Starting phenix.real_space_refine on Wed Mar 4 21:43:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v0h_20998/03_2026/6v0h_20998.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v0h_20998/03_2026/6v0h_20998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v0h_20998/03_2026/6v0h_20998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v0h_20998/03_2026/6v0h_20998.map" model { file = "/net/cci-nas-00/data/ceres_data/6v0h_20998/03_2026/6v0h_20998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v0h_20998/03_2026/6v0h_20998.cif" } resolution = 3.6 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= 0.000 sd= 0.007 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 24 5.16 5 C 10542 2.51 5 N 2922 2.21 5 O 3114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16602 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2767 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Chain: "B" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2767 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Chain: "C" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2767 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Chain: "D" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2767 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Chain: "E" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2767 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Chain: "F" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2767 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 18, 'TRANS': 344} Time building chain proxies: 3.36, per 1000 atoms: 0.20 Number of scatterers: 16602 At special positions: 0 Unit cell: (110.04, 111.35, 112.66, 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 24 16.00 O 3114 8.00 N 2922 7.00 C 10542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 877.4 milliseconds 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 23 sheets defined 15.2% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.869A pdb=" N ASN A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.562A pdb=" N ILE A 714 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 744 removed outlier: 4.488A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 802 removed outlier: 3.843A pdb=" N VAL A 802 " --> pdb=" O GLN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 835 removed outlier: 4.107A pdb=" N ILE A 834 " --> pdb=" O PHE A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 870 removed outlier: 4.126A pdb=" N ARG A 869 " --> pdb=" O LYS A 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 567 removed outlier: 3.869A pdb=" N ASN B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 600 Processing helix chain 'B' and resid 612 through 617 Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 711 through 715 removed outlier: 3.562A pdb=" N ILE B 714 " --> pdb=" O LEU B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 744 removed outlier: 4.487A pdb=" N ARG B 743 " --> pdb=" O ILE B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 802 removed outlier: 3.843A pdb=" N VAL B 802 " --> pdb=" O GLN B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 835 removed outlier: 4.108A pdb=" N ILE B 834 " --> pdb=" O PHE B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 870 removed outlier: 4.127A pdb=" N ARG B 869 " --> pdb=" O LYS B 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 567 removed outlier: 3.810A pdb=" N ASN C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 600 Processing helix chain 'C' and resid 611 through 617 removed outlier: 3.966A pdb=" N GLN C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 631 Processing helix chain 'C' and resid 711 through 715 removed outlier: 3.571A pdb=" N ILE C 714 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 removed outlier: 4.483A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 802 removed outlier: 3.841A pdb=" N VAL C 802 " --> pdb=" O GLN C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 835 removed outlier: 4.508A pdb=" N ILE C 834 " --> pdb=" O PHE C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 870 removed outlier: 4.248A pdb=" N ARG C 869 " --> pdb=" O LYS C 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 567 removed outlier: 3.868A pdb=" N ASN D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 600 Processing helix chain 'D' and resid 612 through 617 Processing helix chain 'D' and resid 626 through 631 Processing helix chain 'D' and resid 711 through 715 removed outlier: 3.563A pdb=" N ILE D 714 " --> pdb=" O LEU D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 744 removed outlier: 4.486A pdb=" N ARG D 743 " --> pdb=" O ILE D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 802 removed outlier: 3.843A pdb=" N VAL D 802 " --> pdb=" O GLN D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 835 removed outlier: 4.107A pdb=" N ILE D 834 " --> pdb=" O PHE D 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 870 removed outlier: 4.126A pdb=" N ARG D 869 " --> pdb=" O LYS D 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 567 removed outlier: 3.869A pdb=" N ASN E 565 " --> pdb=" O PRO E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 600 Processing helix chain 'E' and resid 612 through 617 Processing helix chain 'E' and resid 626 through 631 Processing helix chain 'E' and resid 711 through 715 removed outlier: 3.563A pdb=" N ILE E 714 " --> pdb=" O LEU E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 744 removed outlier: 4.486A pdb=" N ARG E 743 " --> pdb=" O ILE E 739 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 802 removed outlier: 3.844A pdb=" N VAL E 802 " --> pdb=" O GLN E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 830 through 835 removed outlier: 4.108A pdb=" N ILE E 834 " --> pdb=" O PHE E 830 " (cutoff:3.500A) Processing helix chain 'E' and resid 865 through 870 removed outlier: 4.126A pdb=" N ARG E 869 " --> pdb=" O LYS E 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 567 removed outlier: 3.869A pdb=" N ASN F 565 " --> pdb=" O PRO F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 600 Processing helix chain 'F' and resid 612 through 617 Processing helix chain 'F' and resid 626 through 631 Processing helix chain 'F' and resid 711 through 715 removed outlier: 3.562A pdb=" N ILE F 714 " --> pdb=" O LEU F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 739 through 744 removed outlier: 4.487A pdb=" N ARG F 743 " --> pdb=" O ILE F 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 798 through 802 removed outlier: 3.843A pdb=" N VAL F 802 " --> pdb=" O GLN F 799 " (cutoff:3.500A) Processing helix chain 'F' and resid 830 through 835 removed outlier: 4.108A pdb=" N ILE F 834 " --> pdb=" O PHE F 830 " (cutoff:3.500A) Processing helix chain 'F' and resid 865 through 870 removed outlier: 4.126A pdb=" N ARG F 869 " --> pdb=" O LYS F 866 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 521 removed outlier: 6.506A pdb=" N ASP A 554 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL A 546 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP A 556 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 533 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 602 through 607 removed outlier: 9.260A pdb=" N TYR A 624 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE A 573 " --> pdb=" O TYR A 624 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 636 through 641 removed outlier: 7.238A pdb=" N GLU A 674 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU A 668 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN A 676 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU A 666 " --> pdb=" O GLN A 676 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS A 678 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE A 653 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 721 