Starting phenix.real_space_refine on Mon Sep 14 07:27:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vsj_21377/09_2026/6vsj_21377.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vsj_21377/09_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_21377/09_2026/6vsj_21377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vsj_21377/09_2026/6vsj_21377.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vsj_21377/09_2026/6vsj_21377.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vsj_21377/09_2026/6vsj_21377.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vsj_21377/09_2026/6vsj_21377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vsj_21377/09_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 chiralities: 1 Restraints were copied for chains: B, C, E, F Time building chain proxies: 11.34, per 1000 atoms: 0.39 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: 2.37 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: 1.10 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: 7.41 Time building geometry restraints manager: 3.15 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: 15043 16.60 - 33.20: 1834 33.20 - 49.80: 415 49.80 - 66.40: 72 66.40 - 83.01: 27 Dihedral angle restraints: 17391 sinusoidal: 6657 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 17388 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: 0.08 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.860 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 15.040 83.006 10383 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/Z covalent geometry : bond 0.00845 / 0.40 (29394) covalent geometry : angle 1.01740 / 0.59 (40032) SS BOND : bond 0.01012 / 0.62 ( 48) SS BOND : angle 2.88040 / 1.73 ( 96) hydrogen bonds : bond 0.30550 / 20.71 ( 774) hydrogen bonds : angle 10.35683 / 7.31 ( 2079) link_NAG-ASN : bond 0.00255 / 0.11 ( 9) link_NAG-ASN : angle 3.74569 / 2.36 ( 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 : 1.141 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: 0.1957 time to fit residues: 143.8761 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 : 1.082 ------------------------------------------------------------------------------- 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... 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 = 0.3550 r_free = 0.3550 target = 0.087832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.071095 restraints weight = 87685.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.073389 restraints weight = 51713.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.074979 restraints weight = 35909.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.076118 restraints weight = 27741.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.076931 restraints weight = 22920.075| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1665 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= 0.163 Angle : 0.679 12.581 40155 Z= 0.367 Chirality : 0.045 0.237 4536 Planarity : 0.005 0.101 5208 Dihedral : 6.866 58.484 4034 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.11 % Allowed : 15.90 % Favored : 80.98 % 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: -3.20 (0.12), residues: 3663 helix: -1.85 (0.16), residues: 729 sheet: -2.05 (0.20), residues: 612 loop : -2.34 (0.12), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 399 TYR 0.019 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/Z covalent geometry : bond 0.00353 / 0.16 (29394) covalent geometry : angle 0.66622 / 0.36 (40032) SS BOND : bond 0.00585 / 0.33 ( 48) SS BOND : angle 2.56370 / 1.53 ( 96) hydrogen bonds : bond 0.05472 / 3.70 ( 774) hydrogen bonds : angle 6.62891 / 4.68 ( 2079) link_NAG-ASN : bond 0.00307 / 0.14 ( 9) link_NAG-ASN : angle 1.98088 / 1.21 ( 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 450 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 352 time to evaluate : 1.117 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: 0.8405 (t0) cc_final: 0.7808 (t0) REVERT: A 184 PRO cc_start: 0.8575 (Cg_exo) cc_final: 0.8349 (Cg_endo) REVERT: A 431 LEU cc_start: 0.8929 (mt) cc_final: 0.8713 (mt) REVERT: A 748 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6698 (tm-30) REVERT: A 749 MET cc_start: 0.7150 (mtt) cc_final: 0.6529 (mtt) REVERT: A 964 ASN cc_start: 0.8229 (t0) cc_final: 0.8016 (t0) REVERT: A 998 ILE cc_start: 0.9400 (mt) cc_final: 0.9163 (tt) REVERT: A 1029 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8166 (tm-30) REVERT: A 1064 ASP cc_start: 0.8474 (t0) cc_final: 0.8261 (t0) REVERT: A 1068 ILE cc_start: 0.9444 (mt) cc_final: 0.9186 (mm) REVERT: