Starting phenix.real_space_refine on Fri Mar 6 12:20:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x6a_33019/03_2026/7x6a_33019.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x6a_33019/03_2026/7x6a_33019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x6a_33019/03_2026/7x6a_33019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x6a_33019/03_2026/7x6a_33019.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x6a_33019/03_2026/7x6a_33019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x6a_33019/03_2026/7x6a_33019.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.061 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 129 5.16 5 C 19682 2.51 5 N 5168 2.21 5 O 5900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30879 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8548 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8548 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 8551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8551 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 817 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 817 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 817 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Time building chain proxies: 6.88, per 1000 atoms: 0.22 Number of scatterers: 30879 At special positions: 0 Unit cell: (175.48, 154.08, 208.65, 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 129 16.00 O 5900 8.00 N 5168 7.00 C 19682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 90 " distance=2.03 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: 2.40 Conformation dependent library (CDL) restraints added in 1.5 seconds 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7380 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 63 sheets defined 18.9% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.719A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 762 through 783 removed outlier: 3.550A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.562A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.640A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.611A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 933 through 941 removed outlier: 3.606A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.961A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.577A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 4.052A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.883A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.613A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.797A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.438A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 762 through 783 removed outlier: 3.883A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.589A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.563A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.743A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 932 Processing helix chain 'B' and resid 933 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.837A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.657A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1150 removed outlier: 3.760A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B1150 " --> pdb=" O ASP B1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.665A pdb=" N ASN D 370 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 4.228A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.637A pdb=" N ASP D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR D 421 " --> pdb=" O ASN D 417 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 422' Processing helix chain 'D' and resid 619 through 623 Processing helix chain 'D' and resid 737 through 742 Processing helix chain 'D' and resid 747 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 760 through 783 removed outlier: 3.779A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU D 780 " --> pdb=" O LYS D 776 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 824 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 913 through 919 removed outlier: 3.823A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.634A pdb=" N LYS D 933 " --> pdb=" O SER D 929 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.868A pdb=" N GLN D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN D 955 " --> pdb=" O VAL D 951 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 956 " --> pdb=" O VAL D 952 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN D 957 " --> pdb=" O ASN D 953 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D 958 " --> pdb=" O HIS D 954 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU D 959 " --> pdb=" O ASN D 955 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.347A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP D 994 " --> pdb=" O GLU D 990 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR D1007 " --> pdb=" O SER D1003 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D1013 " --> pdb=" O THR D1009 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER D1021 " --> pdb=" O GLU D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1150 removed outlier: 4.115A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.541A pdb=" N SER L 85 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.020A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.582A pdb=" N SER J 85 " --> pdb=" O SER J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 removed outlier: 3.688A pdb=" N SER K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 31 removed outlier: 3.584A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.976A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 127 removed outlier: 3.646A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 127 removed outlier: 3.579A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.310A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.537A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.139A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.183A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 573 through 576 removed outlier: 6.522A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.517A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.771A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.672A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.575A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.680A pdb=" N ILE A 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 26 through 31 removed outlier: 3.525A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.816A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 104 through 107 removed outlier: 3.622A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.561A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.158A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.060A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AC9, first