Starting phenix.real_space_refine on Fri Mar 6 06:50:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vsj_21377/03_2026/6vsj_21377.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vsj_21377/03_2026/6vsj_21377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vsj_21377/03_2026/6vsj_21377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vsj_21377/03_2026/6vsj_21377.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vsj_21377/03_2026/6vsj_21377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vsj_21377/03_2026/6vsj_21377.map" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 162 5.16 5 C 18189 2.51 5 N 4860 2.21 5 O 5541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28752 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8678 Classifications: {'peptide': 1122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1073} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, E, F Time building chain proxies: 9.48, per 1000 atoms: 0.33 Number of scatterers: 28752 At special positions: 0 Unit cell: (171.72, 170.66, 156.88, 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 162 16.00 O 5541 8.00 N 4860 7.00 C 18189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 158 " distance=2.02 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 187 " distance=2.04 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 246 " distance=2.04 Simple disulfide: pdb=" SG CYS A 284 " - pdb=" SG CYS A 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 425 " distance=2.05 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 564 " distance=2.06 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 547 " distance=2.04 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 633 " distance=2.04 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 682 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 706 " distance=2.02 Simple disulfide: pdb=" SG CYS A 775 " - pdb=" SG CYS A 797 " distance=2.03 Simple disulfide: pdb=" SG CYS A 780 " - pdb=" SG CYS A 786 " distance=2.02 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 905 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1093 " distance=2.04 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 158 " distance=2.02 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 158 " distance=2.02 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 187 " distance=2.04 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 187 " distance=2.04 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 165 " - pdb=" SG CYS C 246 " distance=2.04 Simple disulfide: pdb=" SG CYS B 284 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS C 284 " - pdb=" SG CYS C 294 " distance=2.03 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS C 329 " - pdb=" SG CYS C 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 425 " distance=2.05 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 425 " distance=2.05 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 564 " distance=2.06 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 564 " distance=2.06 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 507 " distance=2.03 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 507 " distance=2.04 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 547 " distance=2.04 Simple disulfide: pdb=" SG CYS C 541 " - pdb=" SG CYS C 547 " distance=2.04 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 633 " distance=2.04 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 633 " distance=2.04 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 706 " distance=2.02 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 706 " distance=2.02 Simple disulfide: pdb=" SG CYS B 775 " - pdb=" SG CYS B 797 " distance=2.03 Simple disulfide: pdb=" SG CYS C 775 " - pdb=" SG CYS C 797 " distance=2.03 Simple disulfide: pdb=" SG CYS B 780 " - pdb=" SG CYS B 786 " distance=2.02 Simple disulfide: pdb=" SG CYS C 780 " - pdb=" SG CYS C 786 " distance=2.02 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 905 " distance=2.03 Simple disulfide: pdb=" SG CYS C 894 " - pdb=" SG CYS C 905 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1093 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1093 " distance=2.04 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 192 " " NAG A1302 " - " ASN A 435 " " NAG B1301 " - " ASN B 192 " " NAG B1302 " - " ASN B 435 " " NAG C1301 " - " ASN C 192 " " NAG C1302 " - " ASN C 435 " " NAG D 301 " - " ASN D 89 " " NAG E 301 " - " ASN E 89 " " NAG F 301 " - " ASN F 89 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.2 seconds 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6864 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 69 sheets defined 23.7% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.769A pdb=" N LYS A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 357 through 365 removed outlier: 3.504A pdb=" N TYR A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.864A pdb=" N LEU A 403 " --> pdb=" O GLN A 400 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 404 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 444 through 451 removed outlier: 4.247A pdb=" N GLY A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 664 removed outlier: 3.556A pdb=" N PHE A 662 " --> pdb=" O CYS A 658 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 663 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 664 " --> pdb=" O TYR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 780 removed outlier: 3.517A pdb=" N PHE A 778 " --> pdb=" O ASP A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 791 removed outlier: 3.892A pdb=" N ARG A 787 " --> pdb=" O ASN A 783 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 788 " --> pdb=" O THR A 784 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 823 removed outlier: 3.744A pdb=" N CYS A 797 " --> pdb=" O TYR A 793 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 805 " --> pdb=" O ASN A 801 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 822 " --> pdb=" O VAL A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 880 removed outlier: 3.921A pdb=" N ASP A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 896 removed outlier: 3.862A pdb=" N GLU A 889 " --> pdb=" O VAL A 885 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A 893 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N CYS A 894 " --> pdb=" O ALA A 890 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR A 895 " --> pdb=" O TYR A 891 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY A 896 " --> pdb=" O ASN A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 910 removed outlier: 3.562A pdb=" N ASN A 910 " --> pdb=" O VAL A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 934 Processing helix chain 'A' and resid 947 through 956 removed outlier: 4.292A pdb=" N GLN A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 959 No H-bonds generated for 'chain 'A' and resid 957 through 959' Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.597A pdb=" N LEU A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 989 removed outlier: 4.303A pdb=" N LYS A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP A 989 " --> pdb=" O GLN A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1015 removed outlier: 3.611A pdb=" N LYS A 997 " --> pdb=" O SER A 993 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 998 " --> pdb=" O ALA A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1018 No H-bonds generated for 'chain 'A' and resid 1016 through 1018' Processing helix chain 'A' and resid 1026 through 1034 removed outlier: 3.684A pdb=" N THR A1032 " --> pdb=" O GLN A1028 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A1033 " --> pdb=" O GLU A1029 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A1034 " --> pdb=" O ILE A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1082 removed outlier: 3.593A pdb=" N ALA A1041 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP A1044 " --> pdb=" O LYS A1040 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A1046 " --> pdb=" O GLN A1042 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 113 through 117 removed outlier: 3.536A pdb=" N MET D 117 " --> pdb=" O MET D 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.770A pdb=" N LYS B 293 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 357 through 365 removed outlier: 3.504A pdb=" N TYR B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.864A pdb=" N LEU B 403 " --> pdb=" O GLN B 400 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 404 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'B' and resid 444 through 451 removed outlier: 4.248A pdb=" N GLY B 451 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 664 removed outlier: 3.557A pdb=" N PHE B 662 " --> pdb=" O CYS B 658 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 663 " --> pdb=" O SER B 659 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 664 " --> pdb=" O TYR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 780 removed outlier: 3.517A pdb=" N PHE B 778 " --> pdb=" O ASP B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 791 removed outlier: 3.893A pdb=" N ARG B 787 " --> pdb=" O ASN B 783 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 788 " --> pdb=" O THR B 784 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN B 789 " --> pdb=" O ALA B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 823 removed outlier: 3.743A pdb=" N CYS B 797 " --> pdb=" O TYR B 793 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 805 " --> pdb=" O ASN B 801 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN B 817 " --> pdb=" O ASN B 813 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 822 " --> pdb=" O VAL B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 880 removed outlier: 3.920A pdb=" N ASP B 874 " --> pdb=" O SER B 870 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 879 " --> pdb=" O LEU B 875 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 896 removed outlier: 3.862A pdb=" N GLU B 889 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 893 " --> pdb=" O GLU B 889 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N CYS B 894 " --> pdb=" O ALA B 890 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR B 895 " --> pdb=" O TYR B 891 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY B 896 " --> pdb=" O ASN B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 910 removed outlier: 3.561A pdb=" N ASN B 910 " --> pdb=" O VAL B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 934 Processing helix chain 'B' and resid 947 through 956 removed outlier: 4.292A pdb=" N GLN B 953 " --> pdb=" O SER B 949 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 954 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 955 " --> pdb=" O SER B 951 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 959 No H-bonds generated for 'chain 'B' and resid 957 through 959' Processing helix chain 'B' and resid 961 through 966 removed outlier: 3.598A pdb=" N LEU B 966 " --> pdb=" O THR B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 989 removed outlier: 4.303A pdb=" N LYS B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP B 989 " --> pdb=" O GLN B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1015 removed