A 1091 ASN cc_start: 0.7894 (t0) cc_final: 0.7021 (t0) REVERT: D 68 TYR cc_start: 0.8450 (m-80) cc_final: 0.8054 (m-80) REVERT: D 110 GLN cc_start: 0.7185 (mt0) cc_final: 0.6959 (mm-40) REVERT: D 111 MET cc_start: 0.7884 (tmm) cc_final: 0.7639 (tmm) REVERT: D 120 TYR cc_start: 0.6590 (m-80) cc_final: 0.6340 (m-80) REVERT: D 124 MET cc_start: 0.7173 (tmm) cc_final: 0.6823 (tmm) REVERT: B 26 ASN cc_start: 0.8388 (t0) cc_final: 0.7870 (t0) REVERT: B 184 PRO cc_start: 0.8548 (Cg_exo) cc_final: 0.8309 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8814 (mt) cc_final: 0.8531 (mt) REVERT: B 940 TRP cc_start: 0.6647 (t-100) cc_final: 0.6262 (t-100) REVERT: B 956 ILE cc_start: 0.8586 (mt) cc_final: 0.8292 (pt) REVERT: B 1015 GLN cc_start: 0.8804 (tp-100) cc_final: 0.8218 (mm-40) REVERT: B 1029 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8179 (tm-30) REVERT: B 1091 ASN cc_start: 0.7681 (t0) cc_final: 0.6741 (t0) REVERT: E 111 MET cc_start: 0.7775 (tmm) cc_final: 0.7501 (tmm) REVERT: E 120 TYR cc_start: 0.6173 (m-80) cc_final: 0.5851 (m-80) REVERT: E 124 MET cc_start: 0.6969 (tmm) cc_final: 0.6501 (tmm) REVERT: C 26 ASN cc_start: 0.8545 (t0) cc_final: 0.7976 (t0) REVERT: C 184 PRO cc_start: 0.8601 (Cg_exo) cc_final: 0.8308 (Cg_endo) REVERT: C 349 LYS cc_start: 0.8238 (tttt) cc_final: 0.7981 (tptm) REVERT: C 431 LEU cc_start: 0.8954 (mt) cc_final: 0.8727 (mt) REVERT: C 637 ARG cc_start: 0.7293 (ptt180) cc_final: 0.6761 (ptp-170) REVERT: C 748 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6712 (tm-30) REVERT: C 814 MET cc_start: 0.8827 (mmp) cc_final: 0.8545 (tpp) REVERT: C 940 TRP cc_start: 0.6621 (t-100) cc_final: 0.6268 (t-100) REVERT: C 1064 ASP cc_start: 0.8491 (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: 0.7828 (tmm) cc_final: 0.7542 (tmm) REVERT: F 124 MET cc_start: 0.7311 (tmm) cc_final: 0.6836 (tmm) outliers start: 98 outliers final: 53 residues processed: 422 average time/residue: 0.1804 time to fit residues: 126.0051 Evaluate side-chains 330 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 277 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 537 SER 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 537 SER 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 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: 6.9990 chunk 299 optimal weight: 10.0000 chunk 15 optimal weight: 0.0570 chunk 206 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 226 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 301 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 343 optimal weight: 5.9990 overall best weight: 1.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 ASN A 400 GLN A 759 HIS 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 674 ASN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 GLN ** 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 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1114 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.087801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.071249 restraints weight = 87250.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.073550 restraints weight = 51074.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075169 restraints weight = 35296.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.076321 restraints weight = 27091.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.077105 restraints weight = 22316.438| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29451 Z= 0.159 Angle : 0.643 10.226 40155 Z= 0.345 Chirality : 0.045 0.206 4536 Planarity : 0.005 0.078 5208 Dihedral : 6.192 55.451 4020 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.10 % Allowed : 16.48 % Favored : 79.43 % 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: -2.81 (0.13), residues: 3663 helix: -0.98 (0.18), residues: 729 sheet: -2.05 (0.19), residues: 636 loop : -2.20 (0.12), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 668 TYR 0.015 0.001 TYR B1111 PHE 0.018 0.002 PHE F 138 TRP 0.011 0.001 TRP A 940 HIS 0.003 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (29394) covalent geometry : angle 0.63037 / 0.34 (40032) SS BOND : bond 0.00523 / 0.29 ( 48) SS BOND : angle 2.51112 / 1.55 ( 96) hydrogen bonds : bond 0.04756 / 3.19 ( 774) hydrogen bonds : angle 5.95476 / 4.19 ( 2079) link_NAG-ASN : bond 0.00308 / 0.14 ( 9) link_NAG-ASN : angle 1.70454 / 1.05 ( 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: 129 poor density : 307 time to evaluate : 1.259 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: A 26 ASN cc_start: 0.8515 (t0) cc_final: 0.7863 (t0) REVERT: A 137 TYR cc_start: 0.8610 (m-80) cc_final: 0.8405 (m-10) REVERT: A 184 PRO cc_start: 0.8551 (Cg_exo) cc_final: 0.8332 (Cg_endo) REVERT: A 347 GLU cc_start: 0.8446 (mp0) cc_final: 0.8126 (pm20) REVERT: A 748 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6836 (tm-30) REVERT: A 749 MET cc_start: 0.7157 (mtt) cc_final: 0.6526 (mtt) REVERT: A 963 MET cc_start: 0.8272 (ttt) cc_final: 0.8068 (tmm) REVERT: A 998 ILE cc_start: 0.9366 (mt) cc_final: 0.9143 (tt) REVERT: A 1068 ILE cc_start: 0.9449 (mt) cc_final: 0.9241 (mm) REVERT: A 1086 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7531 (pp30) REVERT: A 1091 ASN cc_start: 0.7996 (t0) cc_final: 0.7194 (t0) REVERT: D 68 TYR cc_start: 0.8535 (m-80) cc_final: 0.7832 (m-10) REVERT: D 75 ILE cc_start: 0.8051 (mt) cc_final: 0.7665 (mm) REVERT: D 78 GLU cc_start: 0.8002 (pt0) cc_final: 0.7524 (pt0) REVERT: D 110 GLN cc_start: 0.7275 (mt0) cc_final: 0.6943 (mm-40) REVERT: D 111 MET cc_start: 0.7985 (tmm) cc_final: 0.7725 (tmm) REVERT: D 124 MET cc_start: 0.7198 (tmm) cc_final: 0.6746 (tmm) REVERT: B 26 ASN cc_start: 0.8579 (t0) cc_final: 0.7876 (t0) REVERT: B 184 PRO cc_start: 0.8667 (Cg_exo) cc_final: 0.8393 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8809 (mt) cc_final: 0.8554 (mt) REVERT: B 643 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.8045 (m-70) REVERT: B 940 TRP cc_start: 0.6625 (t-100) cc_final: 0.6396 (t-100) REVERT: B 956 ILE cc_start: 0.8626 (mt) cc_final: 0.8323 (pt) REVERT: B 1015 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8252 (mm-40) REVERT: B 1029 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 1068 ILE cc_start: 0.9429 (mt) cc_final: 0.9223 (mm) REVERT: B 1091 ASN cc_start: 0.7837 (t0) cc_final: 0.6930 (t0) REVERT: E 75 ILE cc_start: 0.7990 (mt) cc_final: 0.7630 (mm) REVERT: E 78 GLU cc_start: 0.7732 (pt0) cc_final: 0.7495 (pt0) REVERT: E 91 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8100 (p) REVERT: E 111 MET cc_start: 0.7893 (tmm) cc_final: 0.7570 (tmm) REVERT: E 124 MET cc_start: 0.7042 (tmm) cc_final: 0.6527 (tmm) REVERT: C 26 ASN cc_start: 0.8468 (t0) cc_final: 0.7891 (t0) REVERT: C 184 PRO cc_start: 0.8622 (Cg_exo) cc_final: 0.8307 (Cg_endo) REVERT: C 349 LYS cc_start: 0.8123 (tttt) cc_final: 0.7888 (tptm) REVERT: C 748 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6635 (tm-30) REVERT: C 814 MET cc_start: 0.8826 (mmp) cc_final: 0.8524 (tpp) REVERT: C 940 TRP cc_start: 0.6367 (t-100) cc_final: 0.6133 (t-100) REVERT: C 964 ASN cc_start: 0.8192 (t0) cc_final: 0.7957 (t0) REVERT: C 1064 ASP cc_start: 0.8499 (t0) cc_final: 0.8269 (t0) REVERT: C 1091 ASN cc_start: 0.8088 (t0) cc_final: 0.7227 (t0) REVERT: C 1111 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8465 (p90) REVERT: F 111 MET cc_start: 0.7884 (tmm) cc_final: 0.7586 (tmm) REVERT: F 124 MET cc_start: 0.7485 (tmm) cc_final: 0.6995 (tmm) outliers start: 129 outliers final: 79 residues processed: 402 average time/residue: 0.1716 time to fit residues: 115.9456 Evaluate side-chains 353 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 270 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 125 THR 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 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 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 822 LEU 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 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 564 CYS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 668 ARG 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 822 LEU 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 968 GLU 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 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: 0.9980 chunk 238 optimal weight: 9.9990 chunk 159 optimal weight: 0.7980 chunk 301 optimal weight: 9.9990 chunk 250 optimal weight: 0.6980 chunk 332 optimal weight: 0.0870 chunk 246 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 ASN A 674 ASN A 750 GLN A 789 GLN A 964 ASN A1018 ASN A1086 GLN ** A1114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN B 674 ASN B 688 ASN B 789 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN C 407 ASN C 643 HIS C 674 ASN C 688 ASN C 953 GLN C1018 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.089485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.072911 restraints weight = 86822.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075284 restraints weight = 50697.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.076928 restraints weight = 34870.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.078055 restraints weight = 26667.