_final: 0.9529 (t) REVERT: B 463 PHE cc_start: 0.9584 (m-80) cc_final: 0.8697 (m-80) REVERT: B 533 VAL cc_start: 0.9215 (m) cc_final: 0.8968 (p) REVERT: B 544 GLU cc_start: 0.8185 (pm20) cc_final: 0.7751 (pm20) REVERT: B 629 ASN cc_start: 0.7670 (m110) cc_final: 0.7459 (m110) REVERT: B 638 LYS cc_start: 0.9856 (mttt) cc_final: 0.9356 (mmtm) REVERT: B 640 PHE cc_start: 0.9435 (t80) cc_final: 0.8916 (t80) REVERT: B 642 ILE cc_start: 0.9512 (mm) cc_final: 0.9210 (mm) REVERT: B 681 ARG cc_start: 0.9546 (mtt180) cc_final: 0.9322 (tpp-160) REVERT: B 691 ASN cc_start: 0.9787 (m-40) cc_final: 0.9476 (t0) REVERT: B 696 ARG cc_start: 0.9787 (mtt180) cc_final: 0.9557 (mtp85) REVERT: B 698 GLU cc_start: 0.9638 (mt-10) cc_final: 0.9360 (pt0) REVERT: B 705 TRP cc_start: 0.9230 (t60) cc_final: 0.8969 (t60) REVERT: B 758 PHE cc_start: 0.9395 (m-80) cc_final: 0.9033 (m-80) REVERT: B 781 PHE cc_start: 0.9814 (m-80) cc_final: 0.9334 (m-80) REVERT: C 66 CYS cc_start: 0.8519 (m) cc_final: 0.8311 (m) REVERT: C 424 PHE cc_start: 0.9213 (m-80) cc_final: 0.8790 (m-80) REVERT: C 459 VAL cc_start: 0.9909 (t) cc_final: 0.9585 (p) REVERT: C 463 PHE cc_start: 0.9389 (m-80) cc_final: 0.9047 (m-80) REVERT: C 544 GLU cc_start: 0.8321 (pm20) cc_final: 0.7919 (pm20) REVERT: C 586 LEU cc_start: 0.9581 (mt) cc_final: 0.9376 (pt) REVERT: C 638 LYS cc_start: 0.9800 (mmtt) cc_final: 0.9371 (mmtm) REVERT: C 640 PHE cc_start: 0.9374 (t80) cc_final: 0.8848 (t80) REVERT: C 642 ILE cc_start: 0.9586 (mm) cc_final: 0.9368 (mm) REVERT: C 682 GLU cc_start: 0.9542 (mt-10) cc_final: 0.9325 (pt0) REVERT: C 691 ASN cc_start: 0.9786 (m-40) cc_final: 0.9492 (t0) REVERT: C 698 GLU cc_start: 0.9641 (mt-10) cc_final: 0.9309 (pt0) REVERT: C 705 TRP cc_start: 0.9254 (t60) cc_final: 0.8989 (t60) REVERT: C 757 LYS cc_start: 0.9616 (mttt) cc_final: 0.9271 (mtmt) REVERT: C 781 PHE cc_start: 0.9751 (m-80) cc_final: 0.9429 (m-80) REVERT: C 827 TYR cc_start: 0.8388 (m-80) cc_final: 0.8029 (m-80) REVERT: C 830 LEU cc_start: 0.9884 (pt) cc_final: 0.9406 (tt) REVERT: C 840 GLU cc_start: 0.9651 (mt-10) cc_final: 0.9439 (mt-10) REVERT: D 92 ARG cc_start: 0.4880 (OUTLIER) cc_final: 0.4600 (mtp85) REVERT: D 424 PHE cc_start: 0.9230 (m-80) cc_final: 0.8813 (m-80) REVERT: D 459 VAL cc_start: 0.9895 (t) cc_final: 0.9449 (t) REVERT: D 462 MET cc_start: 0.9781 (mmm) cc_final: 0.9319 (tpt) REVERT: D 463 PHE cc_start: 0.9406 (m-80) cc_final: 0.9090 (m-80) REVERT: D 533 VAL cc_start: 0.9388 (m) cc_final: 0.9181 (p) REVERT: D 574 MET cc_start: 0.7797 (mtt) cc_final: 0.7541 (mmt) REVERT: D 617 PHE cc_start: 0.9761 (t80) cc_final: 0.9401 (t80) REVERT: D 638 LYS cc_start: 0.9865 (mttt) cc_final: 0.9432 (mmtm) REVERT: D 640 PHE cc_start: 0.9458 (t80) cc_final: 0.8891 (t80) REVERT: D 641 SER cc_start: 0.9887 (t) cc_final: 0.9642 (p) REVERT: D 656 PHE cc_start: 0.9618 (m-80) cc_final: 0.9357 (m-10) REVERT: D 681 ARG cc_start: 0.9523 (mtt180) cc_final: 0.9297 (tpp-160) REVERT: D 691 ASN cc_start: 0.9793 (m-40) cc_final: 0.9536 (t0) REVERT: D 696 ARG cc_start: 0.9839 (mtt180) cc_final: 0.9628 (mtp85) REVERT: D 698 GLU cc_start: 0.9652 (mt-10) cc_final: 0.9409 (pt0) REVERT: D 699 GLU cc_start: 0.9599 (pt0) cc_final: 0.9321 (pp20) REVERT: D 705 TRP cc_start: 0.9294 (t60) cc_final: 0.9045 (t60) REVERT: D 744 ARG cc_start: 0.9458 (ptp-110) cc_final: 0.9208 (mmp80) REVERT: D 757 LYS cc_start: 0.9627 (mttt) cc_final: 0.8899 (mtmt) REVERT: D 758 PHE cc_start: 0.9421 (m-80) cc_final: 0.9202 (m-80) REVERT: D 781 PHE cc_start: 0.9512 (m-80) cc_final: 0.9228 (m-80) REVERT: D 827 TYR cc_start: 0.8467 (m-80) cc_final: 0.8032 (m-80) outliers start: 58 outliers final: 36 residues processed: 588 average time/residue: 0.1325 time to fit residues: 113.5250 Evaluate side-chains 516 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 477 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 630 VAL Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 760 THR 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 760 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 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 185 optimal weight: 30.0000 chunk 0 optimal weight: 70.0000 chunk 40 optimal weight: 40.0000 chunk 27 optimal weight: 30.0000 chunk 155 optimal weight: 20.0000 chunk 23 optimal weight: 0.0370 chunk 206 optimal weight: 6.9990 chunk 164 optimal weight: 20.0000 chunk 165 optimal weight: 50.0000 chunk 146 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 overall best weight: 13.4072 ------------------------------------------------------------------------------- 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 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 = 0.3368 r_free = 0.3368 target = 0.072710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.053752 restraints weight = 80185.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.055788 restraints weight = 50540.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.057266 restraints weight = 36538.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.058374 restraints weight = 28728.