strand: chain 'B' and resid 573 through 576 removed outlier: 6.385A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.448A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 719 Processing sheet with id=AD4, first strand: chain 'B' and resid 722 through 728 removed outlier: 3.635A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.617A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 861 " --> pdb=" O LYS B 733 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.886A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 36 through 37 removed outlier: 7.392A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 193 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 90 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 93 " --> pdb=" O TYR D 266 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 51 through 55 removed outlier: 3.553A pdb=" N PHE D 275 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 126 through 127 removed outlier: 3.562A pdb=" N PHE D 106 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY D 107 " --> pdb=" O ARG D 237 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 311 through 318 removed outlier: 3.609A pdb=" N THR D 315 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE D 643 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.637A pdb=" N LYS D 356 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP D 398 " --> pdb=" O VAL D 512 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL D 512 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE D 400 " --> pdb=" O VAL D 510 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL D 510 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE D 402 " --> pdb=" O TYR D 508 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR D 508 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS D 432 " --> pdb=" O LEU D 513 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'D' and resid 539 through 540 Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 660 removed outlier: 3.506A pdb=" N ALA D 694 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL D 656 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR D 696 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN D 658 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN D 675 " --> pdb=" O SER D 691 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 693 " --> pdb=" O SER D 673 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.702A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.989A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 733 through 735 removed outlier: 4.746A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 861 " --> pdb=" O LYS D 733 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER D 735 " --> pdb=" O THR D 859 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.647A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU H 99 " --> pdb=" O ALA H 33 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA H 33 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.647A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 17 through 22 Processing sheet with id=AF6, first strand: chain 'L' and resid 3 through 7 removed outlier: 4.168A pdb=" N VAL L 3 " --> pdb=" O ARG L 26 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA L 19 " --> pdb=" O ILE L 77 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE L 73 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU L 72 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.540A pdb=" N GLN L 40 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.737A pdb=" N ALA G 5 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE G 83 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER G 71 " --> pdb=" O TYR G 80 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.750A pdb=" N ILE G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE G 51 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AG2, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.843A pdb=" N ALA J 19 " --> pdb=" O ILE J 77 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE J 77 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU J 75 " --> pdb=" O LEU J 21 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU J 72 " --> pdb=" O SER J 69 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 13 removed outlier: 4.024A pdb=" N VAL J 13 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU J 35 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR J 51 " --> pdb=" O LEU J 35 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP J 37 " --> pdb=" O LEU J 49 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.503A pdb=" N GLU I 10 " --> pdb=" O LEU I 115 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR I 117 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL I 116 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA I 92 " --> pdb=" O VAL I 116 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA I 97 " --> pdb=" O HIS I 35 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.503A pdb=" N GLU I 10 " --> pdb=" O LEU I 115 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR I 117 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL I 116 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA I 92 " --> pdb=" O VAL I 116 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 18 through 22 removed outlier: 3.854A pdb=" N VAL I 18 " --> pdb=" O ILE I 83 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL I 69 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 3 through 7 removed outlier: 4.438A pdb=" N VAL K 3 " --> pdb=" O ARG K 26 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE K 73 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU K 72 " --> pdb=" O SER K 69 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 12 through 13 removed outlier: 3.520A pdb=" N VAL K 13 " --> pdb=" O GLU K 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'K' and resid 47 through 51 removed outlier: 6.521A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TYR K 51 " --> pdb=" O LEU K 35 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU K 35 " --> pdb=" O TYR K 51 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2442 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: 7.63 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9986 1.35 - 1.47: 8135 1.47 - 1.59: 13352 1.59 - 1.72: 0 1.72 - 1.84: 162 Bond restraints: 31635 Sorted by residual: bond pdb=" C VAL D 620 " pdb=" N PRO D 621 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.06e+00 bond pdb=" C GLN B1142 " pdb=" N PRO B1143 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.20e-02 6.94e+03 1.49e+00 bond pdb=" CA GLY D 257 " pdb=" C GLY D 257 " ideal model delta sigma weight residual 