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.078865 restraints weight = 22045.166| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29451 Z= 0.116 Angle : 0.615 10.529 40155 Z= 0.326 Chirality : 0.044 0.203 4536 Planarity : 0.004 0.071 5208 Dihedral : 5.811 52.037 4019 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.52 % Allowed : 18.06 % Favored : 78.41 % 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: -2.55 (0.13), residues: 3663 helix: -0.66 (0.19), residues: 750 sheet: -1.96 (0.19), residues: 648 loop : -2.05 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 399 TYR 0.014 0.001 TYR B 731 PHE 0.018 0.001 PHE E 138 TRP 0.014 0.001 TRP A 940 HIS 0.004 0.001 HIS C 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (29394) covalent geometry : angle 0.60410 / 0.32 (40032) SS BOND : bond 0.00517 / 0.30 ( 48) SS BOND : angle 2.33986 / 1.41 ( 96) hydrogen bonds : bond 0.04134 / 2.76 ( 774) hydrogen bonds : angle 5.52165 / 3.87 ( 2079) link_NAG-ASN : bond 0.00417 / 0.18 ( 9) link_NAG-ASN : angle 1.58217 / 0.97 ( 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 443 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 332 time to evaluate : 0.988 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: A 26 ASN cc_start: 0.8566 (t0) cc_final: 0.7935 (t0) REVERT: A 137 TYR cc_start: 0.8596 (m-80) cc_final: 0.8318 (m-10) REVERT: A 184 PRO cc_start: 0.8588 (Cg_exo) cc_final: 0.8378 (Cg_endo) REVERT: A 544 ASN cc_start: 0.8418 (t0) cc_final: 0.8217 (t0) REVERT: A 748 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6980 (tm-30) REVERT: A 749 MET cc_start: 0.7138 (mtt) cc_final: 0.6509 (mtt) REVERT: A 963 MET cc_start: 0.8314 (ttt) cc_final: 0.8097 (tmm) REVERT: A 998 ILE cc_start: 0.9304 (mt) cc_final: 0.9021 (pt) REVERT: A 1068 ILE cc_start: 0.9448 (mt) cc_final: 0.9228 (mm) REVERT: A 1091 ASN cc_start: 0.7975 (t0) cc_final: 0.7117 (t0) REVERT: D 57 ASN cc_start: 0.6982 (t0) cc_final: 0.6752 (t0) REVERT: D 68 TYR cc_start: 0.8437 (m-80) cc_final: 0.7775 (m-10) REVERT: D 75 ILE cc_start: 0.8032 (mt) cc_final: 0.7655 (mm) REVERT: D 78 GLU cc_start: 0.7882 (pt0) cc_final: 0.7586 (pt0) REVERT: D 110 GLN cc_start: 0.7233 (mt0) cc_final: 0.6883 (mm-40) REVERT: D 111 MET cc_start: 0.8033 (tmm) cc_final: 0.7779 (tmm) REVERT: D 124 MET cc_start: 0.7134 (tmm) cc_final: 0.6733 (tmm) REVERT: B 184 PRO cc_start: 0.8609 (Cg_exo) cc_final: 0.8334 (Cg_endo) REVERT: B 385 PHE cc_start: 0.8707 (m-10) cc_final: 0.8484 (m-10) REVERT: B 431 LEU cc_start: 0.8758 (mt) cc_final: 0.8508 (mt) REVERT: B 643 HIS cc_start: 0.8324 (OUTLIER) cc_final: 0.7806 (m-70) REVERT: B 749 MET cc_start: 0.7310 (mtt) cc_final: 0.7050 (mtt) REVERT: B 940 TRP cc_start: 0.6565 (t-100) cc_final: 0.6292 (t-100) REVERT: B 1015 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8393 (mm-40) REVERT: B 1029 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8187 (tm-30) REVERT: B 1064 ASP cc_start: 0.8575 (t0) cc_final: 0.8284 (t0) REVERT: B 1068 ILE cc_start: 0.9415 (mt) cc_final: 0.9050 (mm) REVERT: B 1090 ILE cc_start: 0.8556 (mt) cc_final: 0.8322 (mt) REVERT: B 1091 ASN cc_start: 0.7818 (t0) cc_final: 0.7004 (t0) REVERT: E 75 ILE cc_start: 0.7928 (mt) cc_final: 0.7669 (mm) REVERT: E 111 MET cc_start: 0.7932 (tmm) cc_final: 0.7613 (tmm) REVERT: E 124 MET cc_start: 0.7162 (tmm) cc_final: 0.6601 (tmm) REVERT: C 26 ASN cc_start: 0.8637 (t0) cc_final: 0.8043 (t0) REVERT: C 184 PRO cc_start: 0.8575 (Cg_exo) cc_final: 0.8300 (Cg_endo) REVERT: C 373 ASN cc_start: 0.8998 (p0) cc_final: 0.8721 (p0) REVERT: C 735 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7884 (pp) REVERT: C 748 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6596 (tm-30) REVERT: C 814 MET cc_start: 0.8785 (mmp) cc_final: 0.8457 (tpp) REVERT: C 940 TRP cc_start: 0.6216 (t-100) cc_final: 0.5990 (t-100) REVERT: C 1091 ASN cc_start: 0.8061 (t0) cc_final: 0.7155 (t0) REVERT: C 1111 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8400 (p90) REVERT: F 75 ILE cc_start: 0.8095 (mt) cc_final: 0.7802 (mm) REVERT: F 76 ASP cc_start: 0.9049 (p0) cc_final: 0.8597 (p0) REVERT: F 77 LYS cc_start: 0.9171 (mmtm) cc_final: 0.8724 (mmtm) REVERT: F 111 MET cc_start: 0.7909 (tmm) cc_final: 0.7628 (tmm) REVERT: F 124 MET cc_start: 0.7347 (tmm) cc_final: 0.6898 (tmm) outliers start: 111 outliers final: 78 residues processed: 402 average time/residue: 0.1754 time to fit residues: 117.8518 Evaluate side-chains 365 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 283 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 138 THR Chi-restraints excluded: chain A residue 153 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 