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.059187 restraints weight = 23870.341| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18032 Z= 0.213 Angle : 0.769 12.084 24472 Z= 0.386 Chirality : 0.047 0.258 2792 Planarity : 0.005 0.046 3068 Dihedral : 6.035 56.553 2440 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.93 % Favored : 95.89 % Rotamer: Outliers : 3.41 % Allowed : 17.37 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.18), residues: 2188 helix: 0.00 (0.15), residues: 1092 sheet: -2.41 (0.29), residues: 204 loop : -1.27 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 784 TYR 0.016 0.002 TYR C 427 PHE 0.030 0.003 PHE C 860 TRP 0.010 0.001 TRP D 705 HIS 0.005 0.001 HIS C 762 Details of bonding type rmsd covalent geometry : bond 0.00440 (18028) covalent geometry : angle 0.76895 (24472) hydrogen bonds : bond 0.04836 ( 856) hydrogen bonds : angle 5.53330 ( 2388) Misc. bond : bond 0.00135 ( 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 549 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 486 time to evaluate : 0.548 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: A 424 PHE cc_start: 0.9257 (m-80) cc_final: 0.8796 (m-80) REVERT: A 463 PHE cc_start: 0.9473 (m-80) cc_final: 0.9040 (m-80) REVERT: A 551 PHE cc_start: 0.9557 (t80) cc_final: 0.9352 (t80) REVERT: A 638 LYS cc_start: 0.9873 (mttt) cc_final: 0.9654 (mttp) REVERT: A 640 PHE cc_start: 0.9530 (t80) cc_final: 0.9002 (t80) REVERT: A 641 SER cc_start: 0.9846 (t) cc_final: 0.9596 (p) REVERT: A 645 MET cc_start: 0.9517 (mtp) cc_final: 0.9154 (ttm) REVERT: A 651 MET cc_start: 0.9639 (tpp) cc_final: 0.9411 (tpp) REVERT: A 656 PHE cc_start: 0.9592 (m-80) cc_final: 0.9290 (m-10) REVERT: A 677 MET cc_start: 0.9674 (tpp) cc_final: 0.9438 (tpp) REVERT: A 691 ASN cc_start: 0.9808 (m-40) cc_final: 0.9525 (t0) REVERT: A 748 LYS cc_start: 0.9875 (mttt) cc_final: 0.9559 (tptp) REVERT: A 757 LYS cc_start: 0.9600 (mttt) cc_final: 0.9265 (mtmt) REVERT: A 758 PHE cc_start: 0.9447 (m-80) cc_final: 0.9189 (m-80) REVERT: A 781 PHE cc_start: 0.9727 (m-80) cc_final: 0.9197 (m-80) REVERT: A 836 ASP cc_start: 0.9371 (m-30) cc_final: 0.9110 (p0) REVERT: A 840 GLU cc_start: 0.9605 (mt-10) cc_final: 0.9342 (mm-30) REVERT: B 61 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8425 (mp10) REVERT: B 92 ARG cc_start: 0.5379 (OUTLIER) cc_final: 0.4905 (mtp85) REVERT: B 424 PHE cc_start: 0.9240 (m-80) cc_final: 0.8781 (m-80) REVERT: B 463 PHE cc_start: 0.9200 (m-80) cc_final: 0.8714 (m-80) REVERT: B 551 PHE cc_start: 0.9556 (t80) cc_final: 0.9327 (t80) REVERT: B 640 PHE cc_start: 0.9499 (t80) cc_final: 0.8927 (t80) REVERT: B 645 MET cc_start: 0.9569 (mtp) cc_final: 0.9262 (ttm) REVERT: B 677 MET cc_start: 0.9653 (tpp) cc_final: 0.9332 (tmm) REVERT: B 691 ASN cc_start: 0.9806 (m-40) cc_final: 0.9454 (t0) REVERT: B 695 GLN cc_start: 0.9774 (mt0) cc_final: 0.9556 (pt0) REVERT: B 698 GLU cc_start: 0.9636 (mt-10) cc_final: 0.9386 (pt0) REVERT: B 781 PHE cc_start: 0.9758 (m-80) cc_final: 0.9273 (m-80) REVERT: C 46 ASP cc_start: 0.9688 (p0) cc_final: 0.9474 (p0) REVERT: C 60 MET cc_start: 0.8693 (ppp) cc_final: 0.8367 (ppp) REVERT: C 67 ASP cc_start: 0.9363 (t70) cc_final: 0.9139 (p0) REVERT: C 424 PHE cc_start: 0.9189 (m-80) cc_final: 0.8714 (m-80) REVERT: C 551 PHE cc_start: 0.9571 (t80) cc_final: 0.9330 (t80) REVERT: C 638 LYS cc_start: 0.9724 (mmtt) cc_final: 0.9514 (mmmm) REVERT: C 681 ARG cc_start: 0.9576 (mmm160) cc_final: 0.9103 (tpp-160) REVERT: C 682 GLU cc_start: 0.9543 (mt-10) cc_final: 0.9283 (pt0) REVERT: C 691 ASN cc_start: 0.9799 (m-40) cc_final: 0.9557 (t0) REVERT: C 698 GLU cc_start: 0.9618 (mt-10) cc_final: 0.9407 (mt-10) REVERT: C 757 LYS cc_start: 0.9609 (mttt) cc_final: 0.9102 (mtmt) REVERT: C 758 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.9027 (m-80) REVERT: C 833 ILE cc_start: 0.9616 (OUTLIER) cc_final: 0.9413 (mm) REVERT: D 424 PHE cc_start: 0.9218 (m-80) cc_final: 0.8753 (m-80) REVERT: D 463 PHE cc_start: 0.9483 (m-80) cc_final: 0.9277 (m-80) REVERT: D 551 PHE cc_start: 0.9571 (t80) cc_final: 0.9325 (t80) REVERT: D 638 LYS cc_start: 0.9866 (mttt) cc_final: 0.9483 (mmtm) REVERT: D 640 PHE cc_start: 0.9537 (t80) cc_final: 0.8972 (t80) REVERT: D 651 MET cc_start: 0.9539 (mmm) cc_final: 0.9322 (mmm) REVERT: D 656 PHE cc_start: 0.9493 (m-80) cc_final: 0.9246 (m-10) REVERT: D 691 ASN cc_start: 0.9809 (m-40) cc_final: 0.9395 (t0) REVERT: D 695 GLN cc_start: 0.9796 (mt0) cc_final: 0.9467 (mm-40) REVERT: D 698 GLU cc_start: 0.9617 (mt-10) cc_final: 0.9325 (pt0) REVERT: D 744 ARG cc_start: 0.9454 (ptp-110) cc_final: 0.9065 (mmp80) REVERT: D 757 LYS cc_start: 0.9563 (mttt) cc_final: 0.9258 (mtmt) REVERT: D 758 PHE cc_start: 0.9355 (m-80) cc_final: 0.8810 (m-80) REVERT: D 830 LEU cc_start: 0.9855 (pt) cc_final: 0.9365 (tt) REVERT: D 856 LEU cc_start: 0.9543 (tt) cc_final: 0.9328 (pp) outliers start: 63 outliers final: 42 residues processed: 522 average time/residue: 0.1202 time to fit residues: 93.9524 Evaluate side-chains 486 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 440 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 113 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 467 ILE 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 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 467 ILE 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 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 413 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 C residue 833 ILE 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 413 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 67 optimal weight: 40.0000 chunk 121 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 160 optimal weight: 30.0000 chunk 195 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 185 optimal weight: 30.0000 chunk 16 optimal weight: 9.9990 chunk 102 optimal weight: 50.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- 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** C 61 GLN ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 834 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.073414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.054515 restraints weight = 79391.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.056558 restraints weight = 49963.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.058012 restraints weight = 36228.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059133 restraints weight = 28631.