1.514 1.530 -0.016 1.41e-02 5.03e+03 1.32e+00 bond pdb=" C GLN D1142 " pdb=" N PRO D1143 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.28e+00 bond pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.27e+00 ... (remaining 31630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 42067 1.44 - 2.87: 814 2.87 - 4.31: 155 4.31 - 5.74: 28 5.74 - 7.18: 14 Bond angle restraints: 43078 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.46 -3.76 1.22e+00 6.72e-01 9.51e+00 angle pdb=" OG1 THR A 547 " pdb=" CB THR A 547 " pdb=" CG2 THR A 547 " ideal model delta sigma weight residual 109.30 103.28 6.02 2.00e+00 2.50e-01 9.05e+00 angle pdb=" N ILE A 805 " pdb=" CA ILE A 805 " pdb=" C ILE A 805 " ideal model delta sigma weight residual 113.53 110.59 2.94 9.80e-01 1.04e+00 9.02e+00 angle pdb=" OG1 THR A 95 " pdb=" CB THR A 95 " pdb=" CG2 THR A 95 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.95e+00 angle pdb=" OG1 THR D 95 " pdb=" CB THR D 95 " pdb=" CG2 THR D 95 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.95e+00 ... (remaining 43073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 16852 17.60 - 35.21: 1539 35.21 - 52.81: 263 52.81 - 70.42: 58 70.42 - 88.02: 34 Dihedral angle restraints: 18746 sinusoidal: 7232 harmonic: 11514 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.23 -80.77 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CA TRP L 96 " pdb=" C TRP L 96 " pdb=" N PRO L 97 " pdb=" CA PRO L 97 " ideal model delta harmonic sigma weight residual 180.00 141.31 38.69 0 5.00e+00 4.00e-02 5.99e+01 dihedral pdb=" CA TRP K 96 " pdb=" C TRP K 96 " pdb=" N PRO K 97 " pdb=" CA PRO K 97 " ideal model delta harmonic sigma weight residual 180.00 146.41 33.59 0 5.00e+00 4.00e-02 4.51e+01 ... (remaining 18743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3429 0.039 - 0.078: 962 0.078 - 0.117: 383 0.117 - 0.156: 46 0.156 - 0.195: 9 Chirality restraints: 4829 Sorted by residual: chirality pdb=" CB THR B 250 " pdb=" CA THR B 250 " pdb=" OG1 THR B 250 " pdb=" CG2 THR B 250 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" CB ILE A 233 " pdb=" CA ILE A 233 " pdb=" CG1 ILE A 233 " pdb=" CG2 ILE A 233 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CB THR B 547 " pdb=" CA THR B 547 " pdb=" OG1 THR B 547 " pdb=" CG2 THR B 547 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 4826 not shown) Planarity restraints: 5588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP L 96 " 0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO L 97 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO L 97 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO L 97 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 411 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO A 412 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 620 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO B 621 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 621 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 621 " -0.032 5.00e-02 4.00e+02 ... (remaining 5585 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 213 2.56 - 3.15: 23728 3.15 - 3.73: 43913 3.73 - 4.32: 59934 4.32 - 4.90: 102976 Nonbonded interactions: 230764 Sorted by model distance: nonbonded pdb=" O ASN B 185 " pdb=" CD2 LEU B 212 " model vdw 1.981 3.460 nonbonded pdb=" O ALA B 67 " pdb=" OG1 THR B 250 " model vdw 2.177 3.040 nonbonded pdb=" O ALA B 292 " pdb=" OG1 THR B 632 " model vdw 2.179 3.040 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.197 3.040 nonbonded pdb=" O ALA D 67 " pdb=" OG1 THR D 250 " model vdw 2.203 3.040 ... (remaining 230759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 184 or (resid 185 and (name N or name CA or nam \ e C or name O or name CB )) or resid 186 through 1150)) selection = (chain 'B' and (resid 25 through 211 or (resid 212 and (name N or name CA or nam \ e C or name O or name CB )) or resid 213 through 1150)) selection = (chain 'D' and (resid 25 through 184 or (resid 185 and (name N or name CA or nam \ e C or name O or name CB )) or resid 186 through 211 or (resid 212 and (name N o \ r name CA or name C or name O or name CB )) or resid 213 through 1150)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 3.460 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 29.510 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.002 0.038 31677 Z= 0.108 Angle : 0.524 7.180 43162 Z= 0.282 Chirality : 0.042 0.195 4829 Planarity : 0.004 0.089 5588 Dihedral : 14.042 88.023 11240 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.17 % Favored : 93.48 % Rotamer: Outliers : 0.06 % Allowed : 0.15 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.13), residues: 3939 helix: 0.83 (0.22), residues: 636 sheet: -0.09 (0.18), residues: 928 loop : -1.73 (0.12), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 357 TYR 0.011 0.001 TYR I 105 PHE 0.015 0.001 PHE D 562 TRP 0.021 0.001 TRP A 64 HIS 0.004 0.000 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00218 (31635) covalent geometry : angle 0.52267 (43078) SS BOND : bond 0.00208 ( 42) SS BOND : angle 0.98574 ( 84) hydrogen bonds : bond 0.25342 ( 902) hydrogen bonds : angle 8.72892 ( 2442) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 529 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.6498 (tm-30) cc_final: 0.6219 (tp40) REVERT: A 345 THR cc_start: 0.8521 (m) cc_final: 0.8203 (m) REVERT: A 498 ARG cc_start: 0.8006 (ptp-170) cc_final: 0.7729 (ptm160) REVERT: A 584 ILE cc_start: 0.8784 (mm) cc_final: 0.8521 (mp) REVERT: A 586 ASP cc_start: 0.8311 (t70) cc_final: 0.7745 (t0) REVERT: A 708 SER cc_start: 0.7992 (t) cc_final: 0.7737 (m) REVERT: A 779 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8518 (tm-30) REVERT: B 88 ASP cc_start: 0.7819 (t0) cc_final: 0.7064 (t70) REVERT: B 170 TYR cc_start: 0.7887 (t80) cc_final: 0.7580 (t80) REVERT: B 850 ILE cc_start: 0.8729 (mm) cc_final: 0.8524 (mt) REVERT: B 993 ILE cc_start: 0.9203 (pt) cc_final: 0.8794 (mt) REVERT: B 1029 MET cc_start: 0.8531 (tpp) cc_final: 0.8282 (ttm) REVERT: D 128 ILE cc_start: 0.8005 (mt) cc_final: 0.7784 (mp) REVERT: D 237 ARG cc_start: 0.6559 (mmm160) cc_final: 0.6027 (tpp-160) REVERT: H 24 THR cc_start: 0.7767 (m) cc_final: 0.7565 (m) REVERT: H 32 ASN cc_start: 0.6621 (p0) cc_final: 0.5605 (t0) REVERT: H 62 GLN cc_start: 0.5817 (tt0) cc_final: 0.4732 (mm110) REVERT: H 87 LYS cc_start: 0.7355 (mmtm) cc_final: 0.6954 (mptt) REVERT: H 98 ARG cc_start: 0.7901 (tpt-90) cc_final: 0.7662 (mmm160) REVERT: H 100 ARG cc_start: 0.7461 (tpp-160) cc_final: 0.7136 (tpp-160) REVERT: G 48 MET cc_start: 0.5530 (ttp) cc_final: 0.5074 (ttt) REVERT: J 4 MET cc_start: 0.0289 (ttt) cc_final: -0.1106 (mtp) REVERT: J 7 SER cc_start: 0.6533 (m) cc_final: 0.6188 (t) REVERT: I 31 SER cc_start: 0.7269 (p) cc_final: 0.7026 (m) REVERT: I 32 ASN cc_start: 0.6607 (t0) cc_final: 0.5942 (t0) REVERT: I 104 ASP cc_start: 0.7143 (p0) cc_final: 0.6443 (p0) REVERT: I 106 PHE cc_start: 0.8489 (p90) cc_final: 0.8246 (p90) REVERT: I 109 TYR cc_start: 0.7055 (m-80) cc_final: 0.6765 (m-80) REVERT: K 4 MET cc_start: 0.5982 (pmm) cc_final: 0.5740 (mtp) REVERT: K 35 LEU cc_start: 0.7609 (tp) cc_final: 0.7187 (tp) REVERT: K 50 ILE cc_start: 0.7663 (mt) cc_final: 0.7433 (tt) REVERT: K 74 THR cc_start: 0.8684 (m) cc_final: 0.8191 (p) REVERT: K 93 TYR cc_start: 0.7086 (p90) cc_final: 0.6665 (p90) outliers start: 2 outliers final: 0 residues processed: 531 average time/residue: 0.2086 time to fit residues: 174.5021 Evaluate side-chains 283 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.0370 chunk 207 optimal weight: 0.0570 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.0050 overall best weight: 0.