outlier: 3.609A pdb=" N LYS B 997 " --> pdb=" O SER B 993 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE B 998 " --> pdb=" O ALA B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1018 No H-bonds generated for 'chain 'B' and resid 1016 through 1018' Processing helix chain 'B' and resid 1026 through 1034 removed outlier: 3.685A pdb=" N THR B1032 " --> pdb=" O GLN B1028 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG B1033 " --> pdb=" O GLU B1029 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B1034 " --> pdb=" O ILE B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1082 removed outlier: 3.594A pdb=" N ALA B1041 " --> pdb=" O VAL B1037 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP B1044 " --> pdb=" O LYS B1040 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B1045 " --> pdb=" O ALA B1041 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B1046 " --> pdb=" O GLN B1042 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 113 through 117 removed outlier: 3.536A pdb=" N MET E 117 " --> pdb=" O MET E 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 287 through 297 removed outlier: 3.770A pdb=" N LYS C 293 " --> pdb=" O THR C 289 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 357 through 365 removed outlier: 3.504A pdb=" N TYR C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 365 " --> pdb=" O LEU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.864A pdb=" N LEU C 403 " --> pdb=" O GLN C 400 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 404 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 415 Processing helix chain 'C' and resid 444 through 451 removed outlier: 4.248A pdb=" N GLY C 451 " --> pdb=" O ASN C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 664 removed outlier: 3.556A pdb=" N PHE C 662 " --> pdb=" O CYS C 658 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C 663 " --> pdb=" O SER C 659 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN C 664 " --> pdb=" O TYR C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 780 removed outlier: 3.517A pdb=" N PHE C 778 " --> pdb=" O ASP C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 791 removed outlier: 3.893A pdb=" N ARG C 787 " --> pdb=" O ASN C 783 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN C 788 " --> pdb=" O THR C 784 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN C 789 " --> pdb=" O ALA C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 823 removed outlier: 3.743A pdb=" N CYS C 797 " --> pdb=" O TYR C 793 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN C 805 " --> pdb=" O ASN C 801 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 817 " --> pdb=" O ASN C 813 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 822 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 880 removed outlier: 3.921A pdb=" N ASP C 874 " --> pdb=" O SER C 870 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 880 " --> pdb=" O LEU C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 896 removed outlier: 3.862A pdb=" N GLU C 889 " --> pdb=" O VAL C 885 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 893 " --> pdb=" O GLU C 889 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N CYS C 894 " --> pdb=" O ALA C 890 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR C 895 " --> pdb=" O TYR C 891 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY C 896 " --> pdb=" O ASN C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 910 removed outlier: 3.561A pdb=" N ASN C 910 " --> pdb=" O VAL C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 934 Processing helix chain 'C' and resid 947 through 956 removed outlier: 4.292A pdb=" N GLN C 953 " --> pdb=" O SER C 949 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR C 954 " --> pdb=" O LEU C 950 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 959 No H-bonds generated for 'chain 'C' and resid 957 through 959' Processing helix chain 'C' and resid 961 through 966 removed outlier: 3.598A pdb=" N LEU C 966 " --> pdb=" O THR C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 989 removed outlier: 4.303A pdb=" N LYS C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP C 989 " --> pdb=" O GLN C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1015 removed outlier: 3.609A pdb=" N LYS C 997 " --> pdb=" O SER C 993 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE C 998 " --> pdb=" O ALA C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1018 No H-bonds generated for 'chain 'C' and resid 1016 through 1018' Processing helix chain 'C' and resid 1026 through 1034 removed outlier: 3.684A pdb=" N THR C1032 " --> pdb=" O GLN C1028 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C1033 " --> pdb=" O GLU C1029 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C1034 " --> pdb=" O ILE C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1082 removed outlier: 3.594A pdb=" N ALA C1041 " --> pdb=" O VAL C1037 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP C1044 " --> pdb=" O LYS C1040 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C1045 " --> pdb=" O ALA C1041 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C1046 " --> pdb=" O GLN C1042 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 113 through 117 removed outlier: 3.536A pdb=" N MET F 117 " --> pdb=" O MET F 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.732A pdb=" N ASN A 26 " --> pdb=" O VAL A 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 69 removed outlier: 3.784A pdb=" N ARG A 266 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.522A pdb=" N GLY A 83 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A 163 " --> pdb=" O ILE A 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 226 removed outlier: 3.513A pdb=" N THR A 225 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 106 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 261 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG A 257 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 141 removed outlier: 3.635A pdb=" N VAL A 127 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA7, first strand: chain 'A' and resid 151 through 153 removed outlier: 7.285A pdb=" N VAL A 152 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 188 " --> pdb=" O VAL A 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 208 through 209 removed outlier: 3.572A pdb=" N THR A 212 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 306 through 307 Processing sheet with id=AB1, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AB2, first strand: chain 'A' and resid 347 through 351 removed outlier: 4.328A pdb=" N GLU A 347 " --> pdb=" O LYS A 392 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A 392 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 390 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 366 through 369 removed outlier: 3.796A pdb=" N GLN A 366 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS A 428 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 431 " --> pdb=" O CYS A 547 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS A 547 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 464 through 468 Processing sheet with id=AB5, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=AB6, first strand: chain 'A' and resid 517 through 518 removed outlier: 3.765A pdb=" N ILE A 527 " --> pdb=" O GLY A 518 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 581 through 585 removed outlier: 3.505A pdb=" N GLY A 590 " --> pdb=" O TYR A 583 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG A 631 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 630 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASN A 617 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 676 through 677 Processing sheet with id=AB9, first strand: chain 'A' and resid 688 through 694 removed outlier: 7.034A pdb=" N ASN A 688 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR A 727 " --> pdb=" O ASN A 688 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N THR A 690 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG A 724 " --> pdb=" O ASP A 708 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP A 708 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 705 " --> pdb=" O MET A 701 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 699 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 756 through 758 Processing sheet with id=AC2, first strand: chain 'A' and resid 761 through 763 removed outlier: 3.730A pdb=" N GLU A 762 " --> pdb=" O PHE A1112 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 770 through 772 removed outlier: 4.281A pdb=" N LYS A 770 " --> pdb=" O LEU A 915 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 772 " --> pdb=" O LYS A 913 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 913 " --> pdb=" O THR A 772 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 37 through 41 Processing sheet with id=AC5, first strand: chain 'D' and resid 44 through 45 removed outlier: 5.157A pdb=" N THR D 132 " --> pdb=" O MET D 124 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET D 124 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA D 134 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY D 118 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE D 65 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG D 81 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP D 67 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.731A pdb=" N ASN B 26 " --> pdb=" O VAL B 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 64 through 69 removed outlier: 3.783A pdb=" N ARG B 266 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.521A pdb=" N GLY B 83 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR B 163 " --> pdb=" O ILE B 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 225 through 226 removed outlier: 3.512A pdb=" N THR B 225 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 106 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 261 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG B 257 " --> pdb=" O GLN B 109 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 138 through 141 removed outlier: 3.636A pdb=" N VAL B 127 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 143 through 144 Processing sheet with id=AD3, first strand: chain 'B' and resid 151 through 153 removed outlier: 7.285A pdb=" N VAL B 152 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL B 188 " --> pdb=" O VAL B 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.573A pdb=" N THR B 212 " --> pdb=" O HIS B 209 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 306 through 307 Processing sheet with id=AD6, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AD7, first strand: chain 'B' and resid 347 through 351 removed outlier: 4.327A pdb=" N GLU B 347 " --> pdb=" O LYS B 392 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS B 392 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B 390 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 366 through 369 removed outlier: 3.797A pdb=" N GLN B 366 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS B 428 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 431 " --> pdb=" O CYS B 547 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 