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE A 696 " --> pdb=" O GLN A 735 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 748 through 754 removed outlier: 7.055A pdb=" N MET A 789 " --> pdb=" O MET A 779 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N MET A 779 " --> pdb=" O MET A 789 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA A 791 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE A 768 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A 841 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 807 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 808 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 517 through 521 removed outlier: 6.506A pdb=" N ASP B 554 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL B 546 " --> pdb=" O ASP B 554 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP B 556 " --> pdb=" O ILE B 544 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL B 533 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 602 through 607 removed outlier: 9.260A pdb=" N TYR B 624 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE B 573 " --> pdb=" O TYR B 624 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 636 through 641 removed outlier: 7.238A pdb=" N GLU B 674 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU B 668 " --> pdb=" O GLU B 674 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN B 676 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU B 666 " --> pdb=" O GLN B 676 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS B 678 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE B 653 " --> pdb=" O ILE B 660 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 721 " --> pdb=" O ARG B 654 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE B 696 " --> pdb=" O GLN B 735 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 748 through 754 removed outlier: 7.055A pdb=" N MET B 789 " --> pdb=" O MET B 779 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N MET B 779 " --> pdb=" O MET B 789 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA B 791 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE B 768 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 841 " --> pdb=" O VAL B 807 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 807 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE B 808 " --> pdb=" O GLN B 861 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 517 through 520 removed outlier: 6.492A pdb=" N ASP C 554 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL C 546 " --> pdb=" O ASP C 554 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASP C 556 " --> pdb=" O ILE C 544 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL C 533 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N TYR C 624 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N PHE C 573 " --> pdb=" O TYR C 624 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 636 through 641 removed outlier: 7.247A pdb=" N GLU C 674 " --> pdb=" O LEU C 668 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU C 668 " --> pdb=" O GLU C 674 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLN C 676 " --> pdb=" O LEU C 666 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU C 666 " --> pdb=" O GLN C 676 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS C 678 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE C 653 " --> pdb=" O ILE C 660 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 721 " --> pdb=" O ARG C 654 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE C 696 " --> pdb=" O GLN C 735 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N PHE C 732 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR C 638 " --> pdb=" O PHE C 732 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU C 734 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HIS C 640 " --> pdb=" O LEU C 734 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 748 through 754 removed outlier: 7.012A pdb=" N MET C 789 " --> pdb=" O MET C 779 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N MET C 779 " --> pdb=" O MET C 789 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA C 791 " --> pdb=" O THR C 777 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU C 772 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE C 768 " --> pdb=" O GLU C 772 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA C 841 " --> pdb=" O VAL C 807 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 807 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE C 808 " --> pdb=" O GLN C 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 517 through 521 removed outlier: 6.505A pdb=" N ASP D 554 " --> pdb=" O VAL D 546 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL D 546 " --> pdb=" O ASP D 554 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP D 556 " --> pdb=" O ILE D 544 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL D 533 " --> pdb=" O VAL D 540 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 602 through 607 removed outlier: 9.260A pdb=" N TYR D 624 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE D 573 " --> pdb=" O TYR D 624 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 636 through 641 removed outlier: 7.237A pdb=" N GLU D 674 " --> pdb=" O LEU D 668 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU D 668 " --> pdb=" O GLU D 674 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN D 676 " --> pdb=" O LEU D 666 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU D 666 " --> pdb=" O GLN D 676 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS D 678 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE D 653 " --> pdb=" O ILE D 660 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 721 " --> pdb=" O ARG D 654 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE D 696 " --> pdb=" O GLN D 735 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 748 through 754 removed outlier: 7.055A pdb=" N MET D 789 " --> pdb=" O MET D 779 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N MET D 779 " --> pdb=" O MET D 789 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA D 791 " --> pdb=" O THR D 777 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU D 772 " --> pdb=" O PHE D 768 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE D 768 " --> pdb=" O GLU D 772 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA D 841 " --> pdb=" O VAL D 807 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL D 807 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE D 808 " --> pdb=" O GLN D 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 517 through 521 removed outlier: 6.506A pdb=" N ASP E 554 " --> pdb=" O VAL E 546 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL E 546 " --> pdb=" O ASP E 554 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP E 556 " --> pdb=" O ILE E 544 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL E 533 " --> pdb=" O VAL E 540 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 602 through 607 removed outlier: 9.260A pdb=" N TYR E 624 " --> pdb=" O SER E 571 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE E 573 " --> pdb=" O TYR E 624 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 636 through 641 removed outlier: 7.238A pdb=" N GLU E 674 " --> pdb=" O LEU E 668 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU E 668 " --> pdb=" O GLU E 674 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN E 676 " --> pdb=" O LEU E 666 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU E 666 " --> pdb=" O GLN E 676 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS E 678 " --> pdb=" O GLN E 664 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE E 653 " --> pdb=" O ILE E 660 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 721 " --> pdb=" O ARG E 654 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE E 696 " --> pdb=" O GLN E 735 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 748 through 754 removed outlier: 7.055A pdb=" N MET E 789 " --> pdb=" O MET E 779 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N MET E 779 " --> pdb=" O MET E 789 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA E 791 " --> pdb=" O THR E 777 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU E 772 " --> pdb=" O PHE E 768 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE E 768 " --> pdb=" O GLU E 772 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA E 841 " --> pdb=" O VAL E 807 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL E 807 " --> pdb=" O ALA E 841 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE E 808 " --> pdb=" O GLN E 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 517 through 521 removed outlier: 6.506A pdb=" N ASP F 554 " --> pdb=" O VAL F 546 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL F 546 " --> pdb=" O ASP F 554 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP F 556 " --> pdb=" O ILE F 544 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL F 533 " --> pdb=" O VAL F 540 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 602 through 607 removed outlier: 9.260A pdb=" N TYR F 624 " --> pdb=" O SER F 571 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N PHE F 573 " --> pdb=" O TYR F 624 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 636 through 641 removed outlier: 7.237A pdb=" N GLU F 674 " --> pdb=" O LEU F 668 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU F 668 " --> pdb=" O GLU F 674 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN F 676 " --> pdb=" O LEU F 666 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU F 666 " --> pdb=" O GLN F 676 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS F 678 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE F 653 " --> pdb=" O ILE F 660 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL F 721 " --> pdb=" O ARG F 654 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE F 696 " --> pdb=" O GLN F 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 748 through 754 removed outlier: 7.056A pdb=" N MET F 789 " --> pdb=" O MET F 779 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N MET F 779 " --> pdb=" O MET F 789 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA F 791 " --> pdb=" O THR F 777 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU F 772 " --> pdb=" O PHE F 768 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE F 768 " --> pdb=" O GLU F 772 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA F 841 " --> pdb=" O VAL F 807 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL F 807 " --> pdb=" O ALA F 841 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE F 808 " --> pdb=" O GLN F 861 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1050 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: 2.78 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2780 1.32 - 1.44: 4378 1.44 - 1.56: 9719 1.56 - 1.68: 7 1.68 - 1.80: 48 Bond restraints: 16932 Sorted by residual: bond pdb=" C VAL C 581 " pdb=" O VAL C 581 " ideal model delta sigma weight residual 1.234 1.198 0.035 1.17e-02 7.31e+03 9.14e+00 bond pdb=" CG LEU C 588 " pdb=" CD1 LEU C 588 " ideal model delta sigma weight residual 1.521 1.602 -0.081 3.30e-02 9.18e+02 5.96e+00 bond pdb=" CA THR C 589 " pdb=" CB THR C 589 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.57e-02 4.06e+03 2.64e+00 bond pdb=" CB VAL F 590 " pdb=" CG1 VAL F 590 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.51e+00 bond pdb=" CB VAL D 590 " pdb=" CG1 VAL D 590 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.50e+00 ... (remaining 16927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 22183 2.05 - 4.11: 724 4.11 - 6.16: 54 6.16 - 8.22: 14 8.22 - 10.27: 11 Bond angle restraints: 22986 Sorted by residual: angle pdb=" C PRO D 876 " pdb=" N LYS D 877 " pdb=" CA LYS D 877 " ideal model delta sigma weight residual 121.70 128.19 -6.49 1.80e+00 3.09e-01 1.30e+01 angle pdb=" C PRO E 876 " pdb=" N LYS E 877 " pdb=" CA LYS E 877 " ideal model delta sigma weight residual 121.70 128.16 -6.46 1.80e+00 3.09e-01 1.29e+01 angle pdb=" C PRO B 876 " pdb=" N LYS B 877 " pdb=" CA LYS B 877 " ideal model delta sigma weight residual 121.70 128.15 -6.45 1.80e+00 3.09e-01 1.29e+01 angle pdb=" C PRO F 876 " pdb=" N LYS F 877 " pdb=" CA LYS F 877 " ideal model delta sigma weight residual 121.70 128.15 -6.45 1.80e+00 3.09e-01 1.28e+01 angle pdb=" C PRO A 876 " pdb=" N LYS A 877 " pdb=" CA LYS A 877 " ideal model delta sigma weight residual 121.70 128.15 -6.45 1.80e+00 3.09e-01 1.28e+01 ... (remaining 22981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 9611 15.05 - 30.09: 376 30.09 - 45.14: 81 45.14 - 60.18: 0 60.18 - 75.23: 12 Dihedral angle restraints: 10080 sinusoidal: 3948 harmonic: 6132 Sorted by residual: dihedral pdb=" CA THR C 846 " pdb=" C THR C 846 " pdb=" N PRO C 847 " pdb=" CA PRO C 847 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA THR B 846 " pdb=" C THR B 846 " pdb=" N PRO B 847 " pdb=" CA PRO B 847 " ideal model delta harmonic sigma weight residual 180.00 152.67 27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA THR A 846 " pdb=" C THR A 846 " pdb=" N PRO A 847 " pdb=" CA PRO A 847 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 10077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2070 0.065 - 0.129: 490 0.129 - 0.194: 66 0.194 - 0.259: 1 0.259 - 0.324: 1 Chirality restraints: 2628 Sorted by residual: chirality pdb=" CG LEU C 588 " pdb=" CB LEU C 588 " pdb=" CD1 LEU C 588 " pdb=" CD2 LEU C 588 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CG LEU C 767 " pdb=" CB LEU C 767 " pdb=" CD1 LEU C 767 " pdb=" CD2 LEU C 767 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA THR C 846 " pdb=" N THR C 846 " pdb=" C THR C 846 " pdb=" CB THR C 846 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 2625 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 587 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.74e+00 pdb=" C GLY C 587 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY C 587 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU C 588 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 846 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO F 847 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO F 847 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 847 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 846 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO E 847 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 847 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 847 " 0.036 5.00e-02 4.00e+02 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 9 2.47 - 3.08: 10096 3.08 - 3.69: 22824 3.69 - 4.29: 33105 4.29 - 4.90: 55059 Nonbonded interactions: 121093 Sorted by model distance: nonbonded pdb=" O PHE B 833 " pdb=" OG1 THR C 829 " model vdw 1.866 3.040 nonbonded pdb=" NE2 GLN A 528 " pdb=" OE1 GLU B 539 " model vdw 2.297 3.120 nonbonded pdb=" NE2 GLN C 528 " pdb=" OE1 GLU D 539 " model vdw 2.341 3.120 nonbonded pdb=" N TYR C 535 " pdb=" O PHE C 538 " model vdw 2.386 3.120 nonbonded pdb=" N TYR F 535 " pdb=" O PHE F 538 " model vdw 2.401 3.120 ... (remaining 121088 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.270 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 : 0.005 0.081 16932 Z= 0.231 Angle : 0.845 10.272 22986 Z= 0.460 Chirality : 0.054 0.324 2628 Planarity : 0.007 0.064 2988 Dihedral : 9.305 75.229 6180 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.15), residues: 2166 helix: -4.40 (0.15), residues: 228 sheet: -2.05 (0.17), residues: 648 loop : -2.32 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 793 TYR 0.013 0.003 TYR A 798 PHE 0.038 0.003 PHE C 605 TRP 0.018 0.003 TRP