Starting phenix.real_space_refine on Sat Jun 14 23:18:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v0h_20998/06_2025/6v0h_20998.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v0h_20998/06_2025/6v0h_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_20998/06_2025/6v0h_20998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v0h_20998/06_2025/6v0h_20998.map" model { file = "/net/cci-nas-00/data/ceres_data/6v0h_20998/06_2025/6v0h_20998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v0h_20998/06_2025/6v0h_20998.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.68, per 1000 atoms: 0.58 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: 4.87 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.26 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: 5.97 Time building geometry restraints manager: 5.67 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 41.610 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.120 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (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 TRP 0.018 0.003 TRP A 574 HIS 0.006 0.002 HIS A 558 PHE 0.038 0.003 PHE C 605 TYR 0.013 0.003 TYR A 798 ARG 0.004 0.001 ARG E 793 Details of bonding type rmsd hydrogen bonds : bond 0.29367 ( 427) hydrogen bonds : angle 10.12607 ( 1050) covalent geometry : bond 0.00510 (16932) covalent geometry : angle 0.84493 (22986) *********************** 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 : 1.866 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: 0.3692 time to fit residues: 285.8079 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 : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 0.0970 chunk 169 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.181634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.148992 restraints weight = 22536.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153454 restraints weight = 14585.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.156575 restraints weight = 10793.858| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16932 Z= 0.143 Angle : 0.625 7.212 22986 Z= 0.333 Chirality : 0.047 0.154 2628 Planarity : 0.005 0.044 2988 Dihedral : 5.364 21.817 2370 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.23 % Allowed : 12.20 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.16), residues: 2166 helix: -3.63 (0.25), residues: 240 sheet: -1.63 (0.17), residues: 774 loop : -2.07 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 809 HIS 0.003 0.001 HIS C 640 PHE 0.022 0.001 PHE F 833 TYR 0.017 0.002 TYR B 624 ARG 0.008 0.001 ARG C 869 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 427) hydrogen bonds : angle 7.55141 ( 1050) covalent geometry : bond 0.00322 (16932) covalent geometry : angle 0.62462 (22986) *********************** 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 365 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 326 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7600 (mtmt) REVERT: A 716 GLN cc_start: 0.8265 (tt0) cc_final: 0.7856 (pt0) REVERT: A 746 ASP cc_start: 0.6571 (t0) cc_final: 0.6219 (t0) REVERT: A 798 TYR cc_start: 0.8875 (m-80) cc_final: 0.8555 (m-80) REVERT: B 746 ASP cc_start: 0.6441 (t0) cc_final: 0.6043 (t0) REVERT: B 762 ILE cc_start: 0.8820 (mp) cc_final: 0.8608 (mp) REVERT: B 797 ARG cc_start: 0.8199 (mtm110) cc_final: 0.7965 (mtm110) REVERT: B 798 TYR cc_start: 0.8711 (m-80) cc_final: 0.8043 (m-80) REVERT: B 842 THR cc_start: 0.7982 (m) cc_final: 0.7514 (p) REVERT: C 749 SER cc_start: 0.8882 (t) cc_final: 0.8597 (m) REVERT: D 646 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7611 (mtmt) REVERT: D 745 LEU cc_start: 0.8262 (mt) cc_final: 0.8047 (mt) REVERT: D 746 ASP cc_start: 0.6416 (t0) cc_final: 0.5947 (t0) REVERT: D 762 ILE cc_start: 0.8829 (mp) cc_final: 0.8617 (mm) REVERT: D 797 ARG cc_start: 0.8255 (mtm110) cc_final: 0.7892 (mtm110) REVERT: D 798 TYR cc_start: 0.8891 (m-80) cc_final: 0.8219 (m-80) REVERT: E 518 SER cc_start: 0.9073 (m) cc_final: 0.8742 (t) REVERT: E 762 ILE cc_start: 0.8885 (mp) cc_final: 0.8685 (mp) REVERT: E 798 TYR cc_start: 0.8600 (m-10) cc_final: 0.8315 (m-10) REVERT: E 809 TRP cc_start: 0.8576 (p90) cc_final: 0.8272 (p90) REVERT: E 842 THR cc_start: 0.8312 (m) cc_final: 0.7877 (p) REVERT: F 518 SER cc_start: 0.8986 (m) cc_final: 0.8774 (t) REVERT: F 842 THR cc_start: 0.8276 (m) cc_final: 0.7898 (p) outliers start: 39 outliers final: 22 residues processed: 339 average time/residue: 0.2995 time to fit residues: 147.4853 Evaluate side-chains 303 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 279 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 87 optimal weight: 0.7980 chunk 114 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 662 GLN B 662 GLN B 832 GLN C 662 GLN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN D 662 GLN E 570 ASN E 662 GLN E 716 GLN F 662 GLN ** F 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.173191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.142226 restraints weight = 22463.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.146105 restraints weight = 15184.