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 751 ASN A 955 ASN B 26 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 804 GLN B 853 GLN B1142 GLN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.179264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.119673 restraints weight = 57991.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.123768 restraints weight = 30174.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.124462 restraints weight = 18000.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.125155 restraints weight = 17167.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.125367 restraints weight = 14910.457| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 31677 Z= 0.118 Angle : 0.571 13.353 43162 Z= 0.303 Chirality : 0.044 0.175 4829 Planarity : 0.005 0.087 5588 Dihedral : 4.035 37.957 4278 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.19 % Favored : 93.42 % Rotamer: Outliers : 1.23 % Allowed : 7.33 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3939 helix: 1.20 (0.22), residues: 644 sheet: -0.04 (0.17), residues: 981 loop : -1.68 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 98 TYR 0.024 0.001 TYR D 396 PHE 0.020 0.001 PHE D 168 TRP 0.029 0.001 TRP D 633 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00242 (31635) covalent geometry : angle 0.56889 (43078) SS BOND : bond 0.00355 ( 42) SS BOND : angle 1.28130 ( 84) hydrogen bonds : bond 0.04604 ( 902) hydrogen bonds : angle 6.42384 ( 2442) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.8121 (t70) cc_final: 0.7645 (t0) REVERT: A 646 ARG cc_start: 0.7720 (tpt170) cc_final: 0.7394 (tpt170) REVERT: A 779 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8544 (tm-30) REVERT: A 904 TYR cc_start: 0.7270 (m-10) cc_final: 0.6876 (m-10) REVERT: B 65 PHE cc_start: 0.7484 (m-80) cc_final: 0.7071 (m-80) REVERT: B 102 ARG cc_start: 0.8619 (mtt-85) cc_final: 0.8372 (mtt90) REVERT: B 206 LYS cc_start: 0.8636 (tttp) cc_final: 0.7971 (ttpp) REVERT: B 850 ILE cc_start: 0.8640 (mm) cc_final: 0.8350 (mt) REVERT: D 128 ILE cc_start: 0.7464 (mt) cc_final: 0.7198 (mp) REVERT: D 237 ARG cc_start: 0.5903 (mmm160) cc_final: 0.5394 (tpp80) REVERT: D 317 ASN cc_start: 0.8019 (t0) cc_final: 0.7708 (t0) REVERT: D 737 ASP cc_start: 0.7289 (t0) cc_final: 0.7075 (t0) REVERT: D 1017 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7818 (tm-30) REVERT: H 12 ARG cc_start: 0.9081 (mmt-90) cc_final: 0.8795 (tpp80) REVERT: H 32 ASN cc_start: 0.7086 (p0) cc_final: 0.5772 (t0) REVERT: H 62 GLN cc_start: 0.5961 (tt0) cc_final: 0.4853 (mm110) REVERT: L 26 ARG cc_start: 0.7822 (tmm-80) cc_final: 0.7607 (tmm-80) REVERT: G 48 MET cc_start: 0.5085 (ttp) cc_final: 0.4730 (ttt) REVERT: J 4 MET cc_start: 0.0842 (ttt) cc_final: -0.0681 (mtm) REVERT: J 7 SER cc_start: 0.7250 (m) cc_final: 0.6972 (t) REVERT: K 34 ASP cc_start: 0.8609 (m-30) cc_final: 0.8291 (t0) REVERT: K 35 LEU cc_start: 0.7929 (tp) cc_final: 0.7541 (tp) REVERT: K 74 THR cc_start: 0.8579 (m) cc_final: 0.8208 (p) REVERT: K 95 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8207 (t0) outliers start: 42 outliers final: 29 residues processed: 335 average time/residue: 0.1798 time to fit residues: 98.5340 Evaluate side-chains 288 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 108 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 22 optimal weight: 50.0000 chunk 371 optimal weight: 30.0000 chunk 170 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 388 optimal weight: 0.0870 chunk 322 optimal weight: 0.5980 chunk 297 optimal weight: 2.9990 chunk 272 optimal weight: 0.0370 chunk 299 optimal weight: 2.9990 overall best weight: 1.3440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A1083 HIS B 26 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 955 ASN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN H 32 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN I 32 ASN K 6 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.171812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.108665 restraints weight = 57495.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.113712 restraints weight = 30053.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.114057 restraints weight = 19208.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.114860 restraints weight = 15512.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115121 restraints weight = 15054.433| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31677 Z= 0.155 Angle : 0.572 10.690 43162 Z= 0.301 Chirality : 0.044 0.166 4829 Planarity : 0.005 0.083 5588 Dihedral : 4.134 40.604 4278 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.35 % Favored : 93.27 % Rotamer: Outliers : 1.55 % Allowed : 10.00 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.13), residues: 3939 helix: 1.07 (0.22), residues: 645 sheet: -0.12 (0.17), residues: 999 loop : -1.68 (0.12), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 102 TYR 0.020 0.001 TYR L 51 PHE 0.020 0.001 PHE D 329 TRP 0.020 0.001 TRP B 436 HIS 0.007 0.001 HIS D1058 Details of bonding type rmsd covalent geometry : bond 0.00371 (31635) covalent geometry : angle 0.56892 (43078) SS BOND : bond 0.00269 ( 42) SS BOND : angle 1.51857 ( 84) hydrogen bonds : bond 0.04650 ( 902) hydrogen bonds : angle 5.85652 ( 2442) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 288 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7598 (mtt180) cc_final: 0.7231 (mtt180) REVERT: A 207 HIS cc_start: 0.6554 (m170) cc_final: 0.6277 (m170) REVERT: A 779 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8524 (tm-30) REVERT: B 88 ASP cc_start: 0.8217 (t0) cc_final: 0.7977 (t0) REVERT: B 850 ILE cc_start: 0.8712 (mm) cc_final: 0.8485 (mt) REVERT: D 128 ILE cc_start: 0.7534 (mt) cc_final: 0.7277 (mp) REVERT: D 191 GLU cc_start: 0.7306 (tp30) cc_final: 0.6902 (tp30) REVERT: D 237 ARG cc_start: 0.5990 (mmm160) cc_final: 0.5574 (tpp80) REVERT: D 317 ASN cc_start: 