473 THR Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 564 CYS 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 954 TYR Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 968 GLU Chi-restraints excluded: chain A residue 1005 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 42 VAL 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 205 HIS Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 234 ASP 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 751 ILE Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 791 VAL 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 941 SER Chi-restraints excluded: chain B residue 954 TYR 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 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 138 THR 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 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 668 ARG 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 827 THR 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 968 GLU 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 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: 9.9990 chunk 357 optimal weight: 5.9990 chunk 314 optimal weight: 8.9990 chunk 266 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 305 optimal weight: 8.9990 chunk 273 optimal weight: 5.9990 chunk 203 optimal weight: 0.0470 chunk 95 optimal weight: 9.9990 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 325 ASN ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 964 ASN C 145 ASN C 314 GLN C 325 ASN C 400 GLN C 428 HIS ** C 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 GLN ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 GLN ** C 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.084504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.068008 restraints weight = 88791.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.070208 restraints weight = 52064.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.071752 restraints weight = 36055.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.072856 restraints weight = 27753.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.073612 restraints weight = 22939.296| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 29451 Z= 0.332 Angle : 0.773 10.022 40155 Z= 0.407 Chirality : 0.048 0.209 4536 Planarity : 0.005 0.071 5208 Dihedral : 6.192 58.420 4019 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 5.62 % Allowed : 17.81 % Favored : 76.57 % 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: -2.61 (0.13), residues: 3663 helix: -0.35 (0.19), residues: 714 sheet: -2.09 (0.19), residues: 657 loop : -2.18 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1089 TYR 0.022 0.002 TYR B 207 PHE 0.033 0.003 PHE A 393 TRP 0.016 0.002 TRP A 940 HIS 0.006 0.002 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.33 (29394) covalent geometry : angle 0.76057 / 0.40 (40032) SS BOND : bond 0.00680 / 0.42 ( 48) SS BOND : angle 2.86556 / 1.73 ( 96) hydrogen bonds : bond 0.04775 / 3.18 ( 774) hydrogen bonds : angle 5.72611 / 4.01 ( 2079) link_NAG-ASN : bond 0.00403 / 0.19 ( 9) link_NAG-ASN : angle 1.49352 / 0.91 ( 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 435 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 258 time to evaluate : 1.280 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 26 ASN cc_start: 0.8592 (t0) cc_final: 0.7898 (t0) REVERT: A 134 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6503 (p90) REVERT: A 544 ASN cc_start: 0.8520 (t0) cc_final: 0.8279 (t0) REVERT: A 735 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8085 (pp) REVERT: A 749 MET cc_start: 0.7432 (mtt) cc_final: 0.7066 (mtt) REVERT: A 940 TRP cc_start: 0.7023 (t-100) cc_final: 0.6774 (t-100) REVERT: A 998 ILE cc_start: 0.9347 (mt) cc_final: 0.9129 (tt) REVERT: A 1068 ILE cc_start: 0.9469 (mt) cc_final: 0.9239 (mm) REVERT: A 1091 ASN cc_start: 0.8201 (t0) cc_final: 0.7337 (t0) REVERT: D 36 VAL cc_start: 0.6607 (m) cc_final: 0.6357 (m) REVERT: D 68 TYR cc_start: 0.8631 (m-80) cc_final: 0.8157 (m-80) REVERT: D 78 GLU cc_start: 0.8072 (pt0) cc_final: 0.7815 (pt0) REVERT: D 88 MET cc_start: 0.8708 (ttp) cc_final: 0.8404 (ttp) REVERT: D 110 GLN cc_start: 0.7282 (mt0) cc_final: 0.6887 (mm-40) REVERT: D 111 MET cc_start: 0.8005 (tmm) cc_final: 0.7734 (tmm) REVERT: D 124 MET cc_start: 0.7490 (tmm) cc_final: 0.7107 (tmm) REVERT: B 184 PRO cc_start: 0.8594 (Cg_exo) cc_final: 0.8347 (Cg_endo) REVERT: B 431 LEU cc_start: 0.8882 (mt) cc_final: 0.8580 (mt) REVERT: B 643 HIS cc_start: 0.8619 (OUTLIER) cc_final: 0.8035 (m-70) REVERT: B 804 