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.059936 restraints weight = 23918.659| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5639 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= 0.163 Angle : 0.732 12.173 24472 Z= 0.361 Chirality : 0.046 0.180 2792 Planarity : 0.004 0.039 3068 Dihedral : 5.689 55.743 2436 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.43 % Favored : 95.38 % Rotamer: Outliers : 3.30 % Allowed : 21.32 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.18), residues: 2188 helix: 0.11 (0.15), residues: 1104 sheet: -2.15 (0.30), residues: 204 loop : -0.95 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 681 TYR 0.014 0.001 TYR B 707 PHE 0.029 0.002 PHE C 557 TRP 0.006 0.001 TRP B 705 HIS 0.004 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00353 (18028) covalent geometry : angle 0.73223 (24472) hydrogen bonds : bond 0.04432 ( 856) hydrogen bonds : angle 5.33963 ( 2388) Misc. bond : bond 0.00102 ( 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 534 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 473 time to evaluate : 0.459 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: A 92 ARG cc_start: 0.5136 (OUTLIER) cc_final: 0.4683 (mtp85) REVERT: A 424 PHE cc_start: 0.9275 (m-80) cc_final: 0.8796 (m-80) REVERT: A 459 VAL cc_start: 0.9884 (t) cc_final: 0.9487 (p) REVERT: A 463 PHE cc_start: 0.9565 (m-80) cc_final: 0.8992 (m-80) REVERT: A 638 LYS cc_start: 0.9867 (mttt) cc_final: 0.9527 (mmtm) REVERT: A 641 SER cc_start: 0.9815 (t) cc_final: 0.9575 (p) REVERT: A 645 MET cc_start: 0.9447 (mtp) cc_final: 0.9143 (ttm) REVERT: A 651 MET cc_start: 0.9635 (tpp) cc_final: 0.9381 (tpp) REVERT: A 656 PHE cc_start: 0.9552 (m-80) cc_final: 0.9256 (m-10) REVERT: A 691 ASN cc_start: 0.9817 (m-40) cc_final: 0.9590 (t0) REVERT: A 705 TRP cc_start: 0.9274 (t60) cc_final: 0.8986 (t60) REVERT: A 757 LYS cc_start: 0.9588 (mttt) cc_final: 0.9296 (mtmt) REVERT: A 758 PHE cc_start: 0.9464 (m-80) cc_final: 0.8717 (m-80) REVERT: A 836 ASP cc_start: 0.9365 (m-30) cc_final: 0.9014 (p0) REVERT: A 840 GLU cc_start: 0.9587 (mt-10) cc_final: 0.9309 (mm-30) REVERT: B 66 CYS cc_start: 0.8447 (m) cc_final: 0.8213 (m) REVERT: B 92 ARG cc_start: 0.5244 (OUTLIER) cc_final: 0.4677 (mtp85) REVERT: B 424 PHE cc_start: 0.9233 (m-80) cc_final: 0.8763 (m-80) REVERT: B 462 MET cc_start: 0.9737 (tpt) cc_final: 0.9409 (tpt) REVERT: B 619 PHE cc_start: 0.9739 (OUTLIER) cc_final: 0.9012 (t80) REVERT: B 640 PHE cc_start: 0.9530 (t80) cc_final: 0.8943 (t80) REVERT: B 645 MET cc_start: 0.9567 (mtp) cc_final: 0.9308 (ttm) REVERT: B 677 MET cc_start: 0.9702 (tpp) cc_final: 0.9384 (tmm) REVERT: B 691 ASN cc_start: 0.9792 (m-40) cc_final: 0.9566 (t0) REVERT: B 705 TRP cc_start: 0.9252 (t60) cc_final: 0.8981 (t60) REVERT: B 781 PHE cc_start: 0.9713 (m-80) cc_final: 0.9176 (m-80) REVERT: B 782 ILE cc_start: 0.9764 (mp) cc_final: 0.9422 (tp) REVERT: C 67 ASP cc_start: 0.9374 (t70) cc_final: 0.9156 (p0) REVERT: C 424 PHE cc_start: 0.9201 (m-80) cc_final: 0.8726 (m-80) REVERT: C 640 PHE cc_start: 0.9483 (t80) cc_final: 0.8857 (t80) REVERT: C 645 MET cc_start: 0.9614 (mtp) cc_final: 0.9283 (ttm) REVERT: C 681 ARG cc_start: 0.9535 (mmm160) cc_final: 0.9082 (tpp-160) REVERT: C 682 GLU cc_start: 0.9540 (mt-10) cc_final: 0.9284 (pt0) REVERT: C 691 ASN cc_start: 0.9788 (m-40) cc_final: 0.9565 (t0) REVERT: C 705 TRP cc_start: 0.9302 (t60) cc_final: 0.9035 (t60) REVERT: C 757 LYS cc_start: 0.9555 (mttt) cc_final: 0.8864 (mtmt) REVERT: C 758 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8826 (m-80) REVERT: C 830 LEU cc_start: 0.9857 (pt) cc_final: 0.9355 (tt) REVERT: C 832 LYS cc_start: 0.9513 (tttt) cc_final: 0.9218 (tttm) REVERT: C 833 ILE cc_start: 0.9640 (OUTLIER) cc_final: 0.9338 (mm) REVERT: D 424 PHE cc_start: 0.9232 (m-80) cc_final: 0.8764 (m-80) REVERT: D 638 LYS cc_start: 0.9839 (mttt) cc_final: 0.9555 (mmtm) REVERT: D 640 PHE cc_start: 0.9526 (t80) cc_final: 0.9321 (t80) REVERT: D 651 MET cc_start: 0.9617 (mmm) cc_final: 0.9359 (mmm) REVERT: D 681 ARG cc_start: 0.9577 (mmm160) cc_final: 0.9103 (tpp-160) REVERT: D 691 ASN cc_start: 0.9793 (m-40) cc_final: 0.9576 (t0) REVERT: D 705 TRP cc_start: 0.9301 (t60) cc_final: 0.9024 (t60) REVERT: D 712 ASP cc_start: 0.9609 (t0) cc_final: 0.9323 (t0) REVERT: D 757 LYS cc_start: 0.9593 (mttt) cc_final: 0.9322 (mtmt) REVERT: D 758 PHE cc_start: 0.9285 (m-80) cc_final: 0.8547 (m-80) REVERT: D 782 ILE cc_start: 0.9710 (mp) cc_final: 0.9504 (tp) REVERT: D 801 LYS cc_start: 0.9333 (mttp) cc_final: 0.9067 (mmtm) REVERT: D 804 ILE cc_start: 0.9793 (mt) cc_final: 0.9544 (mm) outliers start: 61 outliers final: 49 residues processed: 503 average time/residue: 0.1230 time to fit residues: 92.4420 Evaluate side-chains 490 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 436 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 113 VAL 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 716 VAL Chi-restraints excluded: chain A residue 741 LYS 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 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 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 768 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 483 VAL 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 758 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 833 ILE 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 413 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 642 ILE Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 844 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 134 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 149 optimal weight: 30.0000 chunk 108 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 117 optimal weight: 40.0000 chunk 170 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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** ** 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 = 0.3391 r_free = 0.3391 target = 0.075387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.056528 restraints weight = 77149.