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148722 restraints weight = 11528.048| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16932 Z= 0.226 Angle : 0.646 7.799 22986 Z= 0.341 Chirality : 0.048 0.170 2628 Planarity : 0.005 0.044 2988 Dihedral : 5.364 21.562 2370 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.78 % Allowed : 13.46 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.17), residues: 2166 helix: -3.24 (0.26), residues: 240 sheet: -1.56 (0.17), residues: 822 loop : -1.75 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 809 HIS 0.005 0.001 HIS C 558 PHE 0.025 0.002 PHE B 833 TYR 0.019 0.002 TYR F 624 ARG 0.008 0.001 ARG D 691 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 427) hydrogen bonds : angle 7.20158 ( 1050) covalent geometry : bond 0.00542 (16932) covalent geometry : angle 0.64631 (22986) *********************** 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 361 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 295 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: A 646 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7771 (mtmt) REVERT: A 751 ILE cc_start: 0.8822 (mm) cc_final: 0.8548 (mt) REVERT: A 798 TYR cc_start: 0.8950 (m-80) cc_final: 0.8329 (m-80) REVERT: B 746 ASP cc_start: 0.5989 (t0) cc_final: 0.5594 (t0) REVERT: B 797 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7757 (mtm110) REVERT: B 798 TYR cc_start: 0.8823 (m-80) cc_final: 0.7968 (m-80) REVERT: B 842 THR cc_start: 0.8321 (m) cc_final: 0.7961 (p) REVERT: C 771 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8874 (mt) REVERT: C 835 ARG cc_start: 0.7114 (mtt180) cc_final: 0.6340 (mtm110) REVERT: C 842 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.7932 (p) REVERT: D 646 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7767 (mtmt) REVERT: D 714 ILE cc_start: 0.8113 (mt) cc_final: 0.7654 (pt) REVERT: D 746 ASP cc_start: 0.6403 (t0) cc_final: 0.5871 (t0) REVERT: D 756 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7164 (mt-10) REVERT: D 797 ARG cc_start: 0.8369 (mtm110) cc_final: 0.8133 (mtm110) REVERT: D 798 TYR cc_start: 0.8894 (m-80) cc_final: 0.8350 (m-80) REVERT: D 853 GLN cc_start: 0.7826 (mm110) cc_final: 0.7321 (mp10) REVERT: E 518 SER cc_start: 0.9107 (m) cc_final: 0.8871 (t) REVERT: E 547 ARG cc_start: 0.7570 (ttp80) cc_final: 0.7351 (ttp-110) REVERT: E 591 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: E 673 ASN cc_start: 0.7637 (p0) cc_final: 0.7372 (p0) REVERT: E 695 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7946 (mtp180) REVERT: E 809 TRP cc_start: 0.8662 (p90) cc_final: 0.8253 (p90) REVERT: E 842 THR cc_start: 0.8365 (m) cc_final: 0.8025 (p) REVERT: F 835 ARG cc_start: 0.6795 (mpp80) cc_final: 0.6354 (mpp80) REVERT: F 842 THR cc_start: 0.8577 (m) cc_final: 0.8190 (p) outliers start: 66 outliers final: 35 residues processed: 325 average time/residue: 0.2887 time to fit residues: 139.8379 Evaluate side-chains 304 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 628 THR 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 628 THR 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 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 569 SER 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 771 LEU Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 842 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 646 LYS 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 714 ILE 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 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 121 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 662 GLN A 716 GLN A 853 GLN C 662 GLN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN D 662 GLN E 662 GLN ** E 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN ** F 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 804 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.173318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.144693 restraints weight = 22350.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148072 restraints weight = 15689.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150452 restraints weight = 12207.817| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16932 Z= 0.163 Angle : 0.586 7.823 22986 Z= 0.306 Chirality : 0.046 0.164 2628 Planarity : 0.005 0.045 2988 Dihedral : 5.092 17.358 2370 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.49 % Allowed : 15.69 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.17), residues: 2166 helix: -3.01 (0.27), residues: 240 sheet: -1.56 (0.16), residues: 864 loop : -1.47 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 809 HIS 0.003 0.001 HIS C 558 PHE 0.024 0.002 PHE E 833 TYR 0.016 0.002 TYR C 814 ARG 0.010 0.001 ARG A 695 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 427) hydrogen bonds : angle 6.87692 ( 1050) covalent geometry : bond 0.00387 (16932) covalent geometry : angle 0.58644 (22986) *********************** 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 337 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 646 