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8670 (mm) REVERT: B 940 TRP cc_start: 0.7024 (t-100) cc_final: 0.6778 (t-100) REVERT: B 1015 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8404 (mm-40) REVERT: B 1029 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 1064 ASP cc_start: 0.8594 (t0) cc_final: 0.8305 (t0) REVERT: B 1068 ILE cc_start: 0.9444 (mt) cc_final: 0.9075 (mm) REVERT: B 1090 ILE cc_start: 0.8790 (mt) cc_final: 0.8510 (mt) REVERT: B 1091 ASN cc_start: 0.8123 (t0) cc_final: 0.7355 (t0) REVERT: E 110 GLN cc_start: 0.7458 (mt0) cc_final: 0.6938 (mm-40) REVERT: E 111 MET cc_start: 0.7946 (tmm) cc_final: 0.7634 (tmm) REVERT: E 117 MET cc_start: 0.8480 (tmm) cc_final: 0.7831 (tmm) REVERT: E 124 MET cc_start: 0.7384 (tmm) cc_final: 0.6933 (tmm) REVERT: C 26 ASN cc_start: 0.8642 (t0) cc_final: 0.7948 (t0) REVERT: C 134 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6930 (p90) REVERT: C 184 PRO cc_start: 0.8506 (Cg_exo) cc_final: 0.8234 (Cg_endo) REVERT: C 643 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.7900 (m-70) REVERT: C 735 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8165 (pp) REVERT: C 748 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6727 (tm-30) REVERT: C 814 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8649 (tpp) REVERT: C 940 TRP cc_start: 0.6741 (t-100) cc_final: 0.6454 (t-100) REVERT: C 1091 ASN cc_start: 0.8328 (t0) cc_final: 0.7458 (t0) REVERT: C 1111 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.8584 (p90) REVERT: F 36 VAL cc_start: 0.7182 (m) cc_final: 0.6943 (m) REVERT: F 111 MET cc_start: 0.7991 (tmm) cc_final: 0.7627 (tmm) REVERT: F 124 MET cc_start: 0.7580 (tmm) cc_final: 0.7185 (tmm) outliers start: 177 outliers final: 127 residues processed: 396 average time/residue: 0.1737 time to fit residues: 115.5852 Evaluate side-chains 372 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 235 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 57 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 153 CYS 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 410 PHE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 466 VAL 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 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 735 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 759 HIS 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 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 1100 LEU 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 138 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 205 HIS 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 375 ILE Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 466 VAL 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 941 SER Chi-restraints excluded: chain B residue 954 TYR Chi-restraints excluded: chain B residue 956 ILE 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 1103 VAL 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 57 VAL Chi-restraints excluded: chain C residue 82 ARG 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 153 CYS 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 361 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 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 668 ARG 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 822 LEU Chi-restraints excluded: chain C residue 826 VAL 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 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 1043 ILE 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: 10.0000 chunk 128 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 262 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 346 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 688 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** C 688 ASN ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 GLN C 964 ASN C1018 ASN F 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.085355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.068821 restraints weight = 89058.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.071034 restraints weight = 52940.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.072574 restraints weight = 36969.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.073680 restraints weight = 28648.