547 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 464 through 468 Processing sheet with id=AE1, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AE2, first strand: chain 'B' and resid 517 through 518 removed outlier: 3.766A pdb=" N ILE B 527 " --> pdb=" O GLY B 518 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 581 through 585 removed outlier: 3.506A pdb=" N GLY B 590 " --> pdb=" O TYR B 583 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG B 631 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 630 " --> pdb=" O ASN B 617 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASN B 617 " --> pdb=" O ILE B 630 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 676 through 677 Processing sheet with id=AE5, first strand: chain 'B' and resid 688 through 694 removed outlier: 7.035A pdb=" N ASN B 688 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR B 727 " --> pdb=" O ASN B 688 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N THR B 690 " --> pdb=" O THR B 727 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 724 " --> pdb=" O ASP B 708 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP B 708 " --> pdb=" O ARG B 724 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 705 " --> pdb=" O MET B 701 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 699 " --> pdb=" O VAL B 707 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 756 through 758 Processing sheet with id=AE7, first strand: chain 'B' and resid 761 through 763 removed outlier: 3.729A pdb=" N GLU B 762 " --> pdb=" O PHE B1112 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 770 through 772 removed outlier: 4.281A pdb=" N LYS B 770 " --> pdb=" O LEU B 915 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR B 772 " --> pdb=" O LYS B 913 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS B 913 " --> pdb=" O THR B 772 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 37 through 41 Processing sheet with id=AF1, first strand: chain 'E' and resid 44 through 45 removed outlier: 5.158A pdb=" N THR E 132 " --> pdb=" O MET E 124 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N MET E 124 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA E 134 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY E 118 " --> pdb=" O PHE E 138 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE E 65 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG E 81 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP E 67 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 26 through 27 removed outlier: 6.732A pdb=" N ASN C 26 " --> pdb=" O VAL C 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 64 through 69 removed outlier: 3.784A pdb=" N ARG C 266 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.522A pdb=" N GLY C 83 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR C 163 " --> pdb=" O ILE C 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 225 through 226 removed outlier: 3.512A pdb=" N THR C 225 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 106 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 261 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARG C 257 " --> pdb=" O GLN C 109 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 138 through 141 removed outlier: 3.636A pdb=" N VAL C 127 " --> pdb=" O TYR C 240 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AF8, first strand: chain 'C' and resid 151 through 153 removed outlier: 7.285A pdb=" N VAL C 152 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL C 188 " --> pdb=" O VAL C 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.573A pdb=" N THR C 212 " --> pdb=" O HIS C 209 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 306 through 307 Processing sheet with id=AG2, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AG3, first strand: chain 'C' and resid 347 through 351 removed outlier: 4.329A pdb=" N GLU C 347 " --> pdb=" O LYS C 392 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS C 392 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL C 390 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 366 through 369 removed outlier: 3.796A pdb=" N GLN C 366 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HIS C 428 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 431 " --> pdb=" O CYS C 547 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS C 547 " --> pdb=" O LEU C 431 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 464 through 468 Processing sheet with id=AG6, first strand: chain 'C' and resid 511 through 512 Processing sheet with id=AG7, first strand: chain 'C' and resid 517 through 518 removed outlier: 3.766A pdb=" N ILE C 527 " --> pdb=" O GLY C 518 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 581 through 585 removed outlier: 3.505A pdb=" N GLY C 590 " --> pdb=" O TYR C 583 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG C 631 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 630 " --> pdb=" O ASN C 617 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASN C 617 " --> pdb=" O ILE C 630 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AH1, first strand: chain 'C' and resid 688 through 694 removed outlier: 7.035A pdb=" N ASN C 688 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR C 727 " --> pdb=" O ASN C 688 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N THR C 690 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG C 724 " --> pdb=" O ASP C 708 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP C 708 " --> pdb=" O ARG C 724 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 705 " --> pdb=" O MET C 701 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 699 " --> pdb=" O VAL C 707 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 756 through 758 Processing sheet with id=AH3, first strand: chain 'C' and resid 761 through 763 removed outlier: 3.729A pdb=" N GLU C 762 " --> pdb=" O PHE C1112 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 770 through 772 removed outlier: 4.281A pdb=" N LYS C 770 " --> pdb=" O LEU C 915 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 772 " --> pdb=" O LYS C 913 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS C 913 " --> pdb=" O THR C 772 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 37 through 41 Processing sheet with id=AH6, first strand: chain 'F' and resid 44 through 45 removed outlier: 5.156A pdb=" N THR F 132 " --> pdb=" O MET F 124 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET F 124 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA F 134 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY F 118 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE F 65 " --> pdb=" O ARG F 81 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG F 81 " --> pdb=" O PHE F 65 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP F 67 " --> pdb=" O ILE F 79 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2079 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: 7.02 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9404 1.34 - 1.47: 7465 1.47 - 1.59: 12318 1.59 - 1.72: 0 1.72 - 1.84: 207 Bond restraints: 29394 Sorted by residual: bond pdb=" C ASN C 442 " pdb=" N PRO C 443 " ideal model delta sigma weight residual 1.332 1.307 0.025 8.20e-03 1.49e+04 9.44e+00 bond pdb=" C ASN A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.332 1.307 0.025 8.20e-03 1.49e+04 9.16e+00 bond pdb=" C ASN B 442 " pdb=" N PRO B 443 " ideal model delta sigma weight residual 1.332 1.308 0.025 8.20e-03 1.49e+04 9.06e+00 bond pdb=" CB TRP C 346 " pdb=" CG TRP C 346 " ideal model delta sigma weight residual 1.498 1.436 0.062 3.10e-02 1.04e+03 4.02e+00 bond pdb=" CB TRP A 346 " pdb=" CG TRP A 346 " ideal model delta sigma weight residual 1.498 1.437 0.061 3.10e-02 1.04e+03 3.93e+00 ... (remaining 29389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 39277 3.02 - 6.04: 701 6.04 - 9.07: 51 9.07 - 12.09: 0 12.09 - 15.11: 3 Bond angle restraints: 40032 Sorted by residual: angle pdb=" CA CYS B 425 " pdb=" CB CYS B 425 " pdb=" SG CYS B 425 " ideal model delta sigma weight residual 114.40 129.51 -15.11 2.30e+00 1.89e-01 4.32e+01 angle pdb=" CA CYS A 425 " pdb=" CB CYS A 425 " pdb=" SG CYS A 425 " ideal model delta sigma weight residual 114.40 129.46 -15.06 2.30e+00 1.89e-01 4.29e+01 angle pdb=" CA CYS C 425 " pdb=" CB CYS C 425 " pdb=" SG CYS C 425 " ideal model delta sigma weight residual 114.40 129.45 -15.05 2.30e+00 1.89e-01 4.28e+01 angle pdb=" N GLY A 103 " pdb=" CA GLY A 103 " pdb=" C GLY A 103 " ideal model delta sigma weight residual 111.85 117.68 -5.83 1.06e+00 8.90e-01 3.02e+01 angle pdb=" N GLY B 103 " pdb=" CA GLY B 103 " pdb=" C GLY B 103 " ideal model delta sigma weight residual 111.85 117.67 -5.82 1.06e+00 8.90e-01 3.01e+01 ... (remaining 40027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 15259 16.60 - 33.20: 1846 33.20 - 49.80: 427 49.80 - 66.40: 84 66.40 - 83.01: 27 Dihedral angle restraints: 17643 sinusoidal: 6909 harmonic: 10734 Sorted by residual: dihedral pdb=" CB CYS B 471 " pdb=" SG CYS B 471 " pdb=" SG CYS B 507 " pdb=" CB CYS B 507 " ideal model delta sinusoidal sigma weight residual -86.00 -164.59 78.59 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS A 471 " pdb=" SG CYS A 471 " pdb=" SG CYS A 507 " pdb=" CB CYS A 507 " ideal model delta sinusoidal sigma weight residual -86.00 -164.58 78.58 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS C 471 " pdb=" SG CYS C 471 " pdb=" SG CYS C 507 " pdb=" CB CYS C 507 " ideal model delta sinusoidal sigma weight residual -86.00 -164.53 78.53 1 1.00e+01 1.00e-02 7.69e+01 ... (remaining 17640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3621 0.069 - 0.137: 800 0.137 - 0.206: 97 0.206 - 0.274: 12 0.274 - 0.343: 6 Chirality restraints: 4536 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 435 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 435 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 435 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 4533 not shown) Planarity restraints: 5217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 938 " 0.059 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO A 939 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 939 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 939 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 938 " 0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO B 939 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 939 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 939 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 938 " 0.059 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO C 939 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO C 939 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 939 " 0.050 5.00e-02 4.00e+02 ... (remaining 5214 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5061 2.75 - 3.29: 27184 3.29 - 3.82: 47044 3.82 - 4.36: 53491 4.36 - 4.90: 89461 Nonbonded interactions: 222241 Sorted by model distance: nonbonded pdb=" OH TYR C1117 " pdb=" OG SER C1159 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR A1117 " pdb=" OG SER A1159 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR B1117 " pdb=" OG SER B1159 " model vdw 2.212 3.040 nonbonded pdb=" O SER B1158 " pdb=" OG