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7796 (mtmt) REVERT: A 751 ILE cc_start: 0.8810 (mm) cc_final: 0.8543 (mt) REVERT: A 779 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7663 (ttm) REVERT: B 606 ASP cc_start: 0.7763 (t0) cc_final: 0.7490 (t0) REVERT: B 695 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.7771 (ttm110) REVERT: B 746 ASP cc_start: 0.6066 (t0) cc_final: 0.5666 (t0) REVERT: B 797 ARG cc_start: 0.8146 (mtm110) cc_final: 0.7898 (mtm110) REVERT: B 830 PHE cc_start: 0.6214 (OUTLIER) cc_final: 0.5069 (p90) REVERT: B 842 THR cc_start: 0.8324 (m) cc_final: 0.7970 (p) REVERT: C 606 ASP cc_start: 0.7610 (t0) cc_final: 0.7389 (t0) REVERT: C 735 GLN cc_start: 0.8249 (mt0) cc_final: 0.8015 (mt0) REVERT: C 835 ARG cc_start: 0.7095 (mtt180) cc_final: 0.6823 (mpp80) REVERT: C 842 THR cc_start: 0.8468 (m) cc_final: 0.8005 (p) REVERT: D 646 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7751 (mtmt) REVERT: D 746 ASP cc_start: 0.6406 (t0) cc_final: 0.5875 (t0) REVERT: D 798 TYR cc_start: 0.8921 (m-80) cc_final: 0.8467 (m-80) REVERT: E 518 SER cc_start: 0.9036 (m) cc_final: 0.8789 (t) REVERT: E 591 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8244 (pt0) REVERT: E 673 ASN cc_start: 0.7611 (p0) cc_final: 0.7379 (p0) REVERT: E 695 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7932 (mtp180) REVERT: E 809 TRP cc_start: 0.8615 (p90) cc_final: 0.8173 (p90) REVERT: E 842 THR cc_start: 0.8316 (m) cc_final: 0.7949 (p) REVERT: F 809 TRP cc_start: 0.8856 (p90) cc_final: 0.8566 (p90) REVERT: F 835 ARG cc_start: 0.6759 (mpp80) cc_final: 0.6418 (mpp80) REVERT: F 842 THR cc_start: 0.8609 (m) cc_final: 0.8244 (p) outliers start: 61 outliers final: 39 residues processed: 305 average time/residue: 0.2913 time to fit residues: 132.5982 Evaluate side-chains 292 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 779 MET 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 714 ILE 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 830 PHE Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 714 ILE 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 C residue 816 LEU Chi-restraints excluded: chain D residue 569 SER 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 780 THR Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain D residue 838 ILE Chi-restraints excluded: chain E residue 591 GLN 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 859 LEU 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 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 160 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 154 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 198 optimal weight: 0.0980 chunk 88 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 188 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 B 662 GLN C 702 GLN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN E 716 GLN F 662 GLN F 702 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.175247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.146418 restraints weight = 22703.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.149887 restraints weight = 15809.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152208 restraints weight = 12225.893| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16932 Z= 0.114 Angle : 0.545 8.820 22986 Z= 0.283 Chirality : 0.046 0.155 2628 Planarity : 0.004 0.041 2988 Dihedral : 4.803 17.797 2370 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.09 % Allowed : 16.78 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.17), residues: 2166 helix: -2.84 (0.28), residues: 240 sheet: -1.42 (0.17), residues: 864 loop : -1.33 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 809 HIS 0.002 0.001 HIS C 558 PHE 0.021 0.001 PHE E 833 TYR 0.011 0.001 TYR E 814 ARG 0.007 0.000 ARG F 797 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 427) hydrogen bonds : angle 6.64081 ( 1050) covalent geometry : bond 0.00268 (16932) covalent geometry : angle 0.54550 (22986) *********************** 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 324 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 270 time to evaluate : 1.711 Fit side-chains revert: symmetry clash REVERT: A 646 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7796 (mtmt) REVERT: A 751 ILE cc_start: 0.8779 (mm) cc_final: 0.8527 (mt) REVERT: A 779 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7614 (ttm) REVERT: B 606 ASP cc_start: 0.7753 (t0) cc_final: 0.7451 (t0) REVERT: B 695 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.7678 (ttm110) REVERT: B 712 ASP cc_start: 0.7691 (p0) cc_final: 0.7455 (p0) REVERT: B 746 ASP cc_start: 0.6037 (t0) cc_final: 0.5546 (t0) REVERT: B 809 TRP cc_start: 0.8652 (p90) cc_final: 0.8080 (p90) REVERT: B 842 THR cc_start: 0.8400 (m) cc_final: 0.8010 (p) REVERT: C 606 ASP cc_start: 0.7681 (t0) cc_final: 0.7422 (t0) REVERT: C 779 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7778 (ttt) REVERT: C 786 ASP cc_start: 0.7681 (m-30) cc_final: 0.7421 (m-30) REVERT: C 814 TYR cc_start: 0.7387 (m-10) cc_final: 0.7118 (m-10) REVERT: C 833 PHE cc_start: 