0.8141 (t0) cc_final: 0.7658 (t0) REVERT: D 988 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7646 (mt-10) REVERT: H 12 ARG cc_start: 0.9084 (mmt-90) cc_final: 0.8800 (tpp80) REVERT: H 32 ASN cc_start: 0.7443 (p0) cc_final: 0.7094 (p0) REVERT: H 62 GLN cc_start: 0.6169 (tt0) cc_final: 0.5023 (mm110) REVERT: L 26 ARG cc_start: 0.7921 (tmm-80) cc_final: 0.7531 (tmm-80) REVERT: G 48 MET cc_start: 0.5123 (ttp) cc_final: 0.4724 (ttt) REVERT: J 4 MET cc_start: 0.1073 (ttt) cc_final: -0.0389 (mtm) REVERT: I 64 PHE cc_start: 0.7254 (m-10) cc_final: 0.7039 (m-80) REVERT: K 34 ASP cc_start: 0.8762 (m-30) cc_final: 0.8394 (t0) REVERT: K 95 ASN cc_start: 0.8816 (m-40) cc_final: 0.8490 (t0) outliers start: 53 outliers final: 42 residues processed: 326 average time/residue: 0.1841 time to fit residues: 98.1846 Evaluate side-chains 298 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 108 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 228 optimal weight: 0.7980 chunk 211 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 297 optimal weight: 3.9990 chunk 287 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 379 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN H 82 GLN ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.170837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108195 restraints weight = 55447.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.111972 restraints weight = 26498.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114450 restraints weight = 17010.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.115958 restraints weight = 13014.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.116936 restraints weight = 11064.894| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31677 Z= 0.119 Angle : 0.534 9.886 43162 Z= 0.280 Chirality : 0.043 0.155 4829 Planarity : 0.004 0.083 5588 Dihedral : 4.057 40.449 4278 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.76 % Favored : 93.88 % Rotamer: Outliers : 1.79 % Allowed : 12.14 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 3939 helix: 1.14 (0.22), residues: 640 sheet: -0.14 (0.17), residues: 1004 loop : -1.66 (0.12), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 995 TYR 0.026 0.001 TYR A 266 PHE 0.020 0.001 PHE A 515 TRP 0.031 0.001 TRP D 633 HIS 0.004 0.001 HIS D1058 Details of bonding type rmsd covalent geometry : bond 0.00274 (31635) covalent geometry : angle 0.53157 (43078) SS BOND : bond 0.00247 ( 42) SS BOND : angle 1.19073 ( 84) hydrogen bonds : bond 0.03928 ( 902) hydrogen bonds : angle 5.42331 ( 2442) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 269 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7065 (mtt180) REVERT: A 646 ARG cc_start: 0.7751 (tpt170) cc_final: 0.7353 (tpt170) REVERT: A 759 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7762 (t80) REVERT: A 779 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8521 (tm-30) REVERT: B 88 ASP cc_start: 0.8131 (t0) cc_final: 0.7819 (t0) REVERT: B 132 GLU cc_start: 0.7594 (pt0) cc_final: 0.7368 (pm20) REVERT: B 206 LYS cc_start: 0.8645 (tttp) cc_final: 0.8314 (ttmt) REVERT: B 495 TYR cc_start: 0.4455 (m-10) cc_final: 0.3712 (m-80) REVERT: B 869 MET cc_start: 0.8099 (mtm) cc_final: 0.7821 (mtt) REVERT: D 92 PHE cc_start: 0.5930 (t80) cc_final: 0.5478 (t80) REVERT: D 128 ILE cc_start: 0.7788 (mt) cc_final: 0.7528 (mp) REVERT: D 170 TYR cc_start: 0.7557 (t80) cc_final: 0.7224 (t80) REVERT: D 191 GLU cc_start: 0.7568 (tp30) cc_final: 0.7162 (tp30) REVERT: D 237 ARG cc_start: 0.6233 (mmm160) cc_final: 0.5957 (tpp80) REVERT: D 988 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7492 (mt-10) REVERT: H 62 GLN cc_start: 0.6292 (tt0) cc_final: 0.5607 (tp40) REVERT: L 26 ARG cc_start: 0.7953 (tmm-80) cc_final: 0.7487 (tmm-80) REVERT: G 48 MET cc_start: 0.5149 (ttp) cc_final: 0.4756 (ttt) REVERT: J 4 MET cc_start: 0.1741 (ttt) cc_final: 0.0516 (mtm) REVERT: K 34 ASP cc_start: 0.8779 (m-30) cc_final: 0.8408 (t0) REVERT: K 81 GLN cc_start: 0.8870 (mt0) cc_final: 0.8660 (mm110) REVERT: K 95 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8385 (t0) outliers start: 61 outliers final: 45 residues processed: 308 average time/residue: 0.1757 time to fit residues: 90.5218 Evaluate side-chains 295 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 248 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 108 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 252 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 330 optimal weight: 1.9990 chunk 287 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 chunk 339 optimal weight: 10.0000 chunk 329 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 296 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1083 HIS B1135 ASN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN I 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.160336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.096518 restraints weight = 56892.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100172 restraints weight = 32366.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.100840 restraints weight = 18861.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.101262 restraints weight = 18615.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.101523 restraints weight = 17540.267| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 31677 Z= 0.225 Angle : 0.636 10.846 43162 Z= 0.333 Chirality : 0.046 0.175 4829 Planarity : 0.005 0.085 5588 Dihedral : 4.482 44.916 4278 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.31 % Favored : 92.31 % Rotamer: Outliers : 2.43 % Allowed : 13.26 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.13), residues: 3939 helix: 0.69 (0.22), residues: 641 sheet: -0.16 (0.17), residues: 966 loop : -1.80 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 357 TYR 0.024 0.002 TYR I 80 PHE 0.026 0.002 PHE A 906 TRP 0.026 0.002 TRP D 633 HIS 0.012 0.001 HIS D1058 Details of bonding type rmsd covalent geometry : bond 0.00551 (31635) covalent geometry : angle 0.63271 (43078) SS BOND : bond 0.00332 ( 42) SS BOND : angle 1.65824 ( 84) hydrogen bonds : bond 0.05265 ( 902) hydrogen bonds : angle 5.54259 ( 2442) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 263 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7472 (t0) REVERT: A 646 ARG cc_start: 0.7570 (tpt170) cc_final: 0.7253 (tpt170) REVERT: A 759 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7943 (t80) REVERT: A 866 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7592 (t) REVERT: B 170 TYR cc_start: 0.8326 (t80) cc_final: 0.7901 (t80) REVERT: B 869 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7863 (mtt) REVERT: D 65 PHE cc_start: 0.8252 (m-10) cc_final: 0.8027 (m-10) REVERT: D 92 PHE cc_start: 0.6245 (t80) cc_final: 0.5880 (t80) REVERT: D 