SER B1158 " model vdw 2.240 3.040 nonbonded pdb=" O SER A1158 " pdb=" OG SER A1158 " model vdw 2.241 3.040 ... (remaining 222236 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 29.510 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.008 0.066 29451 Z= 0.403 Angle : 1.030 15.109 40155 Z= 0.594 Chirality : 0.058 0.343 4536 Planarity : 0.007 0.089 5208 Dihedral : 15.071 83.006 10635 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.64 % Favored : 90.28 % Rotamer: Outliers : 0.95 % Allowed : 11.40 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.11 (0.11), residues: 3663 helix: -3.80 (0.10), residues: 699 sheet: -2.24 (0.19), residues: 588 loop : -2.65 (0.11), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 668 TYR 0.028 0.003 TYR A 203 PHE 0.029 0.003 PHE C 393 TRP 0.017 0.003 TRP A 334 HIS 0.007 0.002 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00845 (29394) covalent geometry : angle 1.01740 (40032) SS BOND : bond 0.01012 ( 48) SS BOND : angle 2.88040 ( 96) hydrogen bonds : bond 0.30550 ( 774) hydrogen bonds : angle 10.35683 ( 2079) link_NAG-ASN : bond 0.00255 ( 9) link_NAG-ASN : angle 3.74569 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 437 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8311 (t0) cc_final: 0.7788 (t0) REVERT: A 137 TYR cc_start: 0.8770 (m-80) cc_final: 0.8272 (m-10) REVERT: A 149 MET cc_start: 0.8374 (ttm) cc_final: 0.8060 (mtp) REVERT: A 399 ARG cc_start: 0.8592 (mmp80) cc_final: 0.8317 (mmp80) REVERT: A 431 LEU cc_start: 0.8806 (mt) cc_final: 0.8511 (mt) REVERT: A 748 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7093 (tm-30) REVERT: A 749 MET cc_start: 0.7229 (mtt) cc_final: 0.6595 (mtt) REVERT: A 1029 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8292 (tm-30) REVERT: A 1068 ILE cc_start: 0.9655 (mt) cc_final: 0.9449 (mm) REVERT: A 1086 GLN cc_start: 0.8334 (pt0) cc_final: 0.8098 (pp30) REVERT: A 1091 ASN cc_start: 0.7834 (t0) cc_final: 0.6911 (t0) REVERT: D 110 GLN cc_start: 0.7215 (mt0) cc_final: 0.6946 (mm-40) REVERT: D 120 TYR cc_start: 0.6796 (m-80) cc_final: 0.6423 (m-80) REVERT: D 124 MET cc_start: 0.7122 (tmm) cc_final: 0.6444 (tmm) REVERT: B 26 ASN cc_start: 0.8474 (t0) cc_final: 0.7947 (t0) REVERT: B 149 MET cc_start: 0.8398 (ttm) cc_final: 0.8059 (mtp) REVERT: B 184 PRO cc_start: 0.8500 (Cg_exo) cc_final: 0.8233 (Cg_endo) REVERT: B 370 LEU cc_start: 0.9652 (tp) cc_final: 0.9368 (tt) REVERT: B 431 LEU cc_start: 0.8706 (mt) cc_final: 0.8384 (mt) REVERT: B 1029 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8312 (tm-30) REVERT: B 1086 GLN cc_start: 0.8300 (pt0) cc_final: 0.8053 (pp30) REVERT: B 1091 ASN cc_start: 0.7707 (t0) cc_final: 0.6780 (t0) REVERT: E 120 TYR cc_start: 0.6890 (m-80) cc_final: 0.5392 (m-80) REVERT: E 124 MET cc_start: 0.6943 (tmm) cc_final: 0.6506 (tmm) REVERT: C 26 ASN cc_start: 0.8693 (t0) cc_final: 0.8118 (t0) REVERT: C 149 MET cc_start: 0.8323 (ttm) cc_final: 0.8108 (mtp) REVERT: C 184 PRO cc_start: 0.8564 (Cg_exo) cc_final: 0.8290 (Cg_endo) REVERT: C 291 GLU cc_start: 0.8834 (tp30) cc_final: 0.8395 (tp30) REVERT: C 431 LEU cc_start: 0.8916 (mt) cc_final: 0.8684 (mt) REVERT: C 747 TYR cc_start: 0.6150 (m-10) cc_final: 0.5583 (m-80) REVERT: C 940 TRP cc_start: 0.6570 (t-100) cc_final: 0.6274 (t-100) REVERT: C 954 TYR cc_start: 0.8232 (m-10) cc_final: 0.8004 (m-80) REVERT: C 1015 GLN cc_start: 0.8992 (tp40) cc_final: 0.8753 (mm-40) REVERT: C 1064 ASP cc_start: 0.8477 (t0) cc_final: 0.8247 (t0) REVERT: C 1086 GLN cc_start: 0.8514 (pt0) cc_final: 0.8201 (pp30) REVERT: C 1091 ASN cc_start: 0.8037 (t0) cc_final: 0.7217 (t0) REVERT: F 120 TYR cc_start: 0.6711 (m-80) cc_final: 0.6209 (m-80) REVERT: F 124 MET cc_start: 0.7184 (tmm) cc_final: 0.6670 (tmm) outliers start: 30 outliers final: 16 residues processed: 461 average time/residue: 0.1813 time to fit residues: 131.7412 Evaluate side-chains 296 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 280 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 407 ASN Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 1063 SER Chi-restraints excluded: chain F residue 121 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 172 ASN A 325 ASN A 353 ASN A 374 ASN A 400 GLN A 412 GLN A 447 ASN A 469 GLN A 530 ASN A 544 ASN A 548 GLN A 606 GLN A 643 HIS A 688 ASN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN A1018 ASN A1104 GLN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN D 128 ASN D 141 HIS B 154 GLN B 172 ASN B 325 ASN B 353 ASN B 400 GLN B 412 GLN B 469 GLN B 530 ASN B 544 ASN B 548 GLN B 606 GLN B 688 ASN B 750 GLN ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1015 GLN B1018 ASN B1104 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN E 141 HIS C 154 GLN C 172 ASN C 325 ASN C 353 ASN C 374 ASN C 400 GLN C 412 GLN C 447 ASN C 469 GLN C 523 HIS C 530 ASN C 544 ASN C 548 GLN C 606 GLN C 688 ASN ** C 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 ASN C1015 GLN C1018 ASN C1104 GLN ** C1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN F 141 HIS Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.087789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.071064 restraints weight = 87571.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.073361 restraints weight = 51588.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.074944 restraints weight = 35786.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.076091 restraints weight = 27656.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.076870 restraints weight = 22831.185| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29451 Z= 0.166 Angle : 0.681 12.411 40155 Z= 0.368 Chirality : 0.045 0.242 4536 Planarity : 0.005 0.104 5208 Dihedral : 7.632 58.587 4286 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.08 % Allowed : 15.84 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.12), residues: 3663 helix: -1.85 (0.16), residues: 729 sheet: -2.04 (0.20), residues: 612 loop : -2.33 (0.12), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 130 TYR 0.018 0.002 TYR D 120 PHE 0.016 0.001 PHE B 393 TRP 0.012 0.001 TRP A 334 HIS 0.003 0.001 HIS C1114 Details of bonding type rmsd covalent geometry : bond 0.00358 (29394) covalent geometry : angle 0.66784 (40032) SS BOND : bond 0.00581 ( 48) SS BOND : angle 2.57858 ( 96) hydrogen bonds : bond 0.05483 ( 774) hydrogen bonds : angle 6.62373 ( 2079) link_NAG-ASN : bond 0.00326 ( 9) link_NAG-ASN : angle 2.09377 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 351 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8393 (t0) cc_final: 0.7797 (t0) REVERT: A 184 PRO cc_start: 0.8573 (Cg_exo) cc_final: 0.8346 (Cg_endo) REVERT: A 431 LEU cc_start: 0.8926 (mt) cc_final: 0.8709 (mt) REVERT: A 748 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6721 (tm-30) REVERT: A 749 MET cc_start: 0.7152 (mtt) cc_final: 0.6516 (mtt) REVERT: A 964 ASN cc_start: 0.8233 (t0) cc_final: 0.7891 (t0) REVERT: A 998 ILE cc_start: 0.9409 (mt) cc_final: 0.9175 (tt) REVERT: A 1029 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8165 (tm-30) REVERT: A 1064 ASP cc_start: 0.8471 (t0) cc_final: 0.8260 (t0) REVERT: A 1068 ILE cc_start: 0.9446 (mt) cc_final: 0.9192 (mm) REVERT: A 1091 ASN cc_start: 0.7894 (t0) cc_final: 0.7022 (t0) REVERT: D 68 TYR cc_start: 0.8451 (m-80) cc_final: 0.8038 (m-80) REVERT: D 110 GLN cc_start: 0.7127 (mt0) cc_final: 0.6905 (mm-40) REVERT: D 111 MET cc_start: 0.7881 (tmm) cc_final: 0.7636 (tmm) REVERT: D 120 TYR cc_start: 0.6608 (m-80) cc_final: 0.6373 (m-80) REVERT: D 124 MET cc_start: 0.7171 (tmm) cc_final: 0.6820 (tmm) REVERT: B 26 ASN cc_start: 0.8392 (t0) cc_final: 0.7877 (t0) REVERT: B 184 PRO cc_start: 0.8545 (Cg_exo) cc_final: 0.8306 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8812 (mt) cc_final: 0.8528 (mt) REVERT: B 940 TRP cc_start: 0.6652 (t-100) cc_final: 0.6251 (t-100) REVERT: B 956 ILE cc_start: 0.8584 (mt) cc_final: 0.8291 (pt) REVERT: B 1015 GLN cc_start: 0.8804 (tp-100) cc_final: 0.8212 (mm-40) REVERT: B 1029 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8166 (tm-30) REVERT: B 1091 ASN cc_start: 0.7678 (t0) cc_final: 0.6736 (t0) REVERT: E 111 MET cc_start: 0.7773 (tmm) cc_final: 0.7497 (tmm) REVERT: E 120 TYR cc_start: 0.6198 (m-80) cc_final: 0.5947 (m-80) REVERT: E 124 MET cc_start: 0.6966 (tmm) cc_final: 0.6496 (tmm) REVERT: C 26 ASN cc_start: 0.8548 (t0) cc_final: 0.7982 (t0) REVERT: C 184 PRO cc_start: 0.8601 (Cg_exo) cc_final: 0.8307 (Cg_endo) REVERT: C 349 LYS cc_start: 0.8239 (tttt) cc_final: 0.7982 (tptm) REVERT: C 431 LEU cc_start: 0.8953 (mt) cc_final: 0.8725 (mt) REVERT: C 637 ARG cc_start: 0.7310 (ptt180) cc_final: 0.6752 (ptp-170) REVERT: C 748 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6718 (tm-30) REVERT: C 814 MET cc_start: 0.8827 (mmp) cc_final: 0.8544 (tpp) REVERT: C 940 TRP cc_start: 0.6617 (t-100) cc_final: 0.6256 (t-100) REVERT: C 1064 ASP cc_start: 0.8488 (t0) cc_final: 0.8258 (t0) REVERT: C 1091 ASN cc_start: 0.7982 (t0) cc_final: 0.7153 (t0) REVERT: F 111 MET cc_start: 0.7826 (tmm) cc_final: 0.7540 (tmm) REVERT: F 124 MET cc_start: 0.7308 (tmm) cc_final: 0.6835 (tmm) outliers start: 97 outliers final: 52 residues processed: 420 average time/residue: 0.1621 time to fit residues: 112.1535 Evaluate side-chains 329 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 1018 ASN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1128 SER Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 116 optimal weight: 2.9990 chunk 299 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 226 optimal weight: 0.2980 chunk 94 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 301 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 343 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A 400 GLN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 GLN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN B 374 ASN B 400 GLN B 447 ASN ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 GLN ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN C 759 HIS ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1086 GLN C1114 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.086865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.070362 restraints weight = 87718.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.072624 restraints weight = 51536.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.074208 restraints weight = 35720.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.075297 restraints weight = 27504.