0.7148 (t80) cc_final: 0.6692 (t80) REVERT: C 842 THR cc_start: 0.8481 (m) cc_final: 0.7994 (p) REVERT: D 646 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7751 (mtmt) REVERT: D 746 ASP cc_start: 0.6432 (t0) cc_final: 0.5905 (t0) REVERT: E 518 SER cc_start: 0.8999 (m) cc_final: 0.8715 (t) REVERT: E 591 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8197 (pt0) REVERT: E 600 LYS cc_start: 0.4384 (OUTLIER) cc_final: 0.3519 (mmtt) REVERT: E 606 ASP cc_start: 0.7426 (t0) cc_final: 0.7142 (t0) REVERT: E 695 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7911 (mtp180) REVERT: E 809 TRP cc_start: 0.8616 (p90) cc_final: 0.8153 (p90) REVERT: E 833 PHE cc_start: 0.6238 (t80) cc_final: 0.6025 (t80) REVERT: E 842 THR cc_start: 0.8326 (m) cc_final: 0.7934 (p) REVERT: F 695 ARG cc_start: 0.7996 (mtp180) cc_final: 0.7751 (mtp-110) REVERT: F 771 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8638 (mt) REVERT: F 809 TRP cc_start: 0.8854 (p90) cc_final: 0.8577 (p90) REVERT: F 842 THR cc_start: 0.8597 (m) cc_final: 0.8227 (p) outliers start: 54 outliers final: 33 residues processed: 300 average time/residue: 0.2796 time to fit residues: 125.9314 Evaluate side-chains 291 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 251 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 816 LEU 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 569 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 646 LYS 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 600 LYS Chi-restraints excluded: chain E residue 714 ILE 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 569 SER Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 727 ASN Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 780 THR Chi-restraints excluded: chain F residue 816 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 36 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 0.0670 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 662 GLN A 716 GLN A 853 GLN B 570 ASN B 662 GLN C 662 GLN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 ASN D 570 ASN D 662 GLN E 662 GLN F 570 ASN F 662 GLN F 702 GLN ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.170742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141799 restraints weight = 22713.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145089 restraints weight = 16000.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147353 restraints weight = 12516.498| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16932 Z= 0.194 Angle : 0.601 8.341 22986 Z= 0.314 Chirality : 0.047 0.159 2628 Planarity : 0.004 0.042 2988 Dihedral : 4.983 16.742 2370 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.12 % Allowed : 16.72 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.18), residues: 2166 helix: -2.70 (0.28), residues: 240 sheet: -1.47 (0.17), residues: 864 loop : -1.25 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 809 HIS 0.004 0.001 HIS C 800 PHE 0.021 0.002 PHE E 833 TYR 0.013 0.002 TYR E 624 ARG 0.007 0.000 ARG F 797 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 427) hydrogen bonds : angle 6.72644 ( 1050) covalent geometry : bond 0.00467 (16932) covalent geometry : angle 0.60125 (22986) *********************** 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 325 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 253 time to evaluate : 2.471 Fit side-chains revert: symmetry clash REVERT: A 646 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7788 (mtmt) REVERT: A 746 ASP cc_start: 0.6328 (t0) cc_final: 0.6124 (t0) REVERT: A 779 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7597 (ttm) REVERT: B 695 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.7727 (ttm110) REVERT: B 714 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7112 (pt) REVERT: B 746 ASP cc_start: 0.5770 (t0) cc_final: 0.5493 (t0) REVERT: B 830 PHE cc_start: 0.6461 (OUTLIER) cc_final: 0.5399 (p90) REVERT: B 842 THR cc_start: 0.8464 (m) cc_final: 0.8144 (p) REVERT: C 779 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7806 (ttt) REVERT: C 786 ASP cc_start: 0.7807 (m-30) cc_final: 0.7577 (m-30) REVERT: C 842 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8183 (p) REVERT: D 646 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7769 (mtmt) REVERT: D 746 ASP cc_start: 0.6370 (t0) cc_final: 0.5897 (t0) REVERT: E 591 GLN cc_start: 0.8513 (pt0) cc_final: 0.8272 (pt0) REVERT: E 600 LYS cc_start: 0.5072 (OUTLIER) cc_final: 0.3719 (mmtt) REVERT: E 606 ASP cc_start: 0.7722 (t0) cc_final: 0.7397 (t0) REVERT: E 809 TRP cc_start: 0.8654 (p90) cc_final: 0.8157 (p90) REVERT: E 816 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7239 (mm) REVERT: E 830 PHE cc_start: 0.6440 (OUTLIER) cc_final: 0.5779 (p90) REVERT: E 842 THR cc_start: 0.8391 (m) cc_final: 0.8057 (p) REVERT: F 771 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8733 (mt) REVERT: F 786 ASP cc_start: 0.7675 (t0) cc_final: 0.7444 (t0) REVERT: F 816 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7241 (mt) REVERT: F 842 THR cc_start: 0.8689 (m) cc_final: 0.8331 (p) outliers start: 