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.058716 restraints weight = 47622.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.060333 restraints weight = 34091.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.061500 restraints weight = 26532.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.062346 restraints weight = 21935.353| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18032 Z= 0.127 Angle : 0.735 12.676 24472 Z= 0.353 Chirality : 0.046 0.184 2792 Planarity : 0.004 0.036 3068 Dihedral : 5.360 54.662 2436 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.66 % Favored : 96.16 % Rotamer: Outliers : 2.81 % Allowed : 23.43 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.18), residues: 2188 helix: -0.04 (0.15), residues: 1148 sheet: -1.87 (0.33), residues: 204 loop : -0.84 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 823 TYR 0.017 0.001 TYR C 707 PHE 0.028 0.002 PHE B 557 TRP 0.004 0.001 TRP A 705 HIS 0.004 0.001 HIS C 762 Details of bonding type rmsd covalent geometry : bond 0.00281 (18028) covalent geometry : angle 0.73467 (24472) hydrogen bonds : bond 0.04154 ( 856) hydrogen bonds : angle 5.03529 ( 2388) Misc. bond : bond 0.00116 ( 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 523 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 471 time to evaluate : 0.523 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: A 92 ARG cc_start: 0.4899 (OUTLIER) cc_final: 0.4459 (mtp85) REVERT: A 127 LEU cc_start: 0.9353 (tp) cc_final: 0.9051 (tp) REVERT: A 424 PHE cc_start: 0.9295 (m-80) cc_final: 0.8822 (m-80) REVERT: A 459 VAL cc_start: 0.9884 (t) cc_final: 0.9421 (p) REVERT: A 462 MET cc_start: 0.9731 (tpt) cc_final: 0.9479 (tpt) REVERT: A 463 PHE cc_start: 0.9602 (m-80) cc_final: 0.9060 (m-80) REVERT: A 638 LYS cc_start: 0.9872 (mttt) cc_final: 0.9531 (mmtm) REVERT: A 640 PHE cc_start: 0.9474 (t80) cc_final: 0.8887 (t80) REVERT: A 641 SER cc_start: 0.9810 (t) cc_final: 0.9495 (p) REVERT: A 656 PHE cc_start: 0.9519 (m-80) cc_final: 0.9192 (m-10) REVERT: A 681 ARG cc_start: 0.9555 (mmm160) cc_final: 0.9076 (tpp-160) REVERT: A 691 ASN cc_start: 0.9826 (m-40) cc_final: 0.9473 (t0) REVERT: A 695 GLN cc_start: 0.9755 (pt0) cc_final: 0.9501 (mm-40) REVERT: A 705 TRP cc_start: 0.9265 (t60) cc_final: 0.8998 (t60) REVERT: A 757 LYS cc_start: 0.9582 (mttt) cc_final: 0.9316 (mtmt) REVERT: A 782 ILE cc_start: 0.9762 (mp) cc_final: 0.9422 (tp) REVERT: A 840 GLU cc_start: 0.9595 (mt-10) cc_final: 0.9373 (mm-30) REVERT: B 66 CYS cc_start: 0.8395 (m) cc_final: 0.8141 (m) REVERT: B 92 ARG cc_start: 0.5118 (OUTLIER) cc_final: 0.4582 (mtp85) REVERT: B 420 TYR cc_start: 0.9584 (t80) cc_final: 0.9151 (t80) REVERT: B 424 PHE cc_start: 0.9244 (m-80) cc_final: 0.8863 (m-80) REVERT: B 462 MET cc_start: 0.9733 (tpt) cc_final: 0.9413 (tpt) REVERT: B 640 PHE cc_start: 0.9505 (t80) cc_final: 0.8876 (t80) REVERT: B 645 MET cc_start: 0.9532 (mtp) cc_final: 0.9252 (ttm) REVERT: B 681 ARG cc_start: 0.9636 (mmm160) cc_final: 0.9168 (tpp-160) REVERT: B 691 ASN cc_start: 0.9796 (m-40) cc_final: 0.9561 (t0) REVERT: B 705 TRP cc_start: 0.9234 (t60) cc_final: 0.8982 (t60) REVERT: B 758 PHE cc_start: 0.9452 (OUTLIER) cc_final: 0.8611 (m-80) REVERT: B 781 PHE cc_start: 0.9711 (m-80) cc_final: 0.9375 (m-80) REVERT: B 782 ILE cc_start: 0.9773 (mp) cc_final: 0.9426 (tp) REVERT: C 112 VAL cc_start: 0.8535 (t) cc_final: 0.8289 (p) REVERT: C 127 LEU cc_start: 0.9357 (tp) cc_final: 0.8901 (tp) REVERT: C 424 PHE cc_start: 0.9216 (m-80) cc_final: 0.8730 (m-80) REVERT: C 588 ASN cc_start: 0.9176 (m110) cc_final: 0.8961 (m110) REVERT: C 619 PHE cc_start: 0.9719 (OUTLIER) cc_final: 0.9059 (t80) REVERT: C 640 PHE cc_start: 0.9495 (t80) cc_final: 0.8770 (t80) REVERT: C 645 MET cc_start: 0.9595 (mtp) cc_final: 0.9341 (ttm) REVERT: C 656 PHE cc_start: 0.9268 (m-10) cc_final: 0.8892 (m-10) REVERT: C 681 ARG cc_start: 0.9511 (mmm160) cc_final: 0.9019 (tpp-160) REVERT: C 682 GLU cc_start: 0.9530 (mt-10) cc_final: 0.9223 (mt-10) REVERT: C 691 ASN cc_start: 0.9793 (m-40) cc_final: 0.9562 (t0) REVERT: C 705 TRP cc_start: 0.9286 (t60) cc_final: 0.9060 (t60) REVERT: C 757 LYS cc_start: 0.9530 (mttt) cc_final: 0.9290 (mtpt) REVERT: C 758 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8340 (m-80) REVERT: C 821 ASP cc_start: 0.9314 (p0) cc_final: 0.9033 (m-30) REVERT: C 830 LEU cc_start: 0.9854 (pt) cc_final: 0.9375 (tt) REVERT: D 127 LEU cc_start: 0.9318 (tp) cc_final: 0.9060 (tp) REVERT: D 424 PHE cc_start: 0.9238 (m-80) cc_final: 0.8764 (m-80) REVERT: D 638 LYS cc_start: 0.9853 (mttt) cc_final: 0.9587 (mmtm) REVERT: D 640 PHE cc_start: 0.9499 (t80) cc_final: 0.8792 (t80) REVERT: D 645 MET cc_start: 0.9842 (mtp) cc_final: 0.8855 (ttm) REVERT: D 651 MET cc_start: 0.9689 (mmm) cc_final: 0.9423 (mmm) REVERT: D 681 ARG cc_start: 0.9547 (mmm160) cc_final: 0.9041 (tpp-160) REVERT: D 691 ASN cc_start: 0.9783 (m-40) cc_final: 0.9576 (t0) REVERT: D 705 TRP cc_start: 0.9308 (t60) cc_final: 0.9056 (t60) REVERT: D 757 LYS cc_start: 0.9578 (mttt) cc_final: 0.9254 (mtmt) REVERT: D 758 PHE cc_start: 0.9306 (m-80) cc_final: 0.8571 (m-80) REVERT: D 821 ASP cc_start: 0.9373 (p0) cc_final: 0.9073 (t0) outliers start: 52 outliers final: 37 residues processed: 494 average time/residue: 0.1177 time to fit residues: 87.0573 Evaluate side-chains 480 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 438 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 615 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 720 PHE 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 822 VAL 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 716 VAL Chi-restraints excluded: chain B residue 758 PHE 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 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 777 THR Chi-restraints excluded: chain C residue 782 ILE 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 D residue 92 ARG 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 777 THR 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 33 optimal weight: 0.8980 chunk 13 optimal weight: 40.0000 chunk 214 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 171 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 210 optimal weight: 40.0000 chunk 19 optimal weight: 40.0000 chunk 124 optimal weight: 5.9990 chunk 152 optimal weight: 40.0000 chunk 141 optimal weight: 7.