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.076119 restraints weight = 22809.528| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29451 Z= 0.196 Angle : 0.668 10.417 40155 Z= 0.358 Chirality : 0.045 0.208 4536 Planarity : 0.005 0.071 5208 Dihedral : 7.046 56.626 4272 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.32 % Allowed : 16.38 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.13), residues: 3663 helix: -0.94 (0.19), residues: 729 sheet: -2.12 (0.19), residues: 636 loop : -2.23 (0.12), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 399 TYR 0.018 0.002 TYR A 311 PHE 0.018 0.002 PHE A 393 TRP 0.011 0.001 TRP A 940 HIS 0.004 0.001 HIS A 643 Details of bonding type rmsd covalent geometry : bond 0.00430 (29394) covalent geometry : angle 0.65482 (40032) SS BOND : bond 0.00784 ( 48) SS BOND : angle 2.58350 ( 96) hydrogen bonds : bond 0.04859 ( 774) hydrogen bonds : angle 6.00050 ( 2079) link_NAG-ASN : bond 0.00309 ( 9) link_NAG-ASN : angle 1.81605 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 300 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8480 (t0) cc_final: 0.7827 (t0) REVERT: A 134 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6713 (p90) REVERT: A 184 PRO cc_start: 0.8566 (Cg_exo) cc_final: 0.8335 (Cg_endo) REVERT: A 347 GLU cc_start: 0.8488 (mp0) cc_final: 0.8150 (pm20) REVERT: A 637 ARG cc_start: 0.6734 (ptp-170) cc_final: 0.6485 (ptt180) REVERT: A 749 MET cc_start: 0.7207 (mtt) cc_final: 0.6856 (mtt) REVERT: A 998 ILE cc_start: 0.9376 (mt) cc_final: 0.9170 (tt) REVERT: A 1068 ILE cc_start: 0.9454 (mt) cc_final: 0.9248 (mm) REVERT: A 1086 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7544 (pp30) REVERT: A 1091 ASN cc_start: 0.8054 (t0) cc_final: 0.7250 (t0) REVERT: D 68 TYR cc_start: 0.8554 (m-80) cc_final: 0.7457 (m-80) REVERT: D 75 ILE cc_start: 0.8110 (mt) cc_final: 0.7762 (mm) REVERT: D 78 GLU cc_start: 0.8030 (pt0) cc_final: 0.7420 (pt0) REVERT: D 110 GLN cc_start: 0.7187 (mt0) cc_final: 0.6900 (mm-40) REVERT: D 111 MET cc_start: 0.7992 (tmm) cc_final: 0.7737 (tmm) REVERT: D 124 MET cc_start: 0.7298 (tmm) cc_final: 0.6828 (tmm) REVERT: B 26 ASN cc_start: 0.8481 (t0) cc_final: 0.7730 (t0) REVERT: B 184 PRO cc_start: 0.8687 (Cg_exo) cc_final: 0.8410 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8838 (mt) cc_final: 0.8566 (mt) REVERT: B 643 HIS cc_start: 0.8535 (OUTLIER) cc_final: 0.8100 (m-70) REVERT: B 749 MET cc_start: 0.7398 (mtt) cc_final: 0.7134 (mtt) REVERT: B 940 TRP cc_start: 0.6705 (t-100) cc_final: 0.6481 (t-100) REVERT: B 956 ILE cc_start: 0.8637 (mt) cc_final: 0.8311 (pt) REVERT: B 1015 GLN cc_start: 0.8746 (tp-100) cc_final: 0.8303 (mm-40) REVERT: B 1029 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8245 (tm-30) REVERT: B 1068 ILE cc_start: 0.9440 (mt) cc_final: 0.9239 (mm) REVERT: B 1091 ASN cc_start: 0.7826 (t0) cc_final: 0.6915 (t0) REVERT: E 75 ILE cc_start: 0.8035 (mt) cc_final: 0.7632 (mm) REVERT: E 78 GLU cc_start: 0.7795 (pt0) cc_final: 0.7574 (pt0) REVERT: E 91 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8122 (p) REVERT: E 111 MET cc_start: 0.7902 (tmm) cc_final: 0.7581 (tmm) REVERT: E 124 MET cc_start: 0.7110 (tmm) cc_final: 0.6610 (tmm) REVERT: C 26 ASN cc_start: 0.8464 (t0) cc_final: 0.7891 (t0) REVERT: C 184 PRO cc_start: 0.8634 (Cg_exo) cc_final: 0.8337 (Cg_endo) REVERT: C 349 LYS cc_start: 0.8174 (tttt) cc_final: 0.7932 (tptm) REVERT: C 637 ARG cc_start: 0.6987 (ptt180) cc_final: 0.5873 (ptp-170) REVERT: C 748 GLU cc_start: 0.6889 (tm-30) cc_final: 0.6617 (tm-30) REVERT: C 814 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8552 (tpp) REVERT: C 1064 ASP cc_start: 0.8547 (t0) cc_final: 0.8283 (t0) REVERT: C 1068 ILE cc_start: 0.9354 (mm) cc_final: 0.9152 (mm) REVERT: C 1091 ASN cc_start: 0.8131 (t0) cc_final: 0.7265 (t0) REVERT: C 1111 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8496 (p90) REVERT: F 111 MET cc_start: 0.7894 (tmm) cc_final: 0.7601 (tmm) REVERT: F 124 MET cc_start: 0.7534 (tmm) cc_final: 0.7058 (tmm) outliers start: 136 outliers final: 83 residues processed: 401 average time/residue: 0.1527 time to fit residues: 102.6072 Evaluate side-chains 361 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 272 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1086 GLN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 954 TYR Chi-restraints excluded: chain B residue 1018 ASN Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 747 TYR Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 814 MET Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 941 SER Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1086 GLN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain C residue 1128 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 121 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 180 optimal weight: 9.9990 chunk 197 optimal weight: 0.6980 chunk 238 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 301 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 332 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 272 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A 674 ASN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 ASN A1018 ASN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN B 674 ASN ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN C 643 HIS C 674 ASN ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 GLN C1018 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.087440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.070875 restraints weight = 87675.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.073159 restraints weight = 51618.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.074764 restraints weight = 35802.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.075900 restraints weight = 27524.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.076631 restraints weight = 22722.387| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29451 Z= 0.155 Angle : 0.642 10.790 40155 Z= 0.340 Chirality : 0.045 0.205 4536 Planarity : 0.004 0.063 5208 Dihedral : 6.742 57.368 4271 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.06 % Allowed : 18.22 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.13), residues: 3663 helix: -0.55 (0.19), residues: 732 sheet: -2.03 (0.18), residues: 666 loop : -2.12 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 668 TYR 0.016 0.001 TYR B1111 PHE 0.021 0.001 PHE E 138 TRP 0.018 0.001 TRP C 940 HIS 0.004 0.001 HIS C 759 Details of bonding type rmsd covalent geometry : bond 0.00343 (29394) covalent geometry : angle 0.62953 (40032) SS BOND : bond 0.00485 ( 48) SS BOND : angle 2.50473 ( 96) hydrogen bonds : bond 0.04310 ( 774) hydrogen bonds : angle 5.64955 ( 2079) link_NAG-ASN : bond 0.00332 ( 9) link_NAG-ASN : angle 1.75745 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 307 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8515 (t0) cc_final: 0.7843 (t0) REVERT: A 134 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6742 (p90) REVERT: A 184 PRO cc_start: 0.8516 (Cg_exo) cc_final: 0.8269 (Cg_endo) REVERT: A 347 GLU cc_start: 0.8374 (mp0) cc_final: 0.8160 (pm20) REVERT: A 642 PHE cc_start: 0.8271 (m-80) cc_final: 0.8065 (m-80) REVERT: A 735 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7953 (pp) REVERT: A 749 MET cc_start: 0.7250 (mtt) cc_final: 0.6842 (mtt) REVERT: A 1068 ILE cc_start: 0.9436 (mt) cc_final: 0.9211 (mm) REVERT: A 1091 ASN cc_start: 0.7984 (t0) cc_final: 0.7179 (t0) REVERT: D 68 TYR cc_start: 0.8491 (m-80) cc_final: 0.7805 (m-10) REVERT: D 75 ILE cc_start: 0.8104 (mt) cc_final: 0.7717 (mm) REVERT: D 78 GLU cc_start: 0.7951 (pt0) cc_final: 0.7634 (pt0) REVERT: D 110 GLN cc_start: 0.7224 (mt0) cc_final: 0.6881 (mm-40) REVERT: D 111 MET cc_start: 0.7955 (tmm) cc_final: 0.7698 (tmm) REVERT: D 124 MET cc_start: 0.7277 (tmm) cc_final: 0.6869 (tmm) REVERT: B 184 PRO cc_start: 0.8524 (Cg_exo) cc_final: 0.8264 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8767 (mt) cc_final: 0.8502 (mt) REVERT: B 643 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.7910 (m-70) REVERT: B 735 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7825 (pp) REVERT: B 749 MET cc_start: 0.7352 (mtt) cc_final: 0.7148 (mtt) REVERT: B 940 TRP cc_start: 0.6687 (t-100) cc_final: 0.6469 (t-100) REVERT: B 956 ILE cc_start: 0.8638 (mt) cc_final: 0.8295 (pt) REVERT: B 1015 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8444 (mm-40) REVERT: B 1029 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8234 (tm-30) REVERT: B 1064 ASP cc_start: 0.8580 (t0) cc_final: 0.8297 (t0) REVERT: B 1068 ILE cc_start: 0.9415 (mt) cc_final: 0.9055 (mm) REVERT: B 1090 ILE cc_start: 0.8618 (mt) cc_final: 0.8375 (mt) REVERT: B 1091 ASN cc_start: 0.7879 (t0) cc_final: 0.7056 (t0) REVERT: E 75 ILE cc_start: 0.8027 (mt) cc_final: 0.7679 (mm) REVERT: E 110 GLN cc_start: 0.7267 (mt0) cc_final: 0.6806 (mm-40) REVERT: E 111 MET cc_start: 0.7938 (tmm) cc_final: 0.7638 (tmm) REVERT: E 124 MET cc_start: 0.7301 (tmm) cc_final: 0.6772 (tmm) REVERT: C 26 ASN cc_start: 0.8494 (t0) cc_final: 0.7937 (t0) REVERT: C 184 PRO cc_start: 0.8560 (Cg_exo) cc_final: 0.8247 (Cg_endo) REVERT: C 735 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7902 (pp) REVERT: C 748 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6658 (tm-30) REVERT: C 814 MET cc_start: 0.8857 (mmp) cc_final: 0.8535 (tpp) REVERT: C 940 TRP cc_start: 0.6521 (t-100) cc_final: 0.6022 (t-100) REVERT: C 964 ASN cc_start: 0.8374 (t0) cc_final: 0.8011 (t0) REVERT: C 1064 ASP cc_start: 0.8466 (t0) cc_final: 0.8193 (t0) REVERT: C 1068 ILE cc_start: 0.9393 (mm) cc_final: 0.9140 (mm) REVERT: C 1091 ASN cc_start: 0.8114 (t0) cc_final: 0.7292 (t0) REVERT: C 1111 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.8520 (p90) REVERT: F 110 GLN cc_start: 0.7415 (mt0) cc_final: 0.6739 (mm-40) REVERT: F 111 MET cc_start: 0.7929 (tmm) cc_final: 0.7655 (tmm) REVERT: F 124 MET cc_start: 0.7455 (tmm) cc_final: 0.7023 (tmm) outliers start: 128 outliers final: 88 residues processed: 391 average time/residue: 0.1500 time to fit residues: 98.7684 Evaluate side-chains 364 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 269 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 731 TYR Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1111 TYR Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 954 TYR Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1015 GLN Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 747 TYR Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 954 TYR Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1128 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 331 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 357 optimal weight: 9.9990 chunk 314 optimal weight: 5.9990 chunk 266 optimal weight: 1.9990 chunk 292 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 305 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A 750 GLN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN ** C 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.086215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.069653 restraints weight = 88522.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.071874 restraints weight = 52420.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073434 restraints weight = 36532.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074541 restraints weight = 28298.