72 outliers final: 47 residues processed: 296 average time/residue: 0.3042 time to fit residues: 139.9686 Evaluate side-chains 301 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 242 time to evaluate : 2.751 ------------------------------------------------------------------------------- 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 670 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 868 TRP Chi-restraints excluded: chain B residue 628 THR 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 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 B residue 868 TRP 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 779 MET 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 727 ASN 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 788 VAL Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain D residue 838 ILE 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 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 145 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 102 optimal weight: 0.0060 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 662 GLN A 716 GLN A 853 GLN C 662 GLN ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 GLN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN D 662 GLN ** E 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.172610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143852 restraints weight = 22572.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147190 restraints weight = 15781.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.149544 restraints weight = 12287.316| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4497 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= 0.132 Angle : 0.564 9.079 22986 Z= 0.292 Chirality : 0.046 0.175 2628 Planarity : 0.004 0.041 2988 Dihedral : 4.753 16.996 2370 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.15 % Allowed : 18.61 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.18), residues: 2166 helix: -2.57 (0.29), residues: 240 sheet: -1.38 (0.17), residues: 864 loop : -1.19 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 809 HIS 0.002 0.001 HIS C 558 PHE 0.025 0.001 PHE B 833 TYR 0.012 0.001 TYR E 814 ARG 0.008 0.000 ARG A 797 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 427) hydrogen bonds : angle 6.59057 ( 1050) covalent geometry : bond 0.00319 (16932) covalent geometry : angle 0.56377 (22986) *********************** 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 300 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 1.804 Fit side-chains REVERT: A 646 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7792 (mtmt) REVERT: A 751 ILE cc_start: 0.8887 (mm) cc_final: 0.8648 (mt) REVERT: A 779 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7607 (ttm) REVERT: B 695 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7708 (ttm110) REVERT: B 746 ASP cc_start: 0.6019 (t0) cc_final: 0.5685 (t0) REVERT: B 830 PHE cc_start: 0.6329 (OUTLIER) cc_final: 0.5464 (p90) REVERT: B 833 PHE cc_start: 0.5976 (t80) cc_final: 0.5733 (t80) REVERT: B 842 THR cc_start: 0.8452 (m) cc_final: 0.8122 (p) REVERT: C 606 ASP cc_start: 0.7550 (t0) cc_final: 0.7308 (t0) REVERT: C 779 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7862 (ttp) REVERT: C 842 THR cc_start: 0.8643 (m) cc_final: 0.8183 (p) REVERT: D 646 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7766 (mtmt) REVERT: D 746 ASP cc_start: 0.6427 (t0) cc_final: 0.5917 (t0) REVERT: E 591 GLN cc_start: 0.8495 (pt0) cc_final: 0.8260 (pt0) REVERT: E 600 LYS cc_start: 0.4881 (OUTLIER) cc_final: 0.3563 (mmtt) REVERT: E 606 ASP cc_start: 0.7732 (t0) cc_final: 0.7404 (t0) REVERT: E 673 ASN cc_start: 0.7649 (p0) cc_final: 0.7387 (p0) REVERT: E 695 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7901 (mtp180) REVERT: E 809 TRP cc_start: 0.8645 (p90) cc_final: 0.8100 (p90) REVERT: E 816 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7187 (mm) REVERT: E 830 PHE cc_start: 0.6240 (OUTLIER) cc_final: 0.5745 (p90) REVERT: E 842 THR cc_start: 0.8381 (m) cc_final: 0.7998 (p) REVERT: F 771 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8697 (mt) REVERT: F 816 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7199 (mt) REVERT: F 842 THR cc_start: 0.8674 (m) cc_final: 0.8289 (p) outliers start: 55 outliers final: 37 residues processed: 277 average time/residue: 0.2614 time to fit residues: 111.4772 Evaluate side-chains 286 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 1.829 ------------------------------------------------------------------------------- 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 779 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 868 TRP 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 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 B residue 868 TRP Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 608 LEU 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 780 THR Chi-restraints excluded: chain E residue 600 LYS 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 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 215 optimal weight: 0.0370 chunk 117 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 163 optimal weight: 0.0970 chunk 87 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 overall best weight: 0.8060 ------------------------------------------------------------------------------- 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 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN F 716 GLN ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.173930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.142667 restraints weight = 22722.