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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 588 ASN ** 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 658 ASN ** 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 = 0.3372 r_free = 0.3372 target = 0.074403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.055603 restraints weight = 78313.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.057741 restraints weight = 48780.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.059320 restraints weight = 35068.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.060457 restraints weight = 27387.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061282 restraints weight = 22716.369| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.6133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18032 Z= 0.136 Angle : 0.737 15.290 24472 Z= 0.354 Chirality : 0.046 0.236 2792 Planarity : 0.004 0.035 3068 Dihedral : 5.244 50.851 2436 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.07 % Favored : 95.75 % Rotamer: Outliers : 2.98 % Allowed : 24.62 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.18), residues: 2188 helix: -0.03 (0.15), residues: 1152 sheet: -1.76 (0.30), residues: 248 loop : -0.85 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 681 TYR 0.030 0.001 TYR D 652 PHE 0.020 0.002 PHE D 656 TRP 0.006 0.001 TRP B 705 HIS 0.004 0.001 HIS D 771 Details of bonding type rmsd covalent geometry : bond 0.00298 (18028) covalent geometry : angle 0.73741 (24472) hydrogen bonds : bond 0.04004 ( 856) hydrogen bonds : angle 5.04787 ( 2388) Misc. bond : bond 0.00110 ( 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 515 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 460 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.5040 (OUTLIER) cc_final: 0.4538 (mtp85) REVERT: A 127 LEU cc_start: 0.9405 (tp) cc_final: 0.9134 (tp) REVERT: A 424 PHE cc_start: 0.9327 (m-80) cc_final: 0.8860 (m-80) REVERT: A 459 VAL cc_start: 0.9889 (t) cc_final: 0.9434 (p) REVERT: A 462 MET cc_start: 0.9746 (tpt) cc_final: 0.9483 (tpt) REVERT: A 463 PHE cc_start: 0.9601 (m-80) cc_final: 0.9061 (m-80) REVERT: A 554 MET cc_start: 0.9221 (ptt) cc_final: 0.9020 (ptt) REVERT: A 638 LYS cc_start: 0.9862 (mttt) cc_final: 0.9535 (mmtm) REVERT: A 640 PHE cc_start: 0.9463 (t80) cc_final: 0.8867 (t80) REVERT: A 641 SER cc_start: 0.9796 (t) cc_final: 0.9546 (p) REVERT: A 645 MET cc_start: 0.9209 (ttm) cc_final: 0.8995 (ttt) REVERT: A 651 MET cc_start: 0.9432 (mmm) cc_final: 0.9193 (mmm) REVERT: A 656 PHE cc_start: 0.9453 (m-80) cc_final: 0.8998 (m-80) REVERT: A 681 ARG cc_start: 0.9554 (mmm160) cc_final: 0.9050 (tpp-160) REVERT: A 691 ASN cc_start: 0.9826 (m-40) cc_final: 0.9477 (t0) REVERT: A 695 GLN cc_start: 0.9756 (pt0) cc_final: 0.9539 (mm-40) REVERT: A 698 GLU cc_start: 0.9467 (pt0) cc_final: 0.9172 (pt0) REVERT: A 705 TRP cc_start: 0.9260 (t60) cc_final: 0.8982 (t60) REVERT: A 757 LYS cc_start: 0.9555 (mttt) cc_final: 0.9352 (mtmt) REVERT: A 782 ILE cc_start: 0.9750 (mp) cc_final: 0.9392 (tp) REVERT: A 840 GLU cc_start: 0.9593 (mt-10) cc_final: 0.9379 (mm-30) REVERT: B 66 CYS cc_start: 0.8421 (m) cc_final: 0.8205 (m) REVERT: B 92 ARG cc_start: 0.5279 (OUTLIER) cc_final: 0.4701 (mtp85) REVERT: B 127 LEU cc_start: 0.9300 (tp) cc_final: 0.8926 (tp) REVERT: B 424 PHE cc_start: 0.9287 (m-80) cc_final: 0.8808 (m-80) REVERT: B 462 MET cc_start: 0.9736 (tpt) cc_final: 0.9421 (tpt) REVERT: B 638 LYS cc_start: 0.9810 (mmtm) cc_final: 0.9543 (mmmm) REVERT: B 640 PHE cc_start: 0.9521 (t80) cc_final: 0.8904 (t80) REVERT: B 645 MET cc_start: 0.9538 (mtp) cc_final: 0.9226 (ttm) REVERT: B 656 PHE cc_start: 0.9287 (m-10) cc_final: 0.8978 (m-10) REVERT: B 681 ARG cc_start: 0.9606 (mmm160) cc_final: 0.9107 (tpp-160) REVERT: B 691 ASN cc_start: 0.9796 (m-40) cc_final: 0.9571 (t0) REVERT: B 705 TRP cc_start: 0.9240 (t60) cc_final: 0.8982 (t60) REVERT: B 758 PHE cc_start: 0.9456 (OUTLIER) cc_final: 0.8879 (m-80) REVERT: B 781 PHE cc_start: 0.9712 (m-80) cc_final: 0.9268 (m-80) REVERT: B 782 ILE cc_start: 0.9765 (mp) cc_final: 0.9397 (tp) REVERT: C 420 TYR cc_start: 0.9570 (t80) cc_final: 0.9115 (t80) REVERT: C 424 PHE cc_start: 0.9234 (m-80) cc_final: 0.8849 (m-80) REVERT: C 462 MET cc_start: 0.9623 (tpt) cc_final: 0.9238 (tpt) REVERT: C 588 ASN cc_start: 0.9217 (m-40) cc_final: 0.8970 (m110) REVERT: C 619 PHE cc_start: 0.9709 (OUTLIER) cc_final: 0.9060 (t80) REVERT: C 640 PHE cc_start: 0.9501 (t80) cc_final: 0.8834 (t80) REVERT: C 645 MET cc_start: 0.9587 (mtp) cc_final: 0.9323 (ttm) REVERT: C 681 ARG cc_start: 0.9503 (mmm160) cc_final: 0.8989 (tpp-160) REVERT: C 682 GLU cc_start: 0.9538 (mt-10) cc_final: 0.9240 (mt-10) REVERT: C 691 ASN cc_start: 0.9793 (m-40) cc_final: 0.9569 (t0) REVERT: C 705 TRP cc_start: 0.9295 (t60) cc_final: 0.9067 (t60) REVERT: C 757 LYS cc_start: 0.9513 (mttt) cc_final: 0.9236 (mtpt) REVERT: C 758 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8539 (m-80) REVERT: C 821 ASP cc_start: 0.9337 (p0) cc_final: 0.9121 (m-30) REVERT: C 830 LEU cc_start: 0.9855 (pt) cc_final: 0.9357 (tt) REVERT: C 844 MET cc_start: 0.9536 (mtm) cc_final: 0.9314 (ptp) REVERT: D 127 LEU cc_start: 0.9357 (tp) cc_final: 0.8742 (tp) REVERT: D 424 PHE cc_start: 0.9259 (m-80) cc_final: 0.8776 (m-80) REVERT: D 638 LYS cc_start: 0.9860 (mttt) cc_final: 0.9609 (mmtm) REVERT: D 640 PHE cc_start: 0.9509 (t80) cc_final: 0.8867 (t80) REVERT: D 645 MET cc_start: 0.9836 (mtp) cc_final: 0.8868 (ttm) REVERT: D 651 MET cc_start: 0.9720 (mmm) cc_final: 0.9460 (mmm) REVERT: D 656 PHE cc_start: 0.9237 (m-10) cc_final: 0.8955 (m-10) REVERT: D 681 ARG cc_start: 0.9533 (mmm160) cc_final: 0.9023 (tpp-160) REVERT: D 691 ASN cc_start: 0.9789 (m-40) cc_final: 0.9580 (t0) REVERT: D 705 TRP cc_start: 0.9300 (t60) cc_final: 0.9042 (t60) REVERT: D 758 PHE cc_start: 0.9358 (m-80) cc_final: 0.8628 (m-80) REVERT: D 821 ASP cc_start: 0.9374 (p0) cc_final: 0.9135 (t0) outliers start: 55 outliers final: 47 residues processed: 490 average time/residue: 0.1157 time to fit residues: 85.4551 Evaluate side-chains 482 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 430 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 413 LEU 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 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 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 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 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 798 ILE Chi-restraints excluded: chain B residue 822 VAL 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 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 777 THR Chi-restraints excluded: chain C residue 782 ILE 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 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 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 777 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 105 optimal weight: 0.0010 chunk 107 optimal weight: 8.9990 chunk 159 optimal weight: 0.4980 chunk 183 optimal weight: 9.9990 chunk 128 optimal weight: 50.0000 chunk 211 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 overall best weight: 4.4992 ------------------------------------------------------------------------------- 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 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.073699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.055194 restraints weight = 80022.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.057410 restraints weight = 48673.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.059026 restraints weight = 34512.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.060200 restraints weight = 26676.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.061101 restraints weight = 21907.417| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18032 Z= 0.126 Angle : 0.749 14.559 24472 Z= 0.359 Chirality : 0.046 0.306 2792 Planarity : 0.004 0.034 3068 Dihedral : 5.138 49.432 2436 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.47 % Favored : 96.34 % Rotamer: Outliers : 3.57 % Allowed : 25.38 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.18), residues: 2188 helix: 0.00 (0.15), residues: 1148 sheet: -1.51 (0.32), residues: 248 loop : -0.80 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 534 TYR 0.021 0.001 TYR D 652 PHE 0.025 0.002 PHE C 781 TRP 0.008 0.001 TRP B 563 HIS 0.004 0.001 HIS D 762 Details of bonding type rmsd covalent geometry : bond 0.00281 (18028) covalent geometry : angle 0.74938 (24472) hydrogen bonds : bond 0.03931 ( 856) hydrogen bonds : angle 5.03269 ( 2388) Misc. bond : bond 0.00098 ( 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 512 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 446 time to evaluate : 0.575 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: 0.5058 (OUTLIER) cc_final: 0.4531 (mtp85) REVERT: A 424 PHE cc_start: 0.9315 (m-80) cc_final: 0.8839 (m-80) REVERT: A 459 VAL cc_start: 0.9897 (t) cc_final: 0.9449 (p) REVERT: A 462 MET cc_start: 0.9741 (tpt) cc_final: 0.9473 (tpt) REVERT: A 463 PHE cc_start: 0.9589 (m-80) cc_final: 0.9064 (m-80) REVERT: A 638 LYS cc_start: 0.9855 (mttt) cc_final: 0.9543 (mmtm) REVERT: A 640 PHE cc_start: 0.9452 (t80) cc_final: 0.8907 (t80) REVERT: A 641 SER cc_start: 0.9787 (t) cc_final: 0.9537 (p) REVERT: A 651 MET cc_start: 0.9504 (mmm) cc_final: 0.9211 (mmm) REVERT: A 656 PHE cc_start: 0.9424 (m-80) cc_final: 0.9029 (m-80) REVERT: A 681 ARG cc_start: 0.9544 (mmm160) cc_final: 0.9253 (mmm160) REVERT: A 691 ASN cc_start: 0.9822 (m-40) cc_final: 0.9600 (t0) REVERT: A 705 TRP cc_start: 0.9251 (t60) cc_final: 0.8975 (t60) REVERT: A 758 PHE cc_start: 0.9466 (m-80) cc_final: 0.8872 (m-80) REVERT: A 840 GLU cc_start: 0.9574 (mt-10) cc_final: 0.9368 (mm-30) REVERT: B 92 ARG cc_start: 0.5247 (OUTLIER) cc_final: 0.4667 (mtp85) REVERT: B 424 PHE cc_start: 0.9293 (m-80) cc_final: 0.8810 (m-80) REVERT: B 462 MET cc_start: 0.9731 (tpt) cc_final: 0.9420 (tpt) REVERT: B 638 LYS cc_start: 0.9827 (mmtm) cc_final: 0.9558 (mmmm) REVERT: B 640 PHE cc_start: 0.9498 (t80) cc_final: 0.8936 (t80) REVERT: B 645 MET cc_start: 0.9506 (mtp) cc_final: 0.9246 (ttm) REVERT: B 681 ARG cc_start: 0.9590 (mmm160) cc_final: 0.9075 (tpp-160) REVERT: B 691 ASN cc_start: 0.9780 (m-40) cc_final: 0.9552 (t0) REVERT: B 705 TRP cc_start: 0.9243 (t60) cc_final: 0.8997 (t60) REVERT: B 758 PHE cc_start: 0.9484 (OUTLIER) cc_final: 0.8929 (m-80) REVERT: B 781 PHE cc_start: 0.9704 (m-80) cc_final: 0.9253 (m-80) REVERT: B 782 ILE cc_start: 0.9769 (mp) cc_final: 0.9407 (tp) REVERT: C 127 LEU cc_start: 0.9171 (tp) cc_final: 0.8657 (tp) REVERT: C 420 TYR cc_start: 0.9563 (t80) cc_final: 0.9115 (t80) REVERT: C 424 PHE cc_start: 0.9230 (m-80) cc_final: 0.8842 (m-80) REVERT: C 462 MET cc_start: 0.9649 (tpt) cc_final: 0.9387 (tpt) REVERT: C 588 ASN cc_start: 0.9221 (m-40) cc_final: 0.8996 (m110) REVERT: C 619 PHE cc_start: 0.9688 (OUTLIER) cc_final: 0.9032 (t80) REVERT: C 640 PHE cc_start: 0.9496 (t80) cc_final: 0.8809 (t80) REVERT: C 645 MET cc_start: 0.9574 (mtp) cc_final: 0.9321 (ttm) REVERT: C 681 ARG cc_start: 0.9484 (mmm160) cc_final: 0.8951 (tpp-160) REVERT: C 682 GLU cc_start: 0.9529 (mt-10) cc_final: 0.9215 (mt-10) REVERT: C 691 ASN cc_start: 0.9786 (m-40) cc_final: 0.9428 (t0) REVERT: C 695 GLN cc_start: 0.9772 (mt0) cc_final: 0.9525 (mm-40) REVERT: C 705 TRP cc_start: 0.9290 (t60) cc_final: 0.9061 (t60) REVERT: C 757 LYS cc_start: 0.9493 (mttt) cc_final: 0.9226 (mtpt) REVERT: C 758 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8730 (m-80) REVERT: C 780 TYR cc_start: 0.9762 (m-10) cc_final: 0.9529 (m-10) REVERT: C 788 GLU cc_start: 0.8823 (pm20) cc_final: 0.8590 (pm20) REVERT: C 821 ASP cc_start: 0.9340 (p0) cc_final: 0.9093 (m-30) REVERT: C 830 LEU cc_start: 0.9842 (pt) cc_final: 0.9295 (tt) REVERT: C 844 MET cc_start: 0.9552 (mtm) cc_final: 0.9351 (ptp) REVERT: C 860 PHE cc_start: 0.9108 (t80) cc_final: 0.8896 (t80) REVERT: D 420 TYR cc_start: 0.9582 (t80) cc_final: 0.9162 (t80) REVERT: D 424 PHE cc_start: 0.9242 (m-80) cc_final: 0.8870 (m-80) REVERT: D 638 LYS cc_start: 0.9855 (mttt) cc_final: 0.9609 (mmtm) REVERT: D 640 PHE cc_start: 0.9483 (t80) cc_final: 0.8889 (t80) REVERT: D 645 MET cc_start: 0.9817 (mtp) cc_final: 0.8766 (ttm) REVERT: D 649 SER cc_start: 0.9770 (p) cc_final: 0.9381 (p) REVERT: D 651 MET cc_start: 0.9726 (mmm) cc_final: 0.9483 (mmm) REVERT: D 656 PHE cc_start: 0.9242 (m-10) cc_final: 0.8809 (m-80) REVERT: D 664 GLN cc_start: 0.9574 (mt0) cc_final: 0.9290 (mm-40) REVERT: D 677 MET cc_start: 0.9680 (tpp) cc_final: 0.9479 (tpp) REVERT: D 681 ARG cc_start: 0.9521 (mmm160) cc_final: 0.9240 (mmm160) REVERT: D 691 ASN cc_start: 0.9783 (m-40) cc_final: 0.9569 (t0) REVERT: D 705 TRP cc_start: 0.9298 (t60) cc_final: 0.9042 (t60) REVERT: D 744 ARG cc_start: 0.9417 (ptp-110) cc_final: 0.8906 (mpt90) REVERT: D 757 LYS cc_start: 0.9557 (OUTLIER) cc_final: 0.8995 (mtmt) REVERT: D 758 PHE cc_start: 0.9342 (m-80) cc_final: 0.8831 (m-80) outliers start: 66 outliers final: 52 residues processed: 484 average time/residue: 0.1164 time to fit residues: 85.3105 Evaluate side-chains 479 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 421 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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 822 VAL Chi-restraints excluded: chain B residue 26 SER 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 413 LEU 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 619 PHE 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 789 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 822 VAL 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 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 782 ILE 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 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 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 757 LYS 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 163 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 210 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 51 optimal weight: 50.0000 chunk 2 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 112 optimal weight: 50.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 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** D 714 ASN ** 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 = 0.3364 r_free = 0.3364 target = 0.074002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.055020 restraints weight = 78053.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.057069 restraints weight = 48819.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.058567 restraints weight = 35643.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.059658 restraints weight = 28082.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.060520 restraints weight = 23414.940| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.6498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18032 Z= 0.143 Angle : 0.759 13.144 24472 Z= 0.367 Chirality : 0.046 0.274 2792 Planarity : 0.004 0.035 3068 Dihedral : 5.138 47.017 2436 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.98 % Favored : 95.84 % Rotamer: Outliers : 3.63 % Allowed : 27.71 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.18), residues: 2188 helix: 0.08 (0.15), residues: 1152 sheet: -1.41 (0.31), residues: 248 loop : -0.83 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 534 TYR 0.028 0.001 TYR D 707 PHE 0.029 0.002 PHE D 551 TRP 0.010 0.001 TRP D 563 HIS 0.010 0.001 HIS B 703 Details of bonding type rmsd covalent geometry : bond 0.00318 (18028) covalent geometry : angle 0.75945 (24472) hydrogen bonds : bond 0.03974 ( 856) hydrogen bonds : angle 5.09469 ( 2388) Misc. bond : bond 0.00103 ( 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 495 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 428 time to evaluate : 0.745 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: A 92 ARG cc_start: 0.5208 (OUTLIER) cc_final: 0.4836 (mtp85) REVERT: A 127 LEU cc_start: 0.9274 (tp) cc_final: 0.8851 (tp) REVERT: A 462 MET cc_start: 0.9753 (tpt) cc_final: 0.9451 (tpt) REVERT: A 638 LYS cc_start: 0.9867 (mttt) cc_final: 0.9566 (mmtm) REVERT: A 640 PHE cc_start: 0.9467 (t80) cc_final: 0.8976 (t80) REVERT: A 641 SER cc_start: 0.9806 (t) cc_final: 0.9535 (p) REVERT: A 645 MET cc_start: 0.9583 (ttt) cc_final: 0.9221 (ttt) REVERT: A 651 MET cc_start: 0.9529 (mmm) cc_final: 0.9252 (mmm) REVERT: A 656 PHE cc_start: 0.9437 (m-80) cc_final: 0.9006 (m-80) REVERT: A 681 ARG cc_start: 0.9538 (mmm160) cc_final: 0.9279 (mmm160) REVERT: A 691 ASN cc_start: 0.9828 (m-40) cc_final: 0.9506 (t0) REVERT: A 695 GLN cc_start: 0.9761 (pt0) cc_final: 0.9502 (mm-40) REVERT: A 698 GLU cc_start: 0.9523 (pt0) cc_final: 0.9318 (pt0) REVERT: A 705 TRP cc_start: 0.9251 (t60) cc_final: 0.8956 (t60) REVERT: A 758 PHE cc_start: 0.9369 (m-80) cc_final: 0.8737 (m-80) REVERT: B 66 CYS cc_start: 0.8264 (m) cc_final: 0.8035 (m) REVERT: B 92 ARG cc_start: 0.5469 (OUTLIER) cc_final: 0.5033 (mtp85) REVERT: B 127 LEU cc_start: 0.9142 (tp) cc_final: 0.8640 (tp) REVERT: B 410 TRP cc_start: 0.8940 (t60) cc_final: 0.8702 (t60) REVERT: B 462 MET cc_start: 0.9737 (tpt) cc_final: 0.9423 (tpt) REVERT: B 638 LYS cc_start: 0.9835 (mmtm) cc_final: 0.9565 (mmmm) REVERT: B 640 PHE cc_start: 0.9524 (t80) cc_final: 0.8770 (t80) REVERT: B 645 MET cc_start: 0.9525 (mtp) cc_final: 0.9238 (ttm) REVERT: B 656 PHE cc_start: 0.9406 (m-10) cc_final: 0.9044 (m-80) REVERT: B 691 ASN cc_start: 0.9791 (m-40) cc_final: 0.9567 (t0) REVERT: B 705 TRP cc_start: 0.9239 (t60) cc_final: 0.8961 (t60) REVERT: B 758 PHE cc_start: 0.9542 (OUTLIER) cc_final: 0.8917 (m-80) REVERT: B 781 PHE cc_start: 0.9708 (m-80) cc_final: 0.9311 (m-80) REVERT: B 782 ILE cc_start: 0.9770 (mp) cc_final: 0.9507 (tp) REVERT: B 830 LEU cc_start: 0.9828 (OUTLIER) cc_final: 0.9305 (tt) REVERT: C 420 TYR cc_start: 0.9571 (t80) cc_final: 0.9121 (t80) REVERT: C 424 PHE cc_start: 0.9240 (m-80) cc_final: 0.8873 (m-80) REVERT: C 462 MET cc_start: 0.9660 (tpt) cc_final: 0.9415 (tpt) REVERT: C 588 ASN cc_start: 0.9245 (m-40) cc_final: 0.9022 (m110) REVERT: C 619 PHE cc_start: 0.9719 (OUTLIER) cc_final: 0.9103 (t80) REVERT: C 640 PHE cc_start: 0.9498 (t80) cc_final: 0.8848 (t80) REVERT: C 645 MET cc_start: 0.9594 (mtp) cc_final: 0.9327 (ttm) REVERT: C 664 GLN cc_start: 0.9569 (mt0) cc_final: 0.9358 (mm-40) REVERT: C 682 GLU cc_start: 0.9551 (mt-10) cc_final: 0.9289 (mt-10) REVERT: C 691 ASN cc_start: 0.9798 (m-40) cc_final: 0.9458 (t0) REVERT: C 695 GLN cc_start: 0.9787 (mt0) cc_final: 0.9528 (mm-40) REVERT: C 705 TRP cc_start: 0.9297 (t60) cc_final: 0.9051 (t60) REVERT: C 757 LYS cc_start: 0.9505 (mttt) cc_final: 0.9291 (mtpt) REVERT: C 758 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8692 (m-80) REVERT: C 788 GLU cc_start: 0.8843 (pm20) cc_final: 0.8571 (pm20) REVERT: C 821 ASP cc_start: 0.9338 (p0) cc_final: 0.9065 (m-30) REVERT: C 830 LEU cc_start: 0.9849 (pt) cc_final: 0.9352 (tt) REVERT: C 844 MET cc_start: 0.9552 (mtm) cc_final: 0.9320 (ptp) REVERT: C 860 PHE cc_start: 0.9121 (t80) cc_final: 0.8877 (t80) REVERT: D 424 PHE cc_start: 0.9271 (m-80) cc_final: 0.8800 (m-80) REVERT: D 638 LYS cc_start: 0.9862 (mttt) cc_final: 0.9635 (mmtm) REVERT: D 640 PHE cc_start: 0.9493 (t80) cc_final: 0.8927 (t80) REVERT: D 649 SER cc_start: 0.9765 (p) cc_final: 0.9409 (p) REVERT: D 664 GLN cc_start: 0.9573 (mt0) cc_final: 0.9301 (mm-40) REVERT: D 681 ARG cc_start: 0.9519 (mmm160) cc_final: 0.9273 (mmm160) REVERT: D 691 ASN cc_start: 0.9790 (m-40) cc_final: 0.9584 (t0) REVERT: D 705 TRP cc_start: 0.9293 (t60) cc_final: 0.9011 (t60) REVERT: D 744 ARG cc_start: 0.9437 (ptp-110) cc_final: 0.8935 (mpt90) REVERT: D 758 PHE cc_start: 0.9390 (m-80) cc_final: 0.8879 (m-80) REVERT: D 821 ASP cc_start: 0.9381 (m-30) cc_final: 0.9153 (p0) REVERT: D 838 LEU cc_start: 0.9773 (tp) cc_final: 0.9385 (pp) outliers start: 67 outliers final: 52 residues processed: 469 average time/residue: 0.1454 time to fit residues: 102.5537 Evaluate side-chains 474 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 416 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 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 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 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 413 LEU 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 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 830 LEU 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 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 782 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL 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 716 VAL Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 799 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.4713 > 50: distance: 13 - 14: 5.843 distance: 13 - 142: 3.515 distance: 14 - 17: 7.560 distance: 15 - 16: 4.405 distance: 18 - 19: 4.583 distance: 19 - 20: 4.976 distance: 19 - 22: 3.990 distance: 20 - 21: 6.205 distance: 20 - 26: 8.449 distance: 22 - 23: 9.011 distance: 23 - 24: 7.019 distance: 23 - 25: 4.689 distance: 26 - 27: 7.716 distance: 27 - 28: 6.690 distance: 27 - 30: 10.123 distance: 28 - 29: 12.126 distance: 28 - 31: 7.147 distance: 31 - 32: 14.190 distance: 32 - 33: 12.969 distance: 32 - 35: 17.095 distance: 33 - 34: 24.008 distance: 33 - 36: 21.482 distance: 36 - 37: 6.096 distance: 37 - 38: 12.519 distance: 37 - 40: 7.552 distance: 38 - 39: 17.223 distance: 38 - 43: 12.512 distance: 40 - 41: 14.845 distance: 40 - 42: 16.598 distance: 43 - 44: 5.323 distance: 44 - 45: 7.581 distance: 45 - 46: 7.766 distance: 45 - 52: 3.225 distance: 47 - 48: 7.469 distance: 48 - 49: 7.253 distance: 49 - 50: 7.018 distance: 49 - 51: 5.833 distance: 52 - 53: 4.406 distance: 53 - 54: 6.150 distance: 53 - 56: 4.558 distance: 56 - 57: 4.529 distance: 57 - 58: 3.024 distance: 60 - 61: 3.983 distance: 61 - 62: 9.079 distance: 61 - 64: 5.337 distance: 62 - 63: 4.016 distance: 62 - 66: 8.245 distance: 64 - 65: 10.483 distance: 66 - 67: 3.005 distance: 67 - 68: 3.126 distance: 68 - 69: 4.203 distance: 68 - 71: 4.148 distance: 71 - 72: 9.405 distance: 72 - 73: 5.166 distance: 72 - 75: 7.732 distance: 73 - 74: 3.572 distance: 73 - 78: 5.496 distance: 75 - 76: 5.716 distance: 75 - 77: 7.971