A 574 HIS 0.006 0.002 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00510 (16932) covalent geometry : angle 0.84493 (22986) hydrogen bonds : bond 0.29367 ( 427) hydrogen bonds : angle 10.12607 ( 1050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 656 LEU cc_start: 0.9186 (mt) cc_final: 0.8939 (mp) REVERT: A 716 GLN cc_start: 0.8122 (tt0) cc_final: 0.7909 (pt0) REVERT: A 835 ARG cc_start: 0.6597 (mtt180) cc_final: 0.6319 (mtp180) REVERT: A 853 GLN cc_start: 0.7736 (mm110) cc_final: 0.7264 (mp10) REVERT: A 870 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7824 (mp0) REVERT: B 735 GLN cc_start: 0.7911 (mt0) cc_final: 0.7654 (mt0) REVERT: B 759 SER cc_start: 0.7571 (t) cc_final: 0.7297 (t) REVERT: B 842 THR cc_start: 0.7712 (m) cc_final: 0.7272 (p) REVERT: C 749 SER cc_start: 0.8976 (t) cc_final: 0.8763 (m) REVERT: C 833 PHE cc_start: 0.7378 (t80) cc_final: 0.7150 (t80) REVERT: D 620 LYS cc_start: 0.7440 (mtmt) cc_final: 0.7162 (mtpt) REVERT: D 853 GLN cc_start: 0.7720 (mm110) cc_final: 0.7278 (mp10) REVERT: E 518 SER cc_start: 0.9127 (m) cc_final: 0.8851 (t) REVERT: E 735 GLN cc_start: 0.7777 (mt0) cc_final: 0.7453 (mt0) REVERT: E 759 SER cc_start: 0.7804 (t) cc_final: 0.7416 (t) REVERT: E 771 LEU cc_start: 0.8762 (mt) cc_final: 0.8527 (mt) REVERT: E 798 TYR cc_start: 0.8490 (m-10) cc_final: 0.8233 (m-10) REVERT: E 809 TRP cc_start: 0.8525 (p90) cc_final: 0.8202 (p90) REVERT: E 833 PHE cc_start: 0.7576 (t80) cc_final: 0.7307 (t80) REVERT: F 518 SER cc_start: 0.9124 (m) cc_final: 0.8898 (t) REVERT: F 842 THR cc_start: 0.8041 (m) cc_final: 0.7728 (p) outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.1668 time to fit residues: 129.4886 Evaluate side-chains 311 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.0170 chunk 212 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 HIS A 570 ASN A 662 GLN B 558 HIS B 662 GLN B 716 GLN C 558 HIS C 662 GLN C 716 GLN D 558 HIS D 570 ASN D 662 GLN D 716 GLN E 558 HIS E 570 ASN E 662 GLN E 716 GLN F 558 HIS F 662 GLN F 716 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.182485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.149513 restraints weight = 22447.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154175 restraints weight = 14230.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.157415 restraints weight = 10387.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.159652 restraints weight = 8296.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.161026 restraints weight = 7040.167| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16932 Z= 0.137 Angle : 0.626 7.478 22986 Z= 0.333 Chirality : 0.047 0.155 2628 Planarity : 0.005 0.045 2988 Dihedral : 5.358 21.027 2370 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.41 % Allowed : 11.68 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.16), residues: 2166 helix: -3.42 (0.30), residues: 192 sheet: -1.63 (0.17), residues: 774 loop : -1.90 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 691 TYR 0.017 0.002 TYR B 624 PHE 0.021 0.001 PHE F 833 TRP 0.030 0.002 TRP C 809 HIS 0.002 0.001 HIS C 640 Details of bonding type rmsd covalent geometry : bond 0.00300 (16932) covalent geometry : angle 0.62580 (22986) hydrogen bonds : bond 0.04887 ( 427) hydrogen bonds : angle 7.59186 ( 1050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 330 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7573 (mtmt) REVERT: A 716 GLN cc_start: 0.8235 (tt0) cc_final: 0.7846 (pt0) REVERT: A 746 ASP cc_start: 0.6523 (t0) cc_final: 0.6216 (t0) REVERT: A 762 ILE cc_start: 0.8776 (mp) cc_final: 0.8574 (mm) REVERT: A 797 ARG cc_start: 0.8330 (mtm110) cc_final: 0.8092 (mtm110) REVERT: A 798 TYR cc_start: 0.8857 (m-80) cc_final: 0.8241 (m-80) REVERT: B 746 ASP cc_start: 0.6394 (t0) cc_final: 0.6008 (t0) REVERT: B 762 ILE cc_start: 0.8802 (mp) cc_final: 0.8591 (mp) REVERT: B 797 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7948 (mtm110) REVERT: B 798 TYR cc_start: 0.8772 (m-80) cc_final: 0.8189 (m-80) REVERT: B 842 THR cc_start: 0.7966 (m) cc_final: 0.7469 (p) REVERT: C 749 SER cc_start: 0.8880 (t) cc_final: 0.8605 (m) REVERT: D 599 LEU cc_start: 0.7401 (mp) cc_final: 0.7138 (mp) REVERT: D 646 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7594 (mtmt) REVERT: D 731 ASP cc_start: 0.7376 (m-30) cc_final: 0.7110 (m-30) REVERT: D 745 LEU cc_start: 0.8231 (mt) cc_final: 0.8005 (mt) REVERT: D 746 ASP cc_start: 0.6365 (t0) cc_final: 0.5916 (t0) REVERT: D 762 ILE cc_start: 0.8812 (mp) cc_final: 0.8609 (mm) REVERT: D 798 TYR cc_start: 0.8886 (m-80) cc_final: 0.8333 (m-80) REVERT: E 518 SER cc_start: 0.9074 (m) cc_final: 0.8670 (t) REVERT: E 606 ASP cc_start: 0.7426 (t0) cc_final: 0.7072 (t0) REVERT: E 798 TYR cc_start: 0.8560 (m-10) cc_final: 0.8294 (m-10) REVERT: E 809 TRP cc_start: 0.8599 (p90) cc_final: 0.8286 (p90) REVERT: E 842 THR cc_start: 0.8324 (m) cc_final: 0.7882 (p) REVERT: F 518 SER cc_start: 0.8977 (m) cc_final: 0.8768 (t) REVERT: F 842 THR cc_start: 0.8289 (m) cc_final: 0.7893 (p) outliers start: 42 outliers final: 22 residues processed: 343 average time/residue: 0.1434 time to fit residues: 71.1413 Evaluate side-chains 302 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 278 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain E residue 642 PHE Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 106 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 208 optimal weight: 0.0470 chunk 155 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 662 GLN D 570 ASN E 570 ASN E 662 GLN E 716 GLN ** E 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 662 GLN ** F 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 804 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.175072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142404 restraints weight = 22837.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.146745 restraints weight = 14816.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.149725 restraints weight = 11007.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.151851 restraints weight = 8900.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.153286 restraints weight = 7604.356| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16932 Z= 0.140 Angle : 0.573 7.205 22986 Z= 0.300 Chirality : 0.046 0.149 2628 Planarity : 0.005 0.050 2988 Dihedral : 4.992 18.941 2370 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.98 % Allowed : 14.20 % Favored : 82.82 % 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 are not related in a simple way. whole: -2.70 (0.17), residues: 2166 helix: -3.24 (0.26), residues: 240 sheet: -1.35 (0.17), residues: 750 loop : -1.73 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 691 TYR 0.017 0.002 TYR F 624 PHE 0.021 0.002 PHE F 833 TRP 0.026 0.002 TRP C 809 HIS 0.003 0.001 HIS E 558 Details of bonding type rmsd covalent geometry : bond 0.00330 (16932) covalent geometry : angle 0.57286 (22986) hydrogen bonds : bond 0.03848 ( 427) hydrogen bonds : angle 7.01083 ( 1050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 299 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 606 ASP cc_start: 0.7901 (t0) cc_final: 0.7539 (t0) REVERT: A 646 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7657 (mtmt) REVERT: A 716 GLN cc_start: 0.8315 (tt0) cc_final: 0.8068 (pt0) REVERT: A 762 ILE cc_start: 0.8854 (mp) cc_final: 0.8652 (mm) REVERT: A 798 TYR cc_start: 0.8933 (m-80) cc_final: 0.8613 (m-80) REVERT: B 695 ARG cc_start: 0.7677 (mtp180) cc_final: 0.7275 (mtp180) REVERT: B 746 ASP cc_start: 0.6287 (t0) cc_final: 0.5808 (t0) REVERT: B 797 ARG cc_start: 0.8178 (mtm110) cc_final: 0.7978 (mtm110) REVERT: B 809 TRP cc_start: 0.8637 (p90) cc_final: 0.8057 (p90) REVERT: B 842 THR cc_start: 0.8201 (m) cc_final: 0.7765 (p) REVERT: C 735 GLN cc_start: 0.8355 (mt0) cc_final: 0.7723 (mt0) REVERT: D 646 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7739 (mtmt) REVERT: D 745 LEU cc_start: 0.8284 (mt) cc_final: 0.8052 (mt) REVERT: D 746 ASP cc_start: 0.6412 (t0) cc_final: 0.5854 (t0) REVERT: D 756 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7469 (mt-10) REVERT: D 762 ILE cc_start: 0.8804 (mp) cc_final: 0.8575 (mm) REVERT: D 786 ASP cc_start: 0.6992 (t0) cc_final: 0.6781 (t0) REVERT: D 797 ARG cc_start: 0.8313 (mtm110) cc_final: 0.7913 (mtm110) REVERT: D 798 TYR cc_start: 0.8880 (m-80) cc_final: 0.8398 (m-80) REVERT: D 853 GLN cc_start: 0.7783 (mm110) cc_final: 0.7251 (mp10) REVERT: E 518 SER cc_start: 0.9098 (m) cc_final: 0.8776 (t) REVERT: E 591 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: E 695 ARG cc_start: 0.8150 (mtm180) cc_final: 0.7662 (ttm110) REVERT: E 809 TRP cc_start: 0.8630 (p90) cc_final: 0.8255 (p90) REVERT: E 842 THR cc_start: 0.8315 (m) cc_final: 0.7914 (p) REVERT: F 518 SER cc_start: 0.8956 (m) cc_final: 0.8733 (t) REVERT: F 833 PHE cc_start: 0.6447 (t80) cc_final: 0.6222 (t80) REVERT: F 842 THR cc_start: 0.8478 (m) cc_final: 0.8106 (p) outliers start: 52 outliers final: 32 residues processed: 321 average time/residue: 0.1289 time to fit residues: 62.0783 Evaluate side-chains 300 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 265 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 727 ASN Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain E residue 591 GLN Chi-restraints excluded: chain E residue 642 PHE Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 711 LEU Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 212 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 132 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 168 optimal weight: 0.1980 chunk 158 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 GLN B 662 GLN C 702 GLN D 570 ASN E 662 GLN E 716 GLN F 570 ASN F 662 GLN F 702 GLN F 804 ASN F 831 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.175116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144027 restraints weight = 22758.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.147960 restraints weight = 15267.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.150683 restraints weight = 11528.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.152682 restraints weight = 9459.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154032 restraints weight = 8156.529| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16932 Z= 0.121 Angle : 0.552 7.939 22986 Z= 0.285 Chirality : 0.045 0.151 2628 Planarity : 0.004 0.039 2988 Dihedral : 4.743 17.340 2370 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.92 % Allowed : 15.81 % Favored : 81.27 % 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 are not related in a simple way. whole: -2.45 (0.17), residues: 2166 helix: -3.00 (0.27), residues: 240 sheet: -1.25 (0.17), residues: 780 loop : -1.51 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 869 TYR 0.011 0.001 TYR E 814 PHE 0.024 0.001 PHE E 833 TRP 0.027 0.002 TRP C 809 HIS 0.002 0.001 HIS C 558 Details of bonding type rmsd covalent geometry : bond 0.00280 (16932) covalent geometry : angle 0.55161 (22986) hydrogen bonds : bond 0.03307 ( 427) hydrogen bonds : angle 6.70303 ( 1050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 275 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7628 (mtmt) REVERT: B 540 VAL cc_start: 0.4101 (OUTLIER) cc_final: 0.3897 (t) REVERT: B 746 ASP cc_start: 0.6288 (t0) cc_final: 0.5840 (t0) REVERT: B 809 TRP cc_start: 0.8588 (p90) cc_final: 0.8060 (p90) REVERT: B 842 THR cc_start: 0.8217 (m) cc_final: 0.7768 (p) REVERT: C 606 ASP cc_start: 0.7520 (t0) cc_final: 0.7259 (t0) REVERT: C 779 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7735 (ttt) REVERT: C 786 ASP cc_start: 0.7031 (m-30) cc_final: 0.6785 (t0) REVERT: C 792 MET cc_start: 0.8387 (ptp) cc_final: 0.8073 (ptp) REVERT: D 540 VAL cc_start: 0.4315 (OUTLIER) cc_final: 0.4005 (t) REVERT: D 606 ASP cc_start: 0.7731 (t0) cc_final: 0.7432 (t0) REVERT: D 646 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7722 (mtmt) REVERT: D 746 ASP cc_start: 0.6383 (t0) cc_final: 0.5854 (t0) REVERT: D 762 ILE cc_start: 0.8797 (mp) cc_final: 0.8596 (mm) REVERT: D 797 ARG cc_start: 0.8318 (mtm110) cc_final: 0.7984 (mtm110) REVERT: D 798 TYR cc_start: 0.8960 (m-80) cc_final: 0.8578 (m-80) REVERT: E 518 SER cc_start: 0.9070 (m) cc_final: 0.8777 (t) REVERT: E 591 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7970 (pt0) REVERT: E 695 ARG cc_start: 0.8187 (mtm180) cc_final: 0.7871 (mtp180) REVERT: E 809 TRP cc_start: 0.8608 (p90) cc_final: 0.8210 (p90) REVERT: E 833 PHE cc_start: 0.6797 (t80) cc_final: 0.6490 (t80) REVERT: E 842 THR cc_start: 0.8306 (m) cc_final: 0.7892 (p) REVERT: F 518 SER cc_start: 0.8956 (m) cc_final: 0.8725 (t) REVERT: F 842 THR cc_start: 0.8527 (m) cc_final: 0.8159 (p) outliers start: 51 outliers final: 31 residues processed: 297 average time/residue: 0.1270 time to fit residues: 57.1210 Evaluate side-chains 285 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 248 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 868 TRP Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 727 ASN Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 868 TRP Chi-restraints excluded: chain E residue 591 GLN Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 711 LEU Chi-restraints excluded: chain F residue 773 VAL Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 112 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 115 optimal weight: 0.0870 chunk 154 optimal weight: 8.9990 chunk 161 optimal weight: 0.0980 chunk 146 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 GLN A 853 GLN B 662 GLN C 702 GLN D 570 ASN E 662 GLN E 716 GLN F 570 ASN F 702 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.172625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144391 restraints weight = 22360.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.147874 restraints weight = 15377.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150298 restraints weight = 11775.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.152029 restraints weight = 9684.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.153244 restraints weight = 8368.524| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16932 Z= 0.126 Angle : 0.540 6.216 22986 Z= 0.280 Chirality : 0.045 0.150 2628 Planarity : 0.004 0.039 2988 Dihedral : 4.640 16.627 2370 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.49 % Allowed : 16.21 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.17), residues: 2166 helix: -2.77 (0.28), residues: 240 sheet: -1.26 (0.17), residues: 792 loop : -1.34 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 797 TYR 0.014 0.001 TYR B 814 PHE 0.028 0.002 PHE B 833 TRP 0.029 0.002 TRP C 809 HIS 0.003 0.001 HIS C 558 Details of bonding type rmsd covalent geometry : bond 0.00297 (16932) covalent geometry : angle 0.53984 (22986) hydrogen bonds : bond 0.03206 ( 427) hydrogen bonds : angle 6.53640 ( 1050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 252 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 606 ASP cc_start: 0.7882 (t0) cc_final: 0.7553 (t0) REVERT: A 646 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7752 (mtmt) REVERT: A 746 ASP cc_start: 0.6447 (t0) cc_final: 0.6212 (t0) REVERT: B 746 ASP cc_start: 0.6300 (t0) cc_final: 0.5868 (t0) REVERT: B 809 TRP cc_start: 0.8625 (p90) cc_final: 0.8083 (p90) REVERT: B 833 PHE cc_start: 0.5937 (t80) cc_final: 0.5638 (t80) REVERT: B 842 THR cc_start: 0.8306 (m) cc_final: 0.7887 (p) REVERT: C 606 ASP cc_start: 0.7494 (t0) cc_final: 0.7224 (t0) REVERT: C 833 PHE cc_start: 0.7242 (t80) cc_final: 0.7020 (t80) REVERT: C 842 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.7921 (p) REVERT: D 606 ASP cc_start: 0.7795 (t0) cc_final: 0.7566 (t0) REVERT: D 646 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7757 (mtmt) REVERT: D 733 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7536 (mm-30) REVERT: D 746 ASP cc_start: 0.6373 (t0) cc_final: 0.5841 (t0) REVERT: D 762 ILE cc_start: 0.8794 (mp) cc_final: 0.8586 (mm) REVERT: D 797 ARG cc_start: 0.8370 (mtm110) cc_final: 0.8024 (mtm110) REVERT: D 798 TYR cc_start: 0.8952 (m-80) cc_final: 0.8518 (m-80) REVERT: E 518 SER cc_start: 0.9017 (m) cc_final: 0.8710 (t) REVERT: E 591 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7974 (pt0) REVERT: E 606 ASP cc_start: 0.7340 (t0) cc_final: 0.7119 (t0) REVERT: E 673 ASN cc_start: 0.7480 (p0) cc_final: 0.7136 (p0) REVERT: E 695 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7893 (mtp180) REVERT: E 809 TRP cc_start: 0.8626 (p90) cc_final: 0.8191 (p90) REVERT: E 842 THR cc_start: 0.8333 (m) cc_final: 0.7919 (p) REVERT: F 518 SER cc_start: 0.9027 (m) cc_final: 0.8768 (t) REVERT: F 603 ILE cc_start: 0.8574 (mt) cc_final: 0.8326 (mp) REVERT: F 606 ASP cc_start: 0.7683 (t0) cc_final: 0.7479 (t0) REVERT: F 695 ARG cc_start: 0.7676 (mtp180) cc_final: 0.7474 (mtp-110) REVERT: F 702 GLN cc_start: 0.5686 (OUTLIER) cc_final: 0.5319 (pm20) REVERT: F 842 THR cc_start: 0.8604 (m) cc_final: 0.8244 (p) outliers start: 61 outliers final: 39 residues processed: 281 average time/residue: 0.1265 time to fit residues: 54.1982 Evaluate side-chains 283 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain D residue 642 PHE Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain E residue 591 GLN Chi-restraints excluded: chain E residue 642 PHE Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 702 GLN Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 773 VAL Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain F residue 835 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 116 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 chunk 185 optimal weight: 0.0670 chunk 15 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 GLN A 853 GLN B 662 GLN D 570 ASN E 662 GLN F 570 ASN F 702 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.177626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.145963 restraints weight = 22850.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.150055 restraints weight = 15279.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.152891 restraints weight = 11543.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.154608 restraints weight = 9423.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.156144 restraints weight = 8213.369| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16932 Z= 0.110 Angle : 0.523 6.000 22986 Z= 0.270 Chirality : 0.045 0.149 2628 Planarity : 0.004 0.053 2988 Dihedral : 4.507 16.510 2370 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.38 % Allowed : 17.12 % Favored : 79.50 % 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 are not related in a simple way. whole: -2.14 (0.18), residues: 2166 helix: -2.64 (0.28), residues: 240 sheet: -1.18 (0.17), residues: 852 loop : -1.19 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 797 TYR 0.017 0.001 TYR B 814 PHE 0.027 0.001 PHE B 833 TRP 0.027 0.002 TRP C 809 HIS 0.002 0.001 HIS C 558 Details of bonding type rmsd covalent geometry : bond 0.00261 (16932) covalent geometry : angle 0.52348 (22986) hydrogen bonds : bond 0.03024 ( 427) hydrogen bonds : angle 6.43404 ( 1050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 258 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 606 ASP cc_start: 0.7812 (t0) cc_final: 0.7607 (t0) REVERT: A 646 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7748 (mtmt) REVERT: A 746 ASP cc_start: 0.6463 (t0) cc_final: 0.6244 (t0) REVERT: B 746 ASP cc_start: 0.6080 (t0) cc_final: 0.5739 (t0) REVERT: B 809 TRP cc_start: 0.8594 (p90) cc_final: 0.8093 (p90) REVERT: B 830 PHE cc_start: 0.6231 (OUTLIER) cc_final: 0.5151 (p90) REVERT: B 833 PHE cc_start: 0.5930 (t80) cc_final: 0.5547 (t80) REVERT: B 842 THR cc_start: 0.8312 (m) cc_final: 0.7882 (p) REVERT: C 842 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.7929 (p) REVERT: D 606 ASP cc_start: 0.7779 (t0) cc_final: 0.7523 (t0) REVERT: D 646 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7750 (mtmt) REVERT: D 733 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: D 746 ASP cc_start: 0.6349 (t0) cc_final: 0.5820 (t0) REVERT: D 797 ARG cc_start: 0.8369 (mtm110) cc_final: 0.8064 (mtm110) REVERT: D 798 TYR cc_start: 0.8911 (m-80) cc_final: 0.8472 (m-80) REVERT: E 518 SER cc_start: 0.8943 (m) cc_final: 0.8535 (t) REVERT: E 591 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: E 600 LYS cc_start: 0.4389 (OUTLIER) cc_final: 0.3549 (mmtt) REVERT: E 606 ASP cc_start: 0.7312 (t0) cc_final: 0.7060 (t0) REVERT: E 673 ASN cc_start: 0.7395 (p0) cc_final: 0.7117 (p0) REVERT: E 695 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7890 (mtp180) REVERT: E 809 TRP cc_start: 0.8609 (p90) cc_final: 0.8164 (p90) REVERT: E 842 THR cc_start: 0.8327 (m) cc_final: 0.7902 (p) REVERT: F 518 SER cc_start: 0.8971 (m) cc_final: 0.8710 (t) REVERT: F 695 ARG cc_start: 0.7875 (mtp180) cc_final: 0.7548 (mtp-110) REVERT: F 771 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8621 (mt) REVERT: F 842 THR cc_start: 0.8602 (m) cc_final: 0.8235 (p) outliers start: 59 outliers final: 35 residues processed: 288 average time/residue: 0.1235 time to fit residues: 54.7071 Evaluate side-chains 287 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain E residue 591 GLN Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 740 THR Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 773 VAL Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 129 optimal weight: 0.2980 chunk 166 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 GLN A 853 GLN B 662 GLN B 832 GLN C 662 GLN C 702 GLN C 716 GLN D 570 ASN E 662 GLN E 716 GLN F 570 ASN F 662 GLN F 716 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.173243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.146082 restraints weight = 22362.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148951 restraints weight = 16515.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.150948 restraints weight = 13242.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.152257 restraints weight = 11280.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.153411 restraints weight = 10065.700| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16932 Z= 0.174 Angle : 0.571 8.268 22986 Z= 0.298 Chirality : 0.046 0.166 2628 Planarity : 0.005 0.079 2988 Dihedral : 4.686 16.919 2370 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.78 % Allowed : 17.24 % Favored : 78.98 % 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 are not related in a simple way. whole: -2.18 (0.18), residues: 2166 helix: -2.53 (0.29), residues: 240 sheet: -1.29 (0.17), residues: 864 loop : -1.18 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 797 TYR 0.016 0.002 TYR E 814 PHE 0.022 0.002 PHE B 833 TRP 0.030 0.002 TRP C 809 HIS 0.003 0.001 HIS E 558 Details of bonding type rmsd covalent geometry : bond 0.00415 (16932) covalent geometry : angle 0.57141 (22986) hydrogen bonds : bond 0.03296 ( 427) hydrogen bonds : angle 6.56272 ( 1050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 256 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 646 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7730 (mtmt) REVERT: A 716 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: B 746 ASP cc_start: 0.5897 (t0) cc_final: 0.5493 (t0) REVERT: B 759 SER cc_start: 0.7941 (p) cc_final: 0.7734 (p) REVERT: B 830 PHE cc_start: 0.6452 (OUTLIER) cc_final: 0.5253 (p90) REVERT: B 842 THR cc_start: 0.8393 (m) cc_final: 0.8024 (p) REVERT: C 606 ASP cc_start: 0.7712 (t0) cc_final: 0.7469 (t0) REVERT: C 842 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8115 (p) REVERT: D 606 ASP cc_start: 0.7757 (t0) cc_final: 0.7543 (t0) REVERT: D 646 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7725 (mtmt) REVERT: D 797 ARG cc_start: 0.8302 (mtm110) cc_final: 0.8020 (mtm110) REVERT: D 798 TYR cc_start: 0.8824 (m-80) cc_final: 0.8377 (m-80) REVERT: E 591 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: E 600 LYS cc_start: 0.4670 (OUTLIER) cc_final: 0.3756 (mmtt) REVERT: E 606 ASP cc_start: 0.7277 (t0) cc_final: 0.7018 (t0) REVERT: E 673 ASN cc_start: 0.7333 (p0) cc_final: 0.7088 (p0) REVERT: E 809 TRP cc_start: 0.8618 (p90) cc_final: 0.8152 (p90) REVERT: E 816 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7283 (mm) REVERT: E 830 PHE cc_start: 0.6418 (OUTLIER) cc_final: 0.5822 (p90) REVERT: E 842 THR cc_start: 0.8369 (m) cc_final: 0.8015 (p) REVERT: F 771 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8704 (mt) REVERT: F 842 THR cc_start: 0.8661 (m) cc_final: 0.8298 (p) outliers start: 66 outliers final: 47 residues processed: 290 average time/residue: 0.1175 time to fit residues: 52.9072 Evaluate side-chains 295 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain E residue 591 GLN Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 642 PHE Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 830 PHE Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 740 THR Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 773 VAL Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 GLN A 853 GLN B 570 ASN C 662 GLN C 716 GLN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 ASN D 570 ASN ** E 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN F 662 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.174065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.145269 restraints weight = 22512.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148683 restraints weight = 15772.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151064 restraints weight = 12251.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152618 restraints weight = 10201.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153857 restraints weight = 8936.908| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16932 Z= 0.144 Angle : 0.552 8.001 22986 Z= 0.286 Chirality : 0.046 0.200 2628 Planarity : 0.004 0.071 2988 Dihedral : 4.643 17.435 2370 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.32 % Allowed : 18.50 % Favored : 78.18 % 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 are not related in a simple way. whole: -2.13 (0.18), residues: 2166 helix: -2.43 (0.29), residues: 240 sheet: -1.28 (0.17), residues: 864 loop : -1.12 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 797 TYR 0.019 0.002 TYR E 814 PHE 0.024 0.002 PHE E 833 TRP 0.025 0.002 TRP F 809 HIS 0.002 0.001 HIS C 558 Details of bonding type rmsd covalent geometry : bond 0.00346 (16932) covalent geometry : angle 0.55184 (22986) hydrogen bonds : bond 0.03091 ( 427) hydrogen bonds : angle 6.53473 ( 1050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 646 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7769 (mtmt) REVERT: A 716 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: B 517 VAL cc_start: 0.8968 (t) cc_final: 0.8559 (p) REVERT: B 746 ASP cc_start: 0.5820 (t0) cc_final: 0.5501 (t0) REVERT: B 809 TRP cc_start: 0.8588 (p90) cc_final: 0.8350 (p90) REVERT: B 830 PHE cc_start: 0.6332 (OUTLIER) cc_final: 0.5216 (p90) REVERT: B 842 THR cc_start: 0.8429 (m) cc_final: 0.8085 (p) REVERT: C 606 ASP cc_start: 0.7579 (t0) cc_final: 0.7354 (t0) REVERT: C 842 THR cc_start: 0.8597 (m) cc_final: 0.8145 (p) REVERT: D 606 ASP cc_start: 0.7865 (t0) cc_final: 0.7598 (t0) REVERT: D 646 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7753 (mtmt) REVERT: D 746 ASP cc_start: 0.6287 (t0) cc_final: 0.5786 (t0) REVERT: D 797 ARG cc_start: 0.8383 (mtm110) cc_final: 0.8099 (mtm110) REVERT: D 798 TYR cc_start: 0.8888 (m-80) cc_final: 0.8388 (m-80) REVERT: E 591 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: E 600 LYS cc_start: 0.4382 (OUTLIER) cc_final: 0.3509 (mmtt) REVERT: E 606 ASP cc_start: 0.7622 (t0) cc_final: 0.7299 (t0) REVERT: E 673 ASN cc_start: 0.7401 (p0) cc_final: 0.7146 (p0) REVERT: E 695 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7974 (mtp180) REVERT: E 809 TRP cc_start: 0.8639 (p90) cc_final: 0.8101 (p90) REVERT: E 816 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7209 (mm) REVERT: E 830 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.5689 (p90) REVERT: E 842 THR cc_start: 0.8396 (m) cc_final: 0.7999 (p) REVERT: F 771 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8668 (mt) REVERT: F 797 ARG cc_start: 0.8413 (mtm110) cc_final: 0.8049 (ttp-110) REVERT: F 816 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7192 (mt) REVERT: F 830 PHE cc_start: 0.5532 (OUTLIER) cc_final: 0.5283 (p90) REVERT: F 842 THR cc_start: 0.8712 (m) cc_final: 0.8359 (p) outliers start: 58 outliers final: 43 residues processed: 276 average time/residue: 0.1150 time to fit residues: 49.1958 Evaluate side-chains 290 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 235 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain E residue 591 GLN Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 642 PHE Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 830 PHE Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 711 LEU Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 740 THR Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 773 VAL Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain F residue 830 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 136 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 163 optimal weight: 0.0670 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 716 GLN A 853 GLN B 570 ASN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 662 GLN F 570 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.175351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148404 restraints weight = 22296.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151347 restraints weight = 16317.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.153377 restraints weight = 13003.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.154832 restraints weight = 11026.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.155903 restraints weight = 9757.088| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16932 Z= 0.115 Angle : 0.535 7.835 22986 Z= 0.277 Chirality : 0.045 0.209 2628 Planarity : 0.004 0.073 2988 Dihedral : 4.490 17.019 2370 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.98 % Allowed : 19.01 % Favored : 78.01 % 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 are not related in a simple way. whole: -2.05 (0.18), residues: 2166 helix: -2.34 (0.30), residues: 240 sheet: -1.23 (0.17), residues: 864 loop : -1.09 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 797 TYR 0.025 0.001 TYR B 814 PHE 0.020 0.001 PHE B 833 TRP 0.028 0.002 TRP C 809 HIS 0.002 0.000 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00279 (16932) covalent geometry : angle 0.53535 (22986) hydrogen bonds : bond 0.02918 ( 427) hydrogen bonds : angle 6.43089 ( 1050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 241 time to evaluate : 0.574 Fit side-chains REVERT: A 646 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7720 (mtmt) REVERT: A 716 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: A 797 ARG cc_start: 0.8297 (mtm110) cc_final: 0.8050 (ttp80) REVERT: B 538 PHE cc_start: 0.4294 (t80) cc_final: 0.4014 (t80) REVERT: B 746 ASP cc_start: 0.5789 (t0) cc_final: 0.5518 (t0) REVERT: B 809 TRP cc_start: 0.8557 (p90) cc_final: 0.8301 (p90) REVERT: B 830 PHE cc_start: 0.6450 (OUTLIER) cc_final: 0.5509 (p90) REVERT: B 842 THR cc_start: 0.8416 (m) cc_final: 0.8061 (p) REVERT: C 842 THR cc_start: 