128 ILE cc_start: 0.7682 (mt) cc_final: 0.7422 (mp) REVERT: D 170 TYR cc_start: 0.7782 (t80) cc_final: 0.7492 (t80) REVERT: D 191 GLU cc_start: 0.7744 (tp30) cc_final: 0.7336 (tp30) REVERT: D 192 PHE cc_start: 0.6516 (m-80) cc_final: 0.6303 (m-80) REVERT: D 237 ARG cc_start: 0.6051 (mmm160) cc_final: 0.5696 (tpp80) REVERT: D 250 THR cc_start: 0.0595 (OUTLIER) cc_final: 0.0296 (m) REVERT: H 32 ASN cc_start: 0.8145 (p0) cc_final: 0.7718 (p0) REVERT: H 62 GLN cc_start: 0.6567 (tt0) cc_final: 0.5754 (tp40) REVERT: L 26 ARG cc_start: 0.8096 (tmm-80) cc_final: 0.7549 (tmm-80) REVERT: G 48 MET cc_start: 0.5574 (ttp) cc_final: 0.5105 (ttt) REVERT: J 4 MET cc_start: 0.1381 (ttt) cc_final: 0.0143 (mtm) REVERT: I 106 PHE cc_start: 0.8981 (p90) cc_final: 0.8453 (p90) REVERT: K 34 ASP cc_start: 0.8845 (m-30) cc_final: 0.8445 (t0) REVERT: K 55 THR cc_start: 0.8604 (t) cc_final: 0.8273 (p) REVERT: K 95 ASN cc_start: 0.9044 (m-40) cc_final: 0.8696 (t0) outliers start: 83 outliers final: 55 residues processed: 322 average time/residue: 0.1824 time to fit residues: 97.0197 Evaluate side-chains 302 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 108 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 39 optimal weight: 0.8980 chunk 302 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 289 optimal weight: 0.3980 chunk 155 optimal weight: 0.0270 chunk 69 optimal weight: 0.9980 chunk 331 optimal weight: 0.9980 chunk 333 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 66 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN L 95 ASN I 39 GLN K 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.163029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.098033 restraints weight = 56589.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.101830 restraints weight = 27710.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104177 restraints weight = 18087.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105728 restraints weight = 14043.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.106605 restraints weight = 12078.340| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31677 Z= 0.101 Angle : 0.535 9.449 43162 Z= 0.279 Chirality : 0.043 0.157 4829 Planarity : 0.004 0.081 5588 Dihedral : 4.157 42.583 4278 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.61 % Favored : 94.01 % Rotamer: Outliers : 1.76 % Allowed : 14.67 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.13), residues: 3939 helix: 1.06 (0.22), residues: 643 sheet: -0.18 (0.17), residues: 982 loop : -1.66 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 403 TYR 0.027 0.001 TYR A 266 PHE 0.017 0.001 PHE I 106 TRP 0.026 0.001 TRP D 104 HIS 0.002 0.000 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00226 (31635) covalent geometry : angle 0.53106 (43078) SS BOND : bond 0.00261 ( 42) SS BOND : angle 1.54313 ( 84) hydrogen bonds : bond 0.03864 ( 902) hydrogen bonds : angle 5.24142 ( 2442) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 248 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 ARG cc_start: 0.7478 (tpt170) cc_final: 0.7083 (tpt170) REVERT: A 697 MET cc_start: 0.8545 (ttm) cc_final: 0.8246 (ttm) REVERT: A 759 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7947 (t80) REVERT: B 88 ASP cc_start: 0.8220 (t0) cc_final: 0.7929 (t0) REVERT: B 132 GLU cc_start: 0.7811 (pt0) cc_final: 0.7567 (pm20) REVERT: B 170 TYR cc_start: 0.8124 (t80) cc_final: 0.7895 (t80) REVERT: B 869 MET cc_start: 0.8108 (mtm) cc_final: 0.7846 (mtt) REVERT: D 92 PHE cc_start: 0.6053 (t80) cc_final: 0.5640 (t80) REVERT: D 102 ARG cc_start: 0.6785 (ptp-170) cc_final: 0.6392 (ptp90) REVERT: D 128 ILE cc_start: 0.7781 (mt) cc_final: 0.7510 (mp) REVERT: D 170 TYR cc_start: 0.7595 (t80) cc_final: 0.7188 (t80) REVERT: D 191 GLU cc_start: 0.7775 (tp30) cc_final: 0.7411 (tp30) REVERT: D 237 ARG cc_start: 0.5988 (mmm160) cc_final: 0.5600 (tpp80) REVERT: D 250 THR cc_start: 0.0440 (OUTLIER) cc_final: 0.0092 (m) REVERT: H 32 ASN cc_start: 0.8099 (p0) cc_final: 0.7657 (p0) REVERT: H 62 GLN cc_start: 0.6468 (tt0) cc_final: 0.5652 (tp40) REVERT: L 26 ARG cc_start: 0.8052 (tmm-80) cc_final: 0.7803 (tmm-80) REVERT: G 48 MET cc_start: 0.4662 (ttp) cc_final: 0.4400 (ttt) REVERT: J 4 MET cc_start: 0.3298 (ttt) cc_final: 0.2646 (mtm) REVERT: I 57 THR cc_start: 0.6585 (OUTLIER) cc_final: 0.6129 (p) REVERT: K 95 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8549 (t0) outliers start: 60 outliers final: 45 residues processed: 293 average time/residue: 0.1791 time to fit residues: 86.7870 Evaluate side-chains 285 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 108 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 161 optimal weight: 3.9990 chunk 358 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 247 optimal weight: 0.0040 chunk 142 optimal weight: 0.6980 chunk 50 optimal weight: 0.0020 chunk 132 optimal weight: 40.0000 chunk 101 optimal weight: 0.0470 chunk 268 optimal weight: 0.0000 chunk 28 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 overall best weight: 0.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 853 GLN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN L 81 GLN K 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.169400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105761 restraints weight = 56905.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109550 restraints weight = 27807.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.112126 restraints weight = 18109.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.113615 restraints weight = 13894.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114567 restraints weight = 11887.670| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 31677 Z= 0.096 Angle : 0.516 10.231 43162 Z= 0.268 Chirality : 0.042 0.190 4829 Planarity : 0.004 0.080 5588 Dihedral : 3.923 40.331 4278 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.79 % Favored : 93.86 % Rotamer: Outliers : 1.99 % Allowed : 14.90 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3939 helix: 1.34 (0.22), residues: 640 sheet: -0.01 (0.17), residues: 960 loop : -1.59 (0.12), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1107 TYR 0.022 0.001 TYR A 266 PHE 0.019 0.001 PHE B 157 TRP 0.026 0.001 TRP D 104 HIS 0.002 0.000 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00212 (31635) covalent geometry : angle 0.51345 (43078) SS BOND : bond 0.00268 ( 42) SS BOND : angle 1.18245 ( 84) hydrogen bonds : bond 0.03270 ( 902) hydrogen bonds : angle 4.98439 ( 2442) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 245 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 ARG cc_start: 0.7479 (tpt170) cc_final: 0.7151 (tpt170) REVERT: A 697 MET cc_start: 0.8438 (ttm) cc_final: 0.8202 (ttm) REVERT: A 759 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8052 (t80) REVERT: B 88 ASP cc_start: 0.8213 (t0) cc_final: 0.7896 (t0) REVERT: B 869 MET cc_start: 0.7987 (mtm) cc_final: 0.7760 (mtt) REVERT: B 1029 MET cc_start: 0.8651 (tpp) cc_final: 0.8444 (ttm) REVERT: D 92 PHE cc_start: 0.5979 (t80) cc_final: 0.5601 (t80) REVERT: D 102 ARG cc_start: 0.6751 (ptp-170) cc_final: 0.6366 (ptp90) REVERT: D 128 ILE cc_start: 0.7876 (mt) cc_final: 0.7632 (mp) REVERT: D 170 TYR cc_start: 0.7552 (t80) cc_final: 0.7152 (t80) REVERT: D 191 GLU cc_start: 0.7843 (tp30) cc_final: 0.7458 (tp30) REVERT: D 237 ARG cc_start: 0.5926 (mmm160) cc_final: 0.5587 (tpp80) REVERT: D 250 THR cc_start: 0.0417 (OUTLIER) cc_final: 0.0066 (m) REVERT: D 606 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8563 (t0) REVERT: H 32 ASN cc_start: 0.8064 (p0) cc_final: 0.7723 (p0) REVERT: H 62 GLN cc_start: 0.6465 (tt0) cc_final: 0.5648 (tp40) REVERT: L 26 ARG cc_start: 0.8095 (tmm-80) cc_final: 0.7571 (tmm-80) REVERT: L 63 ARG cc_start: 0.5464 (mtp85) cc_final: 0.5210 (mtp85) REVERT: G 48 MET cc_start: 0.5199 (ttp) cc_final: 0.4784 (ttt) REVERT: J 4 MET cc_start: 0.2104 (ttt) cc_final: 0.0764 (mtm) REVERT: I 57 THR cc_start: 0.6697 (OUTLIER) cc_final: 0.6249 (p) REVERT: I 109 TYR cc_start: 0.7271 (m-80) cc_final: 0.6591 (m-80) REVERT: K 34 ASP cc_start: 0.8898 (m-30) cc_final: 0.8275 (t0) REVERT: K 95 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8589 (t0) outliers start: 68 outliers final: 52 residues processed: 294 average time/residue: 0.1712 time to fit residues: 83.0344 Evaluate side-chains 293 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 108 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 161 optimal weight: 0.0570 chunk 112 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 356 optimal weight: 40.0000 chunk 138 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 361 optimal weight: 3.9990 chunk 351 optimal weight: 9.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.168316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.105397 restraints weight = 55231.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.109086 restraints weight = 26512.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.111554 restraints weight = 17028.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.112939 restraints weight = 13021.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113910 restraints weight = 11147.563| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31677 Z= 0.102 Angle : 0.519 9.953 43162 Z= 0.269 Chirality : 0.042 0.159 4829 Planarity : 0.004 0.080 5588 Dihedral : 3.910 40.397 4278 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.02 % Favored : 93.58 % Rotamer: Outliers : 1.91 % Allowed : 15.28 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.13), residues: 3939 helix: 1.36 (0.22), residues: 640 sheet: -0.03 (0.17), residues: 946 loop : -1.55 (0.12), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 190 TYR 0.022 0.001 TYR A 266 PHE 0.032 0.001 PHE D 86 TRP 0.026 0.001 TRP D 104 HIS 0.003 0.000 HIS D1058 Details of bonding type rmsd covalent geometry : bond 0.00237 (31635) covalent geometry : angle 0.51681 (43078) SS BOND : bond 0.00226 ( 42) SS BOND : angle 1.27699 ( 84) hydrogen bonds : bond 0.03402 ( 902) hydrogen bonds : angle 4.92489 ( 2442) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 239 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6978 (mtt180) cc_final: 0.6766 (mtt180) REVERT: A 646 ARG cc_start: 0.7497 (tpt170) cc_final: 0.7237 (tpt170) REVERT: A 759 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8143 (t80) REVERT: B 88 ASP cc_start: 0.8199 (t0) cc_final: 0.7883 (t0) REVERT: B 406 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7026 (pt0) REVERT: B 408 SER cc_start: 0.9135 (m) cc_final: 0.8822 (p) REVERT: B 725 GLU cc_start: 0.7941 (tt0) cc_final: 0.7542 (tt0) REVERT: B 869 MET cc_start: 0.8082 (mtm) cc_final: 0.7852 (mtt) REVERT: D 92 PHE cc_start: 0.6211 (t80) cc_final: 0.5793 (t80) REVERT: D 128 ILE cc_start: 0.7906 (mt) cc_final: 0.7653 (mp) REVERT: D 170 TYR cc_start: 0.7682 (t80) cc_final: 0.7332 (t80) REVERT: D 191 GLU cc_start: 0.7879 (tp30) cc_final: 0.7496 (tp30) REVERT: D 237 ARG cc_start: 0.5937 (mmm160) cc_final: 0.5642 (tpp80) REVERT: D 250 THR cc_start: 0.0347 (OUTLIER) cc_final: -0.0021 (m) REVERT: H 32 ASN cc_start: 0.8148 (p0) cc_final: 0.7770 (p0) REVERT: H 62 GLN cc_start: 0.6584 (tt0) cc_final: 0.5774 (tp40) REVERT: L 26 ARG cc_start: 0.8075 (tmm-80) cc_final: 0.7664 (tmm-80) REVERT: G 48 MET cc_start: 0.5124 (ttp) cc_final: 0.4719 (ttt) REVERT: J 4 MET cc_start: 0.2409 (ttt) cc_final: 0.0871 (mtm) REVERT: I 57 THR cc_start: 0.6890 (OUTLIER) cc_final: 0.6465 (p) REVERT: K 31 ILE cc_start: 0.7685 (mm) cc_final: 0.7433 (mm) REVERT: K 34 ASP cc_start: 0.8931 (m-30) cc_final: 0.8354 (t0) REVERT: K 95 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8541 (t0) outliers start: 65 outliers final: 54 residues processed: 286 average time/residue: 0.1839 time to fit residues: 86.2190 Evaluate side-chains 291 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 232 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 108 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 176 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 206 optimal weight: 0.6980 chunk 328 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 389 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 332 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.169570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106777 restraints weight = 57063.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111770 restraints weight = 29530.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.112098 restraints weight = 18201.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.112856 restraints weight = 15925.