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.074390 restraints weight = 23787.502| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.005 0.066 29451 Z= 0.222 Angle : 0.679 11.071 40155 Z= 0.359 Chirality : 0.045 0.207 4536 Planarity : 0.005 0.073 5208 Dihedral : 6.061 56.218 4019 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 5.24 % Allowed : 18.86 % Favored : 75.90 % 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: -2.59 (0.13), residues: 3663 helix: -0.23 (0.20), residues: 717 sheet: -2.10 (0.19), residues: 648 loop : -2.19 (0.12), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 399 TYR 0.017 0.002 TYR A1111 PHE 0.019 0.002 PHE A 393 TRP 0.010 0.002 TRP A 346 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (29394) covalent geometry : angle 0.66685 / 0.35 (40032) SS BOND : bond 0.00751 / 0.44 ( 48) SS BOND : angle 2.60120 / 1.55 ( 96) hydrogen bonds : bond 0.04315 / 2.87 ( 774) hydrogen bonds : angle 5.55784 / 3.89 ( 2079) link_NAG-ASN : bond 0.00313 / 0.14 ( 9) link_NAG-ASN : angle 1.42375 / 0.89 ( 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 419 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 254 time to evaluate : 1.133 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: A 26 ASN cc_start: 0.8564 (t0) cc_final: 0.8067 (t0) REVERT: A 134 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.6546 (p90) REVERT: A 137 TYR cc_start: 0.8703 (m-80) cc_final: 0.8367 (m-10) REVERT: A 544 ASN cc_start: 0.8486 (t0) cc_final: 0.8261 (t0) REVERT: A 735 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8016 (pp) REVERT: A 749 MET cc_start: 0.7418 (mtt) cc_final: 0.7051 (mtt) REVERT: A 940 TRP cc_start: 0.6871 (t-100) cc_final: 0.6628 (t-100) REVERT: A 963 MET cc_start: 0.8286 (ttt) cc_final: 0.8029 (tmm) REVERT: A 998 ILE cc_start: 0.9336 (mt) cc_final: 0.9126 (tt) REVERT: A 1068 ILE cc_start: 0.9456 (mt) cc_final: 0.9230 (mt) REVERT: A 1091 ASN cc_start: 0.8061 (t0) cc_final: 0.7279 (t0) REVERT: A 1166 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.8002 (tp) REVERT: D 68 TYR cc_start: 0.8576 (m-80) cc_final: 0.8134 (m-80) REVERT: D 90 PHE cc_start: 0.8392 (m-80) cc_final: 0.8099 (m-80) REVERT: D 110 GLN cc_start: 0.7287 (mt0) cc_final: 0.6831 (mm-40) REVERT: D 111 MET cc_start: 0.7976 (tmm) cc_final: 0.7711 (tmm) REVERT: D 124 MET cc_start: 0.7535 (tmm) cc_final: 0.7158 (tmm) REVERT: B 134 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.7266 (p90) REVERT: B 184 PRO cc_start: 0.8539 (Cg_exo) cc_final: 0.8298 (Cg_endo) REVERT: B 321 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7779 (ttm-80) REVERT: B 431 LEU cc_start: 0.8805 (mt) cc_final: 0.8521 (mt) REVERT: B 637 ARG cc_start: 0.7697 (ptt180) cc_final: 0.7257 (ptt180) REVERT: B 643 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.7981 (m-70) REVERT: B 668 ARG cc_start: 0.7643 (ptt180) cc_final: 0.7400 (ptt90) REVERT: B 804 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8685 (mm) REVERT: B 940 TRP cc_start: 0.6816 (t-100) cc_final: 0.6584 (t-100) REVERT: B 1015 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8286 (mm-40) REVERT: B 1029 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8199 (tm-30) REVERT: B 1064 ASP cc_start: 0.8589 (t0) cc_final: 0.8270 (t0) REVERT: B 1068 ILE cc_start: 0.9446 (mt) cc_final: 0.9048 (mm) REVERT: B 1090 ILE cc_start: 0.8617 (mt) cc_final: 0.8371 (mt) REVERT: B 1091 ASN cc_start: 0.7935 (t0) cc_final: 0.7229 (t0) REVERT: E 110 GLN cc_start: 0.7405 (mt0) cc_final: 0.6823 (mm-40) REVERT: E 111 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7651 (tmm) REVERT: E 117 MET cc_start: 0.8480 (tmm) cc_final: 0.7864 (tmm) REVERT: C 134 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6856 (p90) REVERT: C 184 PRO cc_start: 0.8482 (Cg_exo) cc_final: 0.8187 (Cg_endo) REVERT: C 643 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.7721 (m-70) REVERT: C 701 MET cc_start: 0.8003 (ttp) cc_final: 0.7778 (ptm) REVERT: C 735 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8062 (pp) REVERT: C 814 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8566 (tpp) REVERT: C 940 TRP cc_start: 0.6545 (t-100) cc_final: 0.6270 (t-100) REVERT: C 1091 ASN cc_start: 0.8192 (t0) cc_final: 0.7355 (t0) REVERT: C 1111 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8576 (p90) REVERT: F 36 VAL cc_start: 0.7178 (m) cc_final: 0.6958 (m) REVERT: F 111 MET cc_start: 0.7957 (tmm) cc_final: 0.7612 (tmm) REVERT: F 124 MET cc_start: 0.7556 (tmm) cc_final: 0.7170 (tmm) outliers start: 165 outliers final: 123 residues processed: 385 average time/residue: 0.1756 time to fit residues: 113.4436 Evaluate side-chains 377 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 240 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 153 CYS 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 436 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 466 VAL 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 575 