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075321 restraints weight = 23477.629| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 29451 Z= 0.209 Angle : 0.662 9.882 40155 Z= 0.351 Chirality : 0.045 0.190 4536 Planarity : 0.005 0.096 5208 Dihedral : 6.661 57.892 4271 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 5.02 % Allowed : 17.90 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.13), residues: 3663 helix: -0.35 (0.20), residues: 729 sheet: -1.99 (0.19), residues: 651 loop : -2.15 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 637 TYR 0.019 0.002 TYR E 120 PHE 0.019 0.002 PHE A 393 TRP 0.016 0.002 TRP A 940 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00464 (29394) covalent geometry : angle 0.64959 (40032) SS BOND : bond 0.00549 ( 48) SS BOND : angle 2.53289 ( 96) hydrogen bonds : bond 0.04328 ( 774) hydrogen bonds : angle 5.57675 ( 2079) link_NAG-ASN : bond 0.00349 ( 9) link_NAG-ASN : angle 1.61542 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 276 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8550 (t0) cc_final: 0.7840 (t0) REVERT: A 134 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6529 (p90) REVERT: A 184 PRO cc_start: 0.8547 (Cg_exo) cc_final: 0.8321 (Cg_endo) REVERT: A 347 GLU cc_start: 0.8396 (mp0) cc_final: 0.8192 (pm20) REVERT: A 505 ASP cc_start: 0.8833 (p0) cc_final: 0.8582 (p0) REVERT: A 940 TRP cc_start: 0.6767 (t-100) cc_final: 0.6503 (t-100) REVERT: A 1068 ILE cc_start: 0.9452 (mt) cc_final: 0.9169 (mm) REVERT: A 1091 ASN cc_start: 0.8024 (t0) cc_final: 0.7341 (t0) REVERT: D 68 TYR cc_start: 0.8520 (m-80) cc_final: 0.7559 (m-80) REVERT: D 75 ILE cc_start: 0.8166 (mt) cc_final: 0.7812 (mm) REVERT: D 78 GLU cc_start: 0.7972 (pt0) cc_final: 0.7469 (pt0) REVERT: D 110 GLN cc_start: 0.7265 (mt0) cc_final: 0.6903 (mm-40) REVERT: D 111 MET cc_start: 0.7993 (tmm) cc_final: 0.7722 (tmm) REVERT: D 124 MET cc_start: 0.7403 (tmm) cc_final: 0.7003 (tmm) REVERT: B 184 PRO cc_start: 0.8513 (Cg_exo) cc_final: 0.8268 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8781 (mt) cc_final: 0.8501 (mt) REVERT: B 643 HIS cc_start: 0.8508 (OUTLIER) cc_final: 0.7911 (m-70) REVERT: B 804 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8693 (mm) REVERT: B 940 TRP cc_start: 0.6706 (t-100) cc_final: 0.6495 (t-100) REVERT: B 956 ILE cc_start: 0.8675 (mt) cc_final: 0.8300 (pt) REVERT: B 1015 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8258 (mm-40) REVERT: B 1029 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8184 (tm-30) REVERT: B 1064 ASP cc_start: 0.8601 (t0) cc_final: 0.8316 (t0) REVERT: B 1068 ILE cc_start: 0.9433 (mt) cc_final: 0.9064 (mm) REVERT: B 1090 ILE cc_start: 0.8682 (mt) cc_final: 0.8428 (mt) REVERT: B 1091 ASN cc_start: 0.7918 (t0) cc_final: 0.7201 (t0) REVERT: E 75 ILE cc_start: 0.8051 (mt) cc_final: 0.7754 (mm) REVERT: E 110 GLN cc_start: 0.7405 (mt0) cc_final: 0.6932 (mm-40) REVERT: E 111 MET cc_start: 0.7934 (tmm) cc_final: 0.7620 (tmm) REVERT: E 117 MET cc_start: 0.8447 (tmm) cc_final: 0.7817 (tmm) REVERT: E 124 MET cc_start: 0.7325 (tmm) cc_final: 0.6844 (tmm) REVERT: C 184 PRO cc_start: 0.8596 (Cg_exo) cc_final: 0.8317 (Cg_endo) REVERT: C 410 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: C 735 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7990 (pp) REVERT: C 748 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6671 (tm-30) REVERT: C 814 MET cc_start: 0.8884 (mmp) cc_final: 0.8581 (tpp) REVERT: C 940 TRP cc_start: 0.6627 (t-100) cc_final: 0.6309 (t-100) REVERT: C 964 ASN cc_start: 0.8329 (t0) cc_final: 0.7970 (t0) REVERT: C 1091 ASN cc_start: 0.8127 (t0) cc_final: 0.7320 (t0) REVERT: C 1111 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.8580 (p90) REVERT: F 36 VAL cc_start: 0.7239 (m) cc_final: 0.6997 (m) REVERT: F 110 GLN cc_start: 0.7405 (mt0) cc_final: 0.6632 (mm-40) REVERT: F 111 MET cc_start: 0.7981 (tmm) cc_final: 0.7654 (tmm) REVERT: F 124 MET cc_start: 0.7568 (tmm) cc_final: 0.7118 (tmm) outliers start: 158 outliers final: 116 residues processed: 393 average time/residue: 0.1476 time to fit residues: 98.4679 Evaluate side-chains 384 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 261 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 954 TYR Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1015 GLN Chi-restraints excluded: chain B residue 1018 ASN Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 410 PHE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 941 SER Chi-restraints excluded: chain C residue 954 TYR Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1018 ASN Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1128 SER Chi-restraints excluded: chain F residue 78 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 59 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 346 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 523 HIS ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 325 ASN B 428 HIS ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN C 314 GLN C 400 GLN C 428 HIS ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.083704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.067219 restraints weight = 90087.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.069395 restraints weight = 53042.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.070915 restraints weight = 36910.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.071989 restraints weight = 28565.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.072688 restraints weight = 23767.742| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 29451 Z= 0.312 Angle : 0.751 11.117 40155 Z= 0.398 Chirality : 0.047 0.219 4536 Planarity : 0.005 0.059 5208 Dihedral : 6.969 59.494 4271 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 5.49 % Allowed : 18.16 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.13), residues: 3663 helix: -0.37 (0.19), residues: 717 sheet: -2.04 (0.20), residues: 609 loop : -2.29 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 668 TYR 0.023 0.002 TYR E 120 PHE 0.028 0.002 PHE A 393 TRP 0.012 0.002 TRP A 940 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00683 (29394) covalent geometry : angle 0.73889 (40032) SS BOND : bond 0.00862 ( 48) SS BOND : angle 2.77263 ( 96) hydrogen bonds : bond 0.04655 ( 774) hydrogen bonds : angle 5.80152 ( 2079) link_NAG-ASN : bond 0.00334 ( 9) link_NAG-ASN : angle 1.60015 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 254 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.8623 (t0) cc_final: 0.8022 (t0) REVERT: A 134 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.6436 (p90) REVERT: A 505 ASP cc_start: 0.8966 (p0) cc_final: 0.8707 (p0) REVERT: A 749 MET cc_start: 0.7641 (mtt) cc_final: 0.7138 (mtt) REVERT: A 940 TRP cc_start: 0.7018 (t-100) cc_final: 0.6577 (t-100) REVERT: A 1068 ILE cc_start: 0.9475 (mt) cc_final: 0.9244 (mt) REVERT: A 1091 ASN cc_start: 0.8048 (t0) cc_final: 0.7365 (t0) REVERT: A 1166 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7999 (tp) REVERT: D 68 TYR cc_start: 0.8777 (m-80) cc_final: 0.8336 (m-80) REVERT: D 78 GLU cc_start: 0.8123 (pt0) cc_final: 0.7920 (pt0) REVERT: D 90 PHE cc_start: 0.8564 (m-80) cc_final: 0.8149 (m-80) REVERT: D 110 GLN cc_start: 0.7346 (mt0) cc_final: 0.6859 (mm-40) REVERT: D 111 MET cc_start: 0.7993 (tmm) cc_final: 0.7726 (tmm) REVERT: D 124 MET cc_start: 0.7476 (tmm) cc_final: 0.7079 (tmm) REVERT: B 134 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.7389 (p90) REVERT: B 184 PRO cc_start: 0.8540 (Cg_exo) cc_final: 0.8310 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8925 (mt) cc_final: 0.8625 (mt) REVERT: B 643 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.8018 (m-70) REVERT: B 749 MET cc_start: 0.7688 (mtt) cc_final: 0.7172 (mtm) REVERT: B 804 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8632 (mm) REVERT: B 936 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6145 (tpt) REVERT: B 940 TRP cc_start: 0.6998 (t-100) cc_final: 0.6748 (t-100) REVERT: B 1015 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8378 (mm-40) REVERT: B 1029 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8261 (tm-30) REVERT: B 1064 ASP cc_start: 0.8411 (t0) cc_final: 0.8102 (t0) REVERT: B 1068 ILE cc_start: 0.9449 (mt) cc_final: 0.9071 (mm) REVERT: B 1090 ILE cc_start: 0.8737 (mt) cc_final: 0.8528 (mt) REVERT: B 1091 ASN cc_start: 0.8040 (t0) cc_final: 0.7322 (t0) REVERT: E 111 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7624 (tmm) REVERT: E 117 MET cc_start: 0.8592 (tmm) cc_final: 0.7953 (tmm) REVERT: C 26 ASN cc_start: 0.8674 (t0) cc_final: 0.7986 (t0) REVERT: C 134 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6932 (p90) REVERT: C 643 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.7825 (m-70) REVERT: C 701 MET cc_start: 0.7969 (ttp) cc_final: 0.7750 (ptm) REVERT: C 735 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8100 (pp) REVERT: C 814 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8651 (tpp) REVERT: C 940 TRP cc_start: 0.7033 (t-100) cc_final: 0.6605 (t-100) REVERT: C 1091 ASN cc_start: 0.8227 (t0) cc_final: 0.7436 (t0) REVERT: C 1111 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.8575 (p90) REVERT: F 36 VAL cc_start: 0.7215 (m) cc_final: 0.6995 (m) REVERT: F 111 MET cc_start: 0.7972 (tmm) cc_final: 0.7610 (tmm) REVERT: F 124 MET cc_start: 0.7600 (tmm) cc_final: 0.7225 (tmm) outliers start: 173 outliers final: 120 residues processed: 396 average time/residue: 0.1554 time to fit residues: 102.6857 Evaluate side-chains 370 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 237 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1111 TYR Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 954 TYR Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1015 GLN Chi-restraints excluded: chain B residue 1018 ASN Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 643 HIS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 814 MET Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 941 SER Chi-restraints excluded: chain C residue 954 TYR Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1128 SER Chi-restraints excluded: chain F residue 78 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 91 optimal weight: 6.9990 chunk 351 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 195 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 348 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 GLN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS B 765 GLN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN C 765 GLN ** C 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.085669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.069135 restraints weight = 89136.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.071366 restraints weight = 52332.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.072949 restraints weight = 36307.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074069 restraints weight = 27973.