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.113180 restraints weight = 14620.503| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31677 Z= 0.107 Angle : 0.523 11.147 43162 Z= 0.270 Chirality : 0.042 0.160 4829 Planarity : 0.004 0.080 5588 Dihedral : 3.912 40.691 4278 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.19 % Favored : 93.40 % Rotamer: Outliers : 2.05 % Allowed : 15.20 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3939 helix: 1.34 (0.22), residues: 644 sheet: 0.02 (0.17), residues: 964 loop : -1.55 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 190 TYR 0.020 0.001 TYR A 266 PHE 0.017 0.001 PHE B 157 TRP 0.031 0.001 TRP D 104 HIS 0.003 0.000 HIS D1058 Details of bonding type rmsd covalent geometry : bond 0.00252 (31635) covalent geometry : angle 0.52039 (43078) SS BOND : bond 0.00233 ( 42) SS BOND : angle 1.20045 ( 84) hydrogen bonds : bond 0.03508 ( 902) hydrogen bonds : angle 4.86715 ( 2442) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 239 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8129 (t80) REVERT: B 88 ASP cc_start: 0.8192 (t0) cc_final: 0.7938 (t0) REVERT: B 406 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7519 (pt0) REVERT: B 408 SER cc_start: 0.9176 (m) cc_final: 0.8897 (p) REVERT: B 725 GLU cc_start: 0.7951 (tt0) cc_final: 0.7575 (tt0) REVERT: B 869 MET cc_start: 0.8078 (mtm) cc_final: 0.7844 (mtt) REVERT: D 92 PHE cc_start: 0.6144 (t80) cc_final: 0.5720 (t80) REVERT: D 128 ILE cc_start: 0.7729 (mt) cc_final: 0.7482 (mp) REVERT: D 170 TYR cc_start: 0.7598 (t80) cc_final: 0.7262 (t80) REVERT: D 191 GLU cc_start: 0.7899 (tp30) cc_final: 0.7479 (tp30) REVERT: D 237 ARG cc_start: 0.5794 (mmm160) cc_final: 0.5470 (tpp80) REVERT: D 250 THR cc_start: 0.0431 (OUTLIER) cc_final: 0.0129 (m) REVERT: H 62 GLN cc_start: 0.6684 (tt0) cc_final: 0.5915 (tp40) REVERT: H 87 LYS cc_start: 0.7550 (mmtm) cc_final: 0.7109 (mmtt) REVERT: H 90 ASP cc_start: 0.7783 (m-30) cc_final: 0.7399 (m-30) REVERT: H 99 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8239 (mt-10) REVERT: L 26 ARG cc_start: 0.8049 (tmm-80) cc_final: 0.7666 (tmm-80) REVERT: G 48 MET cc_start: 0.5512 (ttp) cc_final: 0.5003 (ttt) REVERT: J 4 MET cc_start: 0.1652 (ttt) cc_final: -0.0382 (mtm) REVERT: I 57 THR cc_start: 0.7178 (OUTLIER) cc_final: 0.6770 (p) REVERT: K 31 ILE cc_start: 0.7590 (mm) cc_final: 0.7353 (mm) REVERT: K 34 ASP cc_start: 0.8910 (m-30) cc_final: 0.8388 (t0) REVERT: K 95 ASN cc_start: 0.8794 (m-40) cc_final: 0.8426 (t0) outliers start: 70 outliers final: 58 residues processed: 289 average time/residue: 0.1836 time to fit residues: 88.0613 Evaluate side-chains 299 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 237 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 340 optimal weight: 8.9990 chunk 229 optimal weight: 0.3980 chunk 258 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 380 optimal weight: 6.9990 chunk 284 optimal weight: 7.9990 chunk 209 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 362 optimal weight: 9.9990 chunk 204 optimal weight: 0.0030 overall best weight: 2.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN J 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.160231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.097213 restraints weight = 56611.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.100296 restraints weight = 34566.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102149 restraints weight = 20082.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102321 restraints weight = 17248.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.102631 restraints weight = 16394.714| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 31677 Z= 0.197 Angle : 0.615 9.709 43162 Z= 0.322 Chirality : 0.045 0.161 4829 Planarity : 0.005 0.083 5588 Dihedral : 4.415 45.711 4278 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.93 % Favored : 92.64 % Rotamer: Outliers : 1.85 % Allowed : 15.69 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.13), residues: 3939 helix: 0.87 (0.22), residues: 644 sheet: -0.20 (0.17), residues: 1001 loop : -1.70 (0.12), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 454 TYR 0.025 0.002 TYR B 453 PHE 0.041 0.002 PHE D 86 TRP 0.026 0.002 TRP D 104 HIS 0.011 0.001 HIS D1058 Details of bonding type rmsd covalent geometry : bond 0.00481 (31635) covalent geometry : angle 0.61149 (43078) SS BOND : bond 0.00290 ( 42) SS BOND : angle 1.61029 ( 84) hydrogen bonds : bond 0.05069 ( 902) hydrogen bonds : angle 5.21035 ( 2442) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 232 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8775 (pp) REVERT: A 759 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8093 (t80) REVERT: B 88 ASP cc_start: 0.8106 (t0) cc_final: 0.7886 (t0) REVERT: B 170 TYR cc_start: 0.8338 (t80) cc_final: 0.8101 (t80) REVERT: B 1029 MET cc_start: 0.8607 (tpp) cc_final: 0.8264 (ttm) REVERT: D 128 ILE cc_start: 0.7855 (mt) cc_final: 0.7622 (mp) REVERT: D 170 TYR cc_start: 0.7723 (t80) cc_final: 0.7464 (t80) REVERT: D 237 ARG cc_start: 0.6224 (mmm160) cc_final: 0.5880 (tpp80) REVERT: D 250 THR cc_start: 0.0565 (OUTLIER) cc_final: 0.0237 (m) REVERT: D 606 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8577 (t0) REVERT: H 62 GLN cc_start: 0.6885 (tt0) cc_final: 0.6253 (tp40) REVERT: H 99 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8347 (mt-10) REVERT: L 26 ARG cc_start: 0.8182 (tmm-80) cc_final: 0.7800 (tmm-80) REVERT: G 48 MET cc_start: 0.5437 (ttp) cc_final: 0.4995 (ttt) REVERT: J 4 MET cc_start: 0.1051 (ttt) cc_final: -0.0449 (mtm) REVERT: I 57 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7495 (p) REVERT: K 31 ILE cc_start: 0.7976 (mm) cc_final: 0.7714 (mm) outliers start: 63 outliers final: 49 residues processed: 276 average time/residue: 0.1766 time to fit residues: 80.3420 Evaluate side-chains 274 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 1097 SER Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 130 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 325 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 306 optimal weight: 0.0040 chunk 11 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 288 optimal weight: 0.6980 chunk 233 optimal weight: 6.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN K 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.167449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104523 restraints weight = 56985.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.109562 restraints weight = 29684.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.109880 restraints weight = 18107.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110516 restraints weight = 15845.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110728 restraints weight = 14792.314| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31677 Z= 0.106 Angle : 0.554 9.643 43162 Z= 0.288 Chirality : 0.043 0.166 4829 Planarity : 0.004 0.080 5588 Dihedral : 4.148 43.346 4278 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.97 % Favored : 93.63 % Rotamer: Outliers : 1.70 % Allowed : 16.02 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.13), residues: 3939 helix: 1.16 (0.22), residues: 645 sheet: -0.16 (0.17), residues: 967 loop : -1.61 (0.12), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.018 0.001 TYR A 266 PHE 0.024 0.001 PHE B 490 TRP 0.034 0.001 TRP D 104 HIS 0.003 0.000 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00245 (31635) covalent geometry : angle 0.55232 (43078) SS BOND : bond 0.00235 ( 42) SS BOND : angle 1.23803 ( 84) hydrogen bonds : bond 0.03808 ( 902) hydrogen bonds : angle 4.98244 ( 2442) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6213.93 seconds wall clock time: 107 minutes 38.33 seconds (6458.33 seconds total)