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.147171 restraints weight = 13840.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150203 restraints weight = 9889.829| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16932 Z= 0.148 Angle : 0.566 7.829 22986 Z= 0.294 Chirality : 0.046 0.154 2628 Planarity : 0.004 0.042 2988 Dihedral : 4.729 17.198 2370 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.55 % Allowed : 18.56 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.18), residues: 2166 helix: -2.47 (0.29), residues: 240 sheet: -1.37 (0.17), residues: 864 loop : -1.15 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 809 HIS 0.002 0.001 HIS C 558 PHE 0.030 0.002 PHE E 833 TYR 0.024 0.002 TYR C 814 ARG 0.007 0.000 ARG F 797 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 427) hydrogen bonds : angle 6.54156 ( 1050) covalent geometry : bond 0.00359 (16932) covalent geometry : angle 0.56587 (22986) *********************** 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 313 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 251 time to evaluate : 1.663 Fit side-chains REVERT: A 646 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7814 (mtmt) REVERT: A 695 ARG cc_start: 0.8098 (mtp180) cc_final: 0.7366 (mtp-110) REVERT: A 779 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7656 (ttm) REVERT: B 695 ARG cc_start: 0.8242 (mmm-85) cc_final: 0.7742 (ttm110) REVERT: B 746 ASP cc_start: 0.5964 (t0) cc_final: 0.5674 (t0) REVERT: B 830 PHE cc_start: 0.6318 (OUTLIER) cc_final: 0.5302 (p90) REVERT: B 842 THR cc_start: 0.8435 (m) cc_final: 0.8118 (p) REVERT: C 606 ASP cc_start: 0.7576 (t0) cc_final: 0.7374 (t0) REVERT: C 779 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7891 (ttp) REVERT: C 842 THR cc_start: 0.8678 (m) cc_final: 0.8233 (p) REVERT: D 646 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7797 (mtmt) REVERT: D 746 ASP cc_start: 0.6553 (t0) cc_final: 0.6017 (t0) REVERT: E 591 GLN cc_start: 0.8442 (pt0) cc_final: 0.8199 (pt0) REVERT: E 600 LYS cc_start: 0.4922 (OUTLIER) cc_final: 0.3586 (mmtt) REVERT: E 606 ASP cc_start: 0.7814 (t0) cc_final: 0.7421 (t0) REVERT: E 673 ASN cc_start: 0.7719 (p0) cc_final: 0.7454 (p0) REVERT: E 695 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7930 (mtp180) REVERT: E 738 THR cc_start: 0.6592 (OUTLIER) cc_final: 0.6127 (p) REVERT: E 816 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7211 (mm) REVERT: E 830 PHE cc_start: 0.6301 (OUTLIER) cc_final: 0.5646 (p90) REVERT: E 842 THR cc_start: 0.8370 (m) cc_final: 0.7995 (p) REVERT: F 771 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8709 (mt) REVERT: F 786 ASP cc_start: 0.7803 (t0) cc_final: 0.7590 (t0) REVERT: F 816 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7165 (mt) REVERT: F 842 THR cc_start: 0.8641 (m) cc_final: 0.8269 (p) outliers start: 62 outliers final: 42 residues processed: 291 average time/residue: 0.2621 time to fit residues: 117.4657 Evaluate side-chains 297 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 243 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 670 THR Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 868 TRP 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 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 B residue 868 TRP Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 816 LEU 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 780 THR Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain D residue 838 ILE Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 738 THR 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 780 THR Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain F residue 859 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 8 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 154 optimal weight: 0.3980 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 C 702 GLN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 853 GLN ** E 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.172574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141176 restraints weight = 22738.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.145639 restraints weight = 13926.