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074839 restraints weight = 23130.016| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29451 Z= 0.200 Angle : 0.674 10.268 40155 Z= 0.357 Chirality : 0.045 0.194 4536 Planarity : 0.005 0.083 5208 Dihedral : 6.697 56.635 4271 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 4.95 % Allowed : 19.46 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.13), residues: 3663 helix: -0.14 (0.20), residues: 699 sheet: -2.06 (0.19), residues: 651 loop : -2.15 (0.12), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 131 TYR 0.023 0.002 TYR D 120 PHE 0.016 0.002 PHE A 393 TRP 0.010 0.001 TRP A 334 HIS 0.004 0.001 HIS C 428 Details of bonding type rmsd covalent geometry : bond 0.00442 (29394) covalent geometry : angle 0.65958 (40032) SS BOND : bond 0.00519 ( 48) SS BOND : angle 2.85547 ( 96) hydrogen bonds : bond 0.04216 ( 774) hydrogen bonds : angle 5.60877 ( 2079) link_NAG-ASN : bond 0.00305 ( 9) link_NAG-ASN : angle 1.59313 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 260 time to evaluate : 1.101 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 134 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6524 (p90) REVERT: A 701 MET cc_start: 0.7713 (ttp) cc_final: 0.7503 (ptp) REVERT: A 749 MET cc_start: 0.7564 (mtt) cc_final: 0.7126 (mtt) REVERT: A 940 TRP cc_start: 0.6847 (t-100) cc_final: 0.6439 (t-100) REVERT: A 1029 GLU cc_start: 0.8897 (tp30) cc_final: 0.8569 (tp30) REVERT: A 1068 ILE cc_start: 0.9442 (mt) cc_final: 0.9198 (mm) REVERT: A 1091 ASN cc_start: 0.7939 (t0) cc_final: 0.7266 (t0) REVERT: D 68 TYR cc_start: 0.8719 (m-80) cc_final: 0.8306 (m-80) REVERT: D 110 GLN cc_start: 0.7267 (mt0) cc_final: 0.6726 (mm-40) REVERT: D 111 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7739 (tmm) REVERT: D 124 MET cc_start: 0.7671 (tmm) cc_final: 0.7156 (tmm) REVERT: B 26 ASN cc_start: 0.8650 (t0) cc_final: 0.8055 (t0) REVERT: B 134 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.7520 (p90) REVERT: B 184 PRO cc_start: 0.8558 (Cg_exo) cc_final: 0.8317 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8824 (mt) cc_final: 0.8541 (mt) REVERT: B 643 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.7931 (m-70) REVERT: B 668 ARG cc_start: 0.7634 (ptt180) cc_final: 0.7379 (ptt90) REVERT: B 749 MET cc_start: 0.7645 (mtt) cc_final: 0.7105 (mtm) REVERT: B 804 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8664 (mm) REVERT: B 940 TRP cc_start: 0.6734 (t-100) cc_final: 0.6517 (t-100) REVERT: B 956 ILE cc_start: 0.8762 (mt) cc_final: 0.8392 (pt) REVERT: B 1015 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8280 (mm-40) REVERT: B 1029 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8120 (tm-30) REVERT: B 1064 ASP cc_start: 0.8630 (t0) cc_final: 0.8408 (t0) REVERT: B 1068 ILE cc_start: 0.9411 (mt) cc_final: 0.9132 (mm) REVERT: B 1090 ILE cc_start: 0.8615 (mt) cc_final: 0.8305 (mm) REVERT: B 1091 ASN cc_start: 0.8048 (t0) cc_final: 0.7431 (t0) REVERT: E 90 PHE cc_start: 0.8394 (m-80) cc_final: 0.7921 (m-80) REVERT: E 111 MET cc_start: 0.8020 (tmm) cc_final: 0.7676 (tmm) REVERT: E 117 MET cc_start: 0.8433 (tmm) cc_final: 0.7908 (tmm) REVERT: E 124 MET cc_start: 0.7401 (tmm) cc_final: 0.6978 (tmm) REVERT: C 134 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.6894 (p90) REVERT: C 402 ASP cc_start: 0.7655 (m-30) cc_final: 0.7338 (m-30) REVERT: C 633 CYS cc_start: 0.4744 (m) cc_final: 0.4518 (m) REVERT: C 643 HIS cc_start: 0.8413 (OUTLIER) cc_final: 0.7588 (m-70) REVERT: C 701 MET cc_start: 0.7899 (ttp) cc_final: 0.7549 (ptm) REVERT: C 735 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8003 (pp) REVERT: C 814 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8592 (tpp) REVERT: C 940 TRP cc_start: 0.6750 (t-100) cc_final: 0.6331 (t-100) REVERT: C 964 ASN cc_start: 0.8389 (t0) cc_final: 0.8071 (t0) REVERT: C 1091 ASN cc_start: 0.8116 (t0) cc_final: 0.7327 (t0) REVERT: C 1111 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8590 (p90) REVERT: F 36 VAL cc_start: 0.7124 (m) cc_final: 0.6912 (m) REVERT: F 111 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7603 (tmm) REVERT: F 124 MET cc_start: 0.7504 (tmm) cc_final: 0.7067 (tmm) outliers start: 156 outliers final: 125 residues processed: 381 average time/residue: 0.1577 time to fit residues: 100.9559 Evaluate side-chains 375 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 238 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1111 TYR Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 954 TYR Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1015 GLN Chi-restraints excluded: chain B residue 1018 ASN Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 507 CYS Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 643 HIS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 814 MET Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 941 SER Chi-restraints excluded: chain C residue 954 TYR Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1018 ASN Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain C residue 1128 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 111 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 336 optimal weight: 10.0000 chunk 105 optimal weight: 0.0980 chunk 214 optimal weight: 0.9990 chunk 354 optimal weight: 0.4980 chunk 42 optimal weight: 6.9990 chunk 351 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 316 optimal weight: 0.9980 chunk 304 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 252 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN A1114 HIS B 765 GLN B 789 GLN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN C 750 GLN ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.088649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072071 restraints weight = 86801.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074384 restraints weight = 51033.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.076016 restraints weight = 35316.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.077177 restraints weight = 27093.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.077951 restraints weight = 22303.542| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29451 Z= 0.118 Angle : 0.632 11.530 40155 Z= 0.333 Chirality : 0.044 0.192 4536 Planarity : 0.004 0.062 5208 Dihedral : 6.302 53.316 4271 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.62 % Allowed : 20.70 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.13), residues: 3663 helix: 0.08 (0.20), residues: 699 sheet: -1.92 (0.19), residues: 663 loop : -2.03 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1019 TYR 0.026 0.001 TYR F 120 PHE 0.029 0.001 PHE C 988 TRP 0.010 0.001 TRP C 605 HIS 0.003 0.001 HIS D 56 Details of bonding type rmsd covalent geometry : bond 0.00256 (29394) covalent geometry : angle 0.62081 (40032) SS BOND : bond 0.00470 ( 48) SS BOND : angle 2.36682 ( 96) hydrogen bonds : bond 0.03829 ( 774) hydrogen bonds : angle 5.35002 ( 2079) link_NAG-ASN : bond 0.00447 ( 9) link_NAG-ASN : angle 1.53004 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 290 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.6449 (p90) REVERT: A 385 PHE cc_start: 0.8582 (m-10) cc_final: 0.8354 (m-10) REVERT: A 643 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7509 (m-70) REVERT: A 749 MET cc_start: 0.7515 (mtt) cc_final: 0.7041 (mtt) REVERT: A 940 TRP cc_start: 0.6553 (t-100) cc_final: 0.6342 (t-100) REVERT: A 1029 GLU cc_start: 0.8792 (tp30) cc_final: 0.8442 (tp30) REVERT: A 1068 ILE cc_start: 0.9434 (mt) cc_final: 0.9226 (mm) REVERT: A 1091 ASN cc_start: 0.7757 (t0) cc_final: 0.7099 (t0) REVERT: D 88 MET cc_start: 0.8814 (ttp) cc_final: 0.7829 (ppp) REVERT: D 110 GLN cc_start: 0.7230 (mt0) cc_final: 0.6675 (mm-40) REVERT: D 111 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7813 (tmm) REVERT: D 124 MET cc_start: 0.7600 (tmm) cc_final: 0.6994 (tmm) REVERT: B 26 ASN cc_start: 0.8603 (t0) cc_final: 0.7911 (t0) REVERT: B 184 PRO cc_start: 0.8494 (Cg_exo) cc_final: 0.8262 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8835 (mt) cc_final: 0.8623 (mt) REVERT: B 643 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7706 (m-70) REVERT: B 940 TRP cc_start: 0.6596 (t-100) cc_final: 0.6313 (t-100) REVERT: B 1029 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7993 (tm-30) REVERT: B 1068 ILE cc_start: 0.9408 (mt) cc_final: 0.9173 (tp) REVERT: B 1090 ILE cc_start: 0.8574 (mt) cc_final: 0.8319 (mm) REVERT: B 1091 ASN cc_start: 0.7925 (t0) cc_final: 0.7273 (t0) REVERT: E 88 MET cc_start: 0.8670 (ttp) cc_final: 0.7450 (tmm) REVERT: E 90 PHE cc_start: 0.8303 (m-80) cc_final: 0.7557 (m-10) REVERT: E 110 GLN cc_start: 0.7385 (mt0) cc_final: 0.7086 (mt0) REVERT: E 111 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7695 (tmm) REVERT: E 117 MET cc_start: 0.8364 (tmm) cc_final: 0.7889 (tmm) REVERT: C 26 ASN cc_start: 0.8643 (t0) cc_final: 0.8004 (t0) REVERT: C 184 PRO cc_start: 0.8417 (Cg_exo) cc_final: 0.8147 (Cg_endo) REVERT: C 643 HIS cc_start: 0.8200 (OUTLIER) cc_final: 0.7334 (m-70) REVERT: C 735 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7834 (pp) REVERT: C 748 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6653 (tm-30) REVERT: C 826 VAL cc_start: 0.7006 (OUTLIER) cc_final: 0.6781 (t) REVERT: C 867 ARG cc_start: 0.7587 (mtp-110) cc_final: 0.7283 (ptm160) REVERT: C 940 TRP cc_start: 0.6539 (t-100) cc_final: 0.6062 (t-100) REVERT: C 964 ASN cc_start: 0.8300 (t0) cc_final: 0.8008 (t0) REVERT: C 998 ILE cc_start: 0.9337 (mt) cc_final: 0.9089 (tt) REVERT: C 1029 GLU cc_start: 0.8690 (tp30) cc_final: 0.8438 (tp30) REVERT: C 1068 ILE cc_start: 0.9291 (mm) cc_final: 0.9006 (tp) REVERT: C 1091 ASN cc_start: 0.7959 (t0) cc_final: 0.7270 (t0) REVERT: C 1111 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8573 (p90) REVERT: F 111 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7626 (tmm) REVERT: F 124 MET cc_start: 0.7552 (tmm) cc_final: 0.7318 (tmm) outliers start: 114 outliers final: 83 residues processed: 373 average time/residue: 0.1586 time to fit residues: 99.0345 Evaluate side-chains 350 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 257 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 954 TYR Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 643 HIS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 954 TYR Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 111 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 157 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 319 optimal weight: 0.9990 chunk 267 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 328 optimal weight: 2.9990 chunk 250 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 HIS A 544 ASN A 750 GLN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 HIS ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 765 GLN C1018 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.087897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.071104 restraints weight = 87743.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073406 restraints weight = 51511.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.075038 restraints weight = 35647.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076201 restraints weight = 27413.