0.8615 (m) cc_final: 0.8157 (p) REVERT: D 606 ASP cc_start: 0.7760 (t0) cc_final: 0.7538 (t0) REVERT: D 646 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7698 (mtmt) REVERT: D 746 ASP cc_start: 0.6175 (t0) cc_final: 0.5705 (t0) REVERT: D 797 ARG cc_start: 0.8341 (mtm110) cc_final: 0.8017 (mtm110) REVERT: D 798 TYR cc_start: 0.8810 (m-80) cc_final: 0.8335 (m-80) REVERT: E 591 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: E 600 LYS cc_start: 0.4817 (OUTLIER) cc_final: 0.3632 (mmtt) REVERT: E 606 ASP cc_start: 0.7558 (t0) cc_final: 0.7268 (t0) REVERT: E 695 ARG cc_start: 0.8238 (mtm180) cc_final: 0.7911 (mtp180) REVERT: E 809 TRP cc_start: 0.8584 (p90) cc_final: 0.8083 (p90) REVERT: E 816 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7172 (mm) REVERT: E 830 PHE cc_start: 0.6419 (OUTLIER) cc_final: 0.5785 (p90) REVERT: E 842 THR cc_start: 0.8375 (m) cc_final: 0.7972 (p) REVERT: F 771 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8675 (mt) REVERT: F 797 ARG cc_start: 0.8285 (mtm110) cc_final: 0.8005 (ttp-110) REVERT: F 816 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7158 (mt) REVERT: F 842 THR cc_start: 0.8673 (m) cc_final: 0.8290 (p) outliers start: 52 outliers final: 37 residues processed: 270 average time/residue: 0.1236 time to fit residues: 51.2797 Evaluate side-chains 279 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain E residue 591 GLN Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 830 PHE Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 740 THR Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 773 VAL Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 164 optimal weight: 0.5980 chunk 206 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 86 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 214 optimal weight: 0.0040 chunk 129 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 GLN B 570 ASN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 853 GLN E 662 GLN F 570 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.178161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144595 restraints weight = 22846.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149517 restraints weight = 13828.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.152901 restraints weight = 9857.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155154 restraints weight = 7771.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.156837 restraints weight = 6544.755| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16932 Z= 0.119 Angle : 0.541 7.471 22986 Z= 0.280 Chirality : 0.045 0.207 2628 Planarity : 0.004 0.071 2988 Dihedral : 4.408 16.794 2370 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.69 % Allowed : 19.76 % Favored : 77.55 % 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 are not related in a simple way. whole: -2.00 (0.18), residues: 2166 helix: -2.25 (0.30), residues: 240 sheet: -1.19 (0.17), residues: 864 loop : -1.06 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 797 TYR 0.028 0.001 TYR E 814 PHE 0.022 0.001 PHE F 833 TRP 0.030 0.002 TRP C 809 HIS 0.002 0.001 HIS C 558 Details of bonding type rmsd covalent geometry : bond 0.00290 (16932) covalent geometry : angle 0.54099 (22986) hydrogen bonds : bond 0.02889 ( 427) hydrogen bonds : angle 6.39944 ( 1050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4332 Ramachandran restraints generated. 2166 Oldfield, 0 Emsley, 2166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 241 time to evaluate : 0.615 Fit side-chains REVERT: A 606 ASP cc_start: 0.7788 (t0) cc_final: 0.7384 (t0) REVERT: A 646 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7767 (mtmt) REVERT: A 716 GLN cc_start: 0.8206 (pm20) cc_final: 0.7832 (pm20) REVERT: A 797 ARG cc_start: 0.8390 (mtm110) cc_final: 0.8091 (ttp80) REVERT: B 538 PHE cc_start: 0.4238 (t80) cc_final: 0.3976 (t80) REVERT: B 746 ASP cc_start: 0.6006 (t0) cc_final: 0.5691 (t0) REVERT: B 809 TRP cc_start: 0.8600 (p90) cc_final: 0.8319 (p90) REVERT: B 830 PHE cc_start: 0.6354 (OUTLIER) cc_final: 0.5351 (p90) REVERT: B 842 THR cc_start: 0.8454 (m) cc_final: 0.8182 (p) REVERT: C 842 THR cc_start: 0.8645 (m) cc_final: 0.8186 (p) REVERT: D 606 ASP cc_start: 0.7932 (t0) cc_final: 0.7690 (t0) REVERT: D 646 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7754 (mtmt) REVERT: D 746 ASP cc_start: 0.6373 (t0) cc_final: 0.5848 (t0) REVERT: D 797 ARG cc_start: 0.8443 (mtm110) cc_final: 0.8092 (mtm110) REVERT: D 798 TYR cc_start: 0.8884 (m-80) cc_final: 0.8352 (m-80) REVERT: E 591 GLN cc_start: 0.8411 (pt0) cc_final: 0.8145 (pt0) REVERT: E 600 LYS cc_start: 0.4604 (OUTLIER) cc_final: 0.3448 (mmtt) REVERT: E 606 ASP cc_start: 0.7678 (t0) cc_final: 0.7316 (t0) REVERT: E 695 ARG cc_start: 0.8270 (mtm180) cc_final: 0.7916 (mtp180) REVERT: E 804 ASN cc_start: 0.8878 (t0) cc_final: 0.8662 (t0) REVERT: E 809 TRP cc_start: 0.8649 (p90) cc_final: 0.8097 (p90) REVERT: E 816 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7154 (mm) REVERT: E 830 PHE cc_start: 0.6346 (OUTLIER) cc_final: 0.5625 (p90) REVERT: E 842 THR cc_start: 0.8371 (m) cc_final: 0.7964 (p) REVERT: F 606 ASP cc_start: 0.7777 (t0) cc_final: 0.7568 (t0) REVERT: F 771 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8593 (mt) REVERT: F 797 ARG cc_start: 0.8413 (mtm110) cc_final: 0.8134 (ttp-110) REVERT: F 816 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7098 (mt) REVERT: F 830 PHE cc_start: 0.5347 (OUTLIER) cc_final: 0.5014 (p90) REVERT: F 842 THR cc_start: 0.8692 (m) cc_final: 0.8304 (p) outliers start: 47 outliers final: 37 residues processed: 268 average time/residue: 0.1168 time to fit residues: 49.0010 Evaluate side-chains 284 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 580 LYS Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 646 LYS Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 780 THR Chi-restraints excluded: chain E residue 788 VAL Chi-restraints excluded: chain E residue 816 LEU Chi-restraints excluded: chain E residue 830 PHE Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain E residue 859 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 740 THR Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 773 VAL Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain F residue 830 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 149 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 173 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 570 ASN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143512 restraints weight = 22816.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148459 restraints weight = 13795.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151722 restraints weight = 9825.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.154038 restraints weight = 7759.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155668 restraints weight = 6524.286| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16932 Z= 0.130 Angle : 0.557 12.411 22986 Z= 0.287 Chirality : 0.046 0.232 2628 Planarity : 0.004 0.048 2988 Dihedral : 4.397 17.938 2370 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.98 % Allowed : 19.93 % Favored : 77.09 % 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 are not related in a simple way. whole: -1.93 (0.18), residues: 2166 helix: -2.15 (0.30), residues: 240 sheet: -1.18 (0.17), residues: 864 loop : -1.01 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 797 TYR 0.023 0.001 TYR B 814 PHE 0.031 0.002 PHE E 833 TRP 0.030 0.002 TRP C 809 HIS 0.002 0.001 HIS A 558 Details of bonding type rmsd covalent geometry : bond 0.00313 (16932) covalent geometry : angle 0.55721 (22986) hydrogen bonds : bond 0.02921 ( 427) hydrogen bonds : angle 6.38569 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2629.88 seconds wall clock time: 45 minutes 59.85 seconds (2759.85 seconds total)