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148693 restraints weight = 10012.764| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16932 Z= 0.169 Angle : 0.580 8.357 22986 Z= 0.303 Chirality : 0.046 0.219 2628 Planarity : 0.004 0.044 2988 Dihedral : 4.782 16.924 2370 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.72 % Allowed : 18.44 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.18), residues: 2166 helix: -2.39 (0.30), residues: 240 sheet: -1.37 (0.17), residues: 864 loop : -1.10 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 809 HIS 0.002 0.001 HIS E 558 PHE 0.027 0.002 PHE C 833 TYR 0.020 0.002 TYR B 814 ARG 0.009 0.000 ARG F 797 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 427) hydrogen bonds : angle 6.60306 ( 1050) covalent geometry : bond 0.00408 (16932) covalent geometry : angle 0.57977 (22986) *********************** 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 309 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 244 time to evaluate : 1.855 Fit side-chains REVERT: A 646 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7817 (mtmt) REVERT: B 695 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7767 (ttm110) REVERT: B 746 ASP cc_start: 0.5979 (t0) cc_final: 0.5688 (t0) REVERT: B 830 PHE cc_start: 0.6441 (OUTLIER) cc_final: 0.5461 (p90) REVERT: B 842 THR cc_start: 0.8449 (m) cc_final: 0.8133 (p) REVERT: C 779 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7938 (ttp) REVERT: C 842 THR cc_start: 0.8742 (m) cc_final: 0.8316 (p) REVERT: D 646 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7782 (mtmt) REVERT: D 746 ASP cc_start: 0.6558 (t0) cc_final: 0.6031 (t0) REVERT: D 797 ARG cc_start: 0.8413 (mtm110) cc_final: 0.8187 (ttp80) REVERT: E 591 GLN cc_start: 0.8421 (pt0) cc_final: 0.8181 (pt0) REVERT: E 600 LYS cc_start: 0.5004 (OUTLIER) cc_final: 0.3654 (mmtt) REVERT: E 606 ASP cc_start: 0.7804 (t0) cc_final: 0.7433 (t0) REVERT: E 673 ASN cc_start: 0.7727 (p0) cc_final: 0.7461 (p0) REVERT: E 695 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7992 (mtp180) REVERT: E 738 THR cc_start: 0.6588 (OUTLIER) cc_final: 0.6129 (p) REVERT: E 809 TRP cc_start: 0.8620 (p90) cc_final: 0.8044 (p90) REVERT: E 816 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7192 (mm) REVERT: E 830 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.5678 (p90) REVERT: E 842 THR cc_start: 0.8378 (m) cc_final: 0.8009 (p) REVERT: F 771 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8722 (mt) REVERT: F 816 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7148 (mt) REVERT: F 842 THR cc_start: 0.8692 (m) cc_final: 0.8332 (p) outliers start: 65 outliers final: 48 residues processed: 287 average time/residue: 0.2569 time to fit residues: 114.5223 Evaluate side-chains 298 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 239 time to evaluate : 1.857 ------------------------------------------------------------------------------- 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 670 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 868 TRP Chi-restraints excluded: chain B residue 628 THR 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 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 B residue 868 TRP Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 779 MET 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 608 LEU 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 780 THR Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain D residue 838 ILE Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 738 THR 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 E residue 868 TRP 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 859 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 165 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 179 optimal weight: 0.0030 chunk 16 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 853 GLN F 570 ASN ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.173573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142264 restraints weight = 22708.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.146705 restraints weight = 13870.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149785 restraints weight = 9936.596| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16932 Z= 0.140 Angle : 0.569 7.404 22986 Z= 0.297 Chirality : 0.046 0.226 2628 Planarity : 0.004 0.047 2988 Dihedral : 4.700 17.944 2370 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.55 % Allowed : 18.84 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.18), residues: 2166 helix: -2.32 (0.30), residues: 240 sheet: -1.33 (0.17), residues: 864 loop : -1.06 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 809 HIS 0.002 0.001 HIS C 558 PHE 0.029 0.002 PHE C 833 TYR 0.026 0.002 TYR B 814 ARG 0.009 0.000 ARG F 797 Details of bonding type rmsd hydrogen bonds : bond 0.03070 ( 427) hydrogen bonds : angle 6.55359 ( 1050) covalent geometry : bond 0.00340 (16932) covalent geometry : angle 0.56875 (22986) ********************** 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 309 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 247 time to evaluate : 1.916 Fit side-chains REVERT: A 646 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7805 (mtmt) REVERT: B 695 ARG cc_start: 0.8248 (mmm-85) cc_final: 0.7743 (ttm110) REVERT: B 746 ASP cc_start: 0.5992 (t0) cc_final: 0.5698 (t0) REVERT: B 830 PHE cc_start: 0.6423 (OUTLIER) cc_final: 0.5398 (p90) REVERT: B 842 THR