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.076952 restraints weight = 22590.788| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29451 Z= 0.149 Angle : 0.645 13.198 40155 Z= 0.337 Chirality : 0.044 0.185 4536 Planarity : 0.004 0.071 5208 Dihedral : 6.259 54.799 4271 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.78 % Allowed : 21.27 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.13), residues: 3663 helix: 0.36 (0.21), residues: 678 sheet: -1.90 (0.19), residues: 645 loop : -1.98 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 637 TYR 0.023 0.001 TYR E 120 PHE 0.026 0.001 PHE D 90 TRP 0.008 0.001 TRP C 536 HIS 0.003 0.001 HIS A1098 Details of bonding type rmsd covalent geometry : bond 0.00334 (29394) covalent geometry : angle 0.63256 (40032) SS BOND : bond 0.00492 ( 48) SS BOND : angle 2.51679 ( 96) hydrogen bonds : bond 0.03879 ( 774) hydrogen bonds : angle 5.24852 ( 2079) link_NAG-ASN : bond 0.00332 ( 9) link_NAG-ASN : angle 1.49760 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 264 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6459 (p90) REVERT: A 385 PHE cc_start: 0.8591 (m-10) cc_final: 0.8352 (m-10) REVERT: A 643 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7532 (m-70) REVERT: A 749 MET cc_start: 0.7554 (mtt) cc_final: 0.7102 (mtt) REVERT: A 940 TRP cc_start: 0.6696 (t-100) cc_final: 0.6325 (t-100) REVERT: A 1029 GLU cc_start: 0.8839 (tp30) cc_final: 0.8468 (tp30) REVERT: A 1068 ILE cc_start: 0.9452 (mt) cc_final: 0.9241 (mm) REVERT: A 1091 ASN cc_start: 0.7823 (t0) cc_final: 0.7150 (t0) REVERT: D 88 MET cc_start: 0.8854 (ttp) cc_final: 0.7857 (ppp) REVERT: D 110 GLN cc_start: 0.7270 (mt0) cc_final: 0.6667 (mm-40) REVERT: D 111 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7812 (tmm) REVERT: D 124 MET cc_start: 0.7597 (tmm) cc_final: 0.6999 (tmm) REVERT: B 26 ASN cc_start: 0.8609 (t0) cc_final: 0.7939 (t0) REVERT: B 431 LEU cc_start: 0.8850 (mt) cc_final: 0.8626 (mt) REVERT: B 643 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7620 (m-70) REVERT: B 749 MET cc_start: 0.7618 (mtt) cc_final: 0.7053 (mtm) REVERT: B 940 TRP cc_start: 0.6693 (t-100) cc_final: 0.6437 (t-100) REVERT: B 1029 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7992 (tm-30) REVERT: B 1068 ILE cc_start: 0.9424 (mt) cc_final: 0.9204 (mm) REVERT: B 1090 ILE cc_start: 0.8609 (mt) cc_final: 0.8336 (mm) REVERT: B 1091 ASN cc_start: 0.7989 (t0) cc_final: 0.7313 (t0) REVERT: E 88 MET cc_start: 0.8657 (ttp) cc_final: 0.7318 (tmm) REVERT: E 90 PHE cc_start: 0.8350 (m-80) cc_final: 0.7611 (m-10) REVERT: E 110 GLN cc_start: 0.7260 (mt0) cc_final: 0.6927 (mt0) REVERT: E 117 MET cc_start: 0.8385 (tmm) cc_final: 0.7915 (tmm) REVERT: C 134 TYR cc_start: 0.7175 (OUTLIER) cc_final: 0.6725 (p90) REVERT: C 184 PRO cc_start: 0.8437 (Cg_exo) cc_final: 0.8160 (Cg_endo) REVERT: C 373 ASN cc_start: 0.9047 (p0) cc_final: 0.8828 (p0) REVERT: C 643 HIS cc_start: 0.8260 (OUTLIER) cc_final: 0.7393 (m-70) REVERT: C 735 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7839 (pp) REVERT: C 748 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6795 (tm-30) REVERT: C 826 VAL cc_start: 0.7173 (OUTLIER) cc_final: 0.6919 (t) REVERT: C 940 TRP cc_start: 0.6695 (t-100) cc_final: 0.6233 (t-100) REVERT: C 964 ASN cc_start: 0.8325 (t0) cc_final: 0.8048 (t0) REVERT: C 1029 GLU cc_start: 0.8714 (tp30) cc_final: 0.8466 (tp30) REVERT: C 1068 ILE cc_start: 0.9320 (mm) cc_final: 0.9055 (tp) REVERT: C 1091 ASN cc_start: 0.7994 (t0) cc_final: 0.7251 (t0) REVERT: C 1111 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8503 (p90) REVERT: F 111 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7654 (tmm) REVERT: F 124 MET cc_start: 0.7557 (tmm) cc_final: 0.7234 (tmm) outliers start: 119 outliers final: 100 residues processed: 351 average time/residue: 0.1511 time to fit residues: 89.2331 Evaluate side-chains 357 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 247 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1111 TYR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 954 TYR Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 643 HIS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 731 TYR Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 954 TYR Chi-restraints excluded: chain C residue 956 ILE Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1018 ASN Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 111 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 109 optimal weight: 0.0770 chunk 190 optimal weight: 6.9990 chunk 330 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 chunk 246 optimal weight: 0.4980 chunk 209 optimal weight: 3.9990 chunk 126 optimal weight: 0.4980 chunk 4 optimal weight: 0.0060 chunk 337 optimal weight: 0.9990 overall best weight: 0.2292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN A 688 ASN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 ASN C1018 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.089253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.072387 restraints weight = 87318.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.074799 restraints weight = 50259.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.076512 restraints weight = 34422.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.077733 restraints weight = 26223.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.078507 restraints weight = 21471.929| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 29451 Z= 0.115 Angle : 0.635 12.293 40155 Z= 0.331 Chirality : 0.044 0.212 4536 Planarity : 0.004 0.078 5208 Dihedral : 6.048 52.716 4271 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.14 % Allowed : 21.97 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.13), residues: 3663 helix: 0.34 (0.20), residues: 702 sheet: -1.81 (0.20), residues: 612 loop : -1.89 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 637 TYR 0.023 0.001 TYR E 120 PHE 0.022 0.001 PHE C 988 TRP 0.013 0.001 TRP C 605 HIS 0.004 0.001 HIS D 56 Details of bonding type rmsd covalent geometry : bond 0.00249 (29394) covalent geometry : angle 0.62559 (40032) SS BOND : bond 0.00430 ( 48) SS BOND : angle 2.20974 ( 96) hydrogen bonds : bond 0.03610 ( 774) hydrogen bonds : angle 5.06411 ( 2079) link_NAG-ASN : bond 0.00421 ( 9) link_NAG-ASN : angle 1.47338 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 285 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.6528 (p90) REVERT: A 205 HIS cc_start: 0.8337 (OUTLIER) cc_final: 0.8083 (m170) REVERT: A 385 PHE cc_start: 0.8466 (m-10) cc_final: 0.8234 (m-10) REVERT: A 643 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.7282 (m-70) REVERT: A 749 MET cc_start: 0.7464 (mtt) cc_final: 0.6992 (mtt) REVERT: A 1029 GLU cc_start: 0.8797 (tp30) cc_final: 0.8371 (tp30) REVERT: A 1068 ILE cc_start: 0.9422 (mt) cc_final: 0.9153 (tp) REVERT: A 1091 ASN cc_start: 0.7669 (t0) cc_final: 0.7028 (t0) REVERT: A 1099 ILE cc_start: 0.8387 (mm) cc_final: 0.8128 (mp) REVERT: D 54 LEU cc_start: 0.7165 (tt) cc_final: 0.6499 (tp) REVERT: D 75 ILE cc_start: 0.8036 (mt) cc_final: 0.7743 (mm) REVERT: D 88 MET cc_start: 0.8843 (ttp) cc_final: 0.7811 (ppp) REVERT: D 110 GLN cc_start: 0.7280 (mt0) cc_final: 0.6653 (mm-40) REVERT: D 111 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7803 (tmm) REVERT: D 124 MET cc_start: 0.7552 (tmm) cc_final: 0.6913 (tmm) REVERT: B 26 ASN cc_start: 0.8633 (t0) cc_final: 0.7981 (t0) REVERT: B 149 MET cc_start: 0.7932 (pmm) cc_final: 0.7622 (pmm) REVERT: B 184 PRO cc_start: 0.8491 (Cg_exo) cc_final: 0.8249 (Cg_endo) REVERT: B 385 PHE cc_start: 0.8525 (m-10) cc_final: 0.8266 (m-10) REVERT: B 643 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.7490 (m-70) REVERT: B 668 ARG cc_start: 0.7536 (ptt180) cc_final: 0.6540 (ptt-90) REVERT: B 823 MET cc_start: 0.6907 (tmm) cc_final: 0.6669 (tmm) REVERT: B 940 TRP cc_start: 0.6604 (t-100) cc_final: 0.6336 (t-100) REVERT: B 1029 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7973 (tm-30) REVERT: B 1068 ILE cc_start: 0.9405 (mt) cc_final: 0.9191 (mm) REVERT: B 1090 ILE cc_start: 0.8493 (mt) cc_final: 0.8206 (mm) REVERT: B 1091 ASN cc_start: 0.7907 (t0) cc_final: 0.7250 (t0) REVERT: B 1099 ILE cc_start: 0.8549 (mm) cc_final: 0.8294 (mm) REVERT: E 88 MET cc_start: 0.8650 (ttp) cc_final: 0.7378 (tmm) REVERT: E 90 PHE cc_start: 0.8221 (m-80) cc_final: 0.7481 (m-10) REVERT: E 91 THR cc_start: 0.8446 (p) cc_final: 0.8130 (p) REVERT: E 110 GLN cc_start: 0.7428 (mt0) cc_final: 0.7096 (mt0) REVERT: E 117 MET cc_start: 0.8351 (tmm) cc_final: 0.7911 (tmm) REVERT: C 26 ASN cc_start: 0.8653 (t0) cc_final: 0.8094 (t0) REVERT: C 184 PRO cc_start: 0.8552 (Cg_exo) cc_final: 0.8265 (Cg_endo) REVERT: C 373 ASN cc_start: 0.8822 (p0) cc_final: 0.8602 (p0) REVERT: C 643 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7251 (m-70) REVERT: C 735 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7736 (pp) REVERT: C 748 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6732 (tm-30) REVERT: C 826 VAL cc_start: 0.6896 (OUTLIER) cc_final: 0.6687 (t) REVERT: C 940 TRP cc_start: 0.6454 (t-100) cc_final: 0.5953 (t-100) REVERT: C 964 ASN cc_start: 0.8354 (t0) cc_final: 0.8076 (t0) REVERT: C 998 ILE cc_start: 0.9309 (mt) cc_final: 0.9042 (tt) REVERT: C 1068 ILE cc_start: 0.9318 (mm) cc_final: 0.8990 (tp) REVERT: C 1091 ASN cc_start: 0.7915 (t0) cc_final: 0.7186 (t0) REVERT: C 1099 ILE cc_start: 0.8653 (mm) cc_final: 0.8326 (mm) REVERT: C 1111 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8447 (p90) REVERT: F 111 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7639 (tmm) REVERT: F 124 MET cc_start: 0.7399 (tmm) cc_final: 0.7044 (tmm) outliers start: 99 outliers final: 76 residues processed: 352 average time/residue: 0.1513 time to fit residues: 90.6269 Evaluate side-chains 346 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 260 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 954 TYR Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1128 SER Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 643 HIS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 880 VAL Chi-restraints excluded: chain C residue 941 SER Chi-restraints excluded: chain C residue 954 TYR Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1111 TYR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 111 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 38 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 353 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 220 optimal weight: 0.0040 chunk 310 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 205 HIS A 688 ASN A 765 GLN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 ASN C 789 GLN C1018 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.086027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.069323 restraints weight = 89306.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.071570 restraints weight = 52257.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.073157 restraints weight = 36288.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074296 restraints weight = 28031.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.075038 restraints weight = 23174.427| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29451 Z= 0.207 Angle : 0.679 11.973 40155 Z= 0.354 Chirality : 0.045 0.187 4536 Planarity : 0.004 0.062 5208 Dihedral : 6.233 56.705 4271 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.40 % Allowed : 22.10 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.14), residues: 3663 helix: 0.50 (0.21), residues: 681 sheet: -1.71 (0.19), residues: 633 loop : -1.94 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 637 TYR 0.022 0.002 TYR A1111 PHE 0.019 0.002 PHE A 393 TRP 0.036 0.002 TRP A 940 HIS 0.004 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00461 (29394) covalent geometry : angle 0.66682 (40032) SS BOND : bond 0.00637 ( 48) SS BOND : angle 2.62666 ( 96) hydrogen bonds : bond 0.03906 ( 774) hydrogen bonds : angle 5.08797 ( 2079) link_NAG-ASN : bond 0.00284 ( 9) link_NAG-ASN : angle 1.49417 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4081.45 seconds wall clock time: 71 minutes 45.86 seconds (4305.86 seconds total)