cc_start: 0.8435 (m) cc_final: 0.8122 (p) REVERT: C 779 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7885 (ttp) REVERT: C 842 THR cc_start: 0.8746 (m) cc_final: 0.8306 (p) REVERT: D 646 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7774 (mtmt) REVERT: D 746 ASP cc_start: 0.6548 (t0) cc_final: 0.6025 (t0) REVERT: D 797 ARG cc_start: 0.8414 (mtm110) cc_final: 0.8200 (ttp80) REVERT: E 591 GLN cc_start: 0.8427 (pt0) cc_final: 0.8185 (pt0) REVERT: E 600 LYS cc_start: 0.5006 (OUTLIER) cc_final: 0.3661 (mmtt) REVERT: E 606 ASP cc_start: 0.7744 (t0) cc_final: 0.7524 (t0) REVERT: E 673 ASN cc_start: 0.7679 (p0) cc_final: 0.7422 (p0) REVERT: E 695 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7905 (mtp180) REVERT: E 738 THR cc_start: 0.6515 (OUTLIER) cc_final: 0.6120 (p) REVERT: E 809 TRP cc_start: 0.8631 (p90) cc_final: 0.8061 (p90) REVERT: E 816 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7189 (mm) REVERT: E 830 PHE cc_start: 0.6393 (OUTLIER) cc_final: 0.5712 (p90) REVERT: E 842 THR cc_start: 0.8368 (m) cc_final: 0.7995 (p) REVERT: F 771 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8714 (mt) REVERT: F 816 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7136 (mt) REVERT: F 842 THR cc_start: 0.8696 (m) cc_final: 0.8332 (p) outliers start: 62 outliers final: 50 residues processed: 287 average time/residue: 0.3264 time to fit residues: 147.5046 Evaluate side-chains 303 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 242 time to evaluate : 1.879 ------------------------------------------------------------------------------- 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 670 THR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 716 GLN Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 868 TRP Chi-restraints excluded: chain B residue 628 THR 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 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 B residue 868 TRP Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 727 ASN Chi-restraints excluded: chain C residue 779 MET 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 608 LEU 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 727 ASN Chi-restraints excluded: chain D residue 733 GLU Chi-restraints excluded: chain D residue 780 THR Chi-restraints excluded: chain D residue 788 VAL Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain D residue 838 ILE Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 695 ARG Chi-restraints excluded: chain E residue 727 ASN Chi-restraints excluded: chain E residue 738 THR 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 E residue 868 TRP 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 859 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.272 > 50: distance: 20 - 127: 15.870 distance: 31 - 130: 25.689 distance: 34 - 146: 11.024 distance: 89 - 95: 15.456 distance: 95 - 96: 9.769 distance: 96 - 97: 20.736 distance: 96 - 99: 7.844 distance: 97 - 98: 11.418 distance: 97 - 104: 5.950 distance: 99 - 100: 11.129 distance: 100 - 101: 12.087 distance: 101 - 102: 9.499 distance: 101 - 103: 15.224 distance: 104 - 105: 12.014 distance: 105 - 106: 11.567 distance: 106 - 107: 19.384 distance: 106 - 108: 13.558 distance: 108 - 109: 13.846 distance: 109 - 110: 8.432 distance: 110 - 111: 15.062 distance: 110 - 117: 14.358 distance: 112 - 113: 8.026 distance: 113 - 114: 6.617 distance: 115 - 116: 12.948 distance: 117 - 118: 14.532 distance: 118 - 119: 15.374 distance: 119 - 120: 13.437 distance: 119 - 127: 27.519 distance: 121 - 122: 16.148 distance: 122 - 123: 21.327 distance: 122 - 124: 12.095 distance: 123 - 125: 8.499 distance: 124 - 126: 15.531 distance: 125 - 126: 6.986 distance: 127 - 128: 20.656 distance: 128 - 129: 27.212 distance: 128 - 131: 19.451 distance: 129 - 130: 41.521 distance: 129 - 138: 9.342 distance: 131 - 132: 32.061 distance: 132 - 133: 11.824 distance: 132 - 134: 19.851 distance: 133 - 135: 4.689 distance: 134 - 136: 11.586 distance: 135 - 137: 10.617 distance: 136 - 137: 11.807 distance: 138 - 139: 30.369 distance: 139 - 140: 4.907 distance: 139 - 142: 6.894 distance: 140 - 141: 7.817 distance: 140 - 146: 27.580 distance: 142 - 143: 13.119 distance: 143 - 144: 13.977 distance: 143 - 145: 25.028 distance: 146 - 147: 19.166 distance: 147 - 148: 26.795 distance: 147 - 150: 17.295 distance: 148 - 149: 17.491 distance: 148 - 154: 42.471 distance: 150 - 151: 24.298 distance: 151 - 153: 36.819 distance: 154 - 155: 13.002 distance: 155 - 156: 7.421 distance: 155 - 158: 39.187 distance: 156 - 157: 27.075 distance: 156 - 163: 13.250 distance: 158 - 159: 33.922 distance: 159 - 160: 39.342 distance: 160 - 161: 35.190 distance: 160 - 162: 48.960 distance: 163 - 164: 14.577 distance: 164 - 165: 12.233 distance: 164 - 167: 10.414 distance: 165 - 166: 7.930 distance: 165 - 172: 11.293 distance: 167 - 168: 11.402 distance: 168 - 169: 11.417 distance: 169 - 170: 5.837 distance: 169 - 171: 12.099 distance: 172 - 173: 7.480 distance: 173 - 174: 24.971 distance: 173 - 176: 7.389 distance: 174 - 175: 19.733 distance: 174 - 178: 28.833 distance: 176 - 177: 6.662