VAL Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 759 HIS 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 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 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 234 ASP Chi-restraints excluded: chain B residue 321 ARG 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 466 VAL 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 956 ILE 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 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 82 ARG 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 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 668 ARG 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 779 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 814 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 VAL 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 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 1043 ILE 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: 8.9990 chunk 351 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 195 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 348 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 765 GLN A1018 ASN A1114 HIS B 765 GLN ** B 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 ASN ** 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 F 110 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.087233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.070657 restraints weight = 88047.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.072929 restraints weight = 51976.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074527 restraints weight = 36104.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.075668 restraints weight = 27857.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.076399 restraints weight = 23037.172| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29451 Z= 0.151 Angle : 0.639 10.882 40155 Z= 0.338 Chirality : 0.044 0.182 4536 Planarity : 0.004 0.078 5208 Dihedral : 5.810 54.074 4019 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 4.83 % Allowed : 19.33 % Favored : 75.84 % 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: -2.45 (0.13), residues: 3663 helix: -0.11 (0.20), residues: 717 sheet: -2.01 (0.19), residues: 642 loop : -2.10 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 131 TYR 0.018 0.001 TYR A1111 PHE 0.014 0.001 PHE B 472 TRP 0.009 0.001 TRP A 346 HIS 0.010 0.001 HIS C1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (29394) covalent geometry : angle 0.62363 / 0.33 (40032) SS BOND : bond 0.00534 / 0.33 ( 48) SS BOND : angle 2.89169 / 1.77 ( 96) hydrogen bonds : bond 0.04015 / 2.67 ( 774) hydrogen bonds : angle 5.41598 / 3.77 ( 2079) link_NAG-ASN : bond 0.00318 / 0.14 ( 9) link_NAG-ASN : angle 1.35783 / 0.85 ( 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 420 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 268 time to evaluate : 1.129 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: A 134 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6539 (p90) REVERT: A 137 TYR cc_start: 0.8696 (m-80) cc_final: 0.8335 (m-10) REVERT: A 385 PHE cc_start: 0.8543 (m-10) cc_final: 0.8318 (m-10) REVERT: A 544 ASN cc_start: 0.8484 (t0) cc_final: 0.8258 (t0) REVERT: A 643 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.7708 (m-70) REVERT: A 735 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7812 (pp) REVERT: A 749 MET cc_start: 0.7395 (mtt) cc_final: 0.7001 (mtt) REVERT: A 940 TRP cc_start: 0.6730 (t-100) cc_final: 0.6372 (t-100) REVERT: A 963 MET cc_start: 0.8288 (ttt) cc_final: 0.8074 (tmm) REVERT: A 1029 GLU cc_start: 0.8870 (tp30) cc_final: 0.8564 (tp30) REVERT: A 1068 ILE cc_start: 0.9419 (mt) cc_final: 0.9180 (mm) REVERT: A 1091 ASN cc_start: 0.7881 (t0) cc_final: 0.7269 (t0) REVERT: D 54 LEU cc_start: 0.7253 (pt) cc_final: 0.6982 (tp) REVERT: D 58 LEU cc_start: 0.8175 (tp) cc_final: 0.7932 (tp) REVERT: D 88 MET cc_start: 0.8666 (ttp) cc_final: 0.7875 (ppp) REVERT: D 90 PHE cc_start: 0.8426 (m-80) cc_final: 0.8040 (m-80) REVERT: D 110 GLN cc_start: 0.7296 (mt0) cc_final: 0.6815 (mm-40) REVERT: D 111 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7779 (tmm) REVERT: D 124 MET cc_start: 0.7594 (tmm) cc_final: 0.7109 (tmm) REVERT: B 184 PRO cc_start: 0.8527 (Cg_exo) cc_final: 0.8290 (Cg_endo) REVERT: B 321 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7860 (ttm-80) REVERT: B 431 LEU cc_start: 0.8822 (mt) cc_final: 0.8579 (mt) REVERT: B 637 ARG cc_start: 0.7609 (ptt180) cc_final: 0.7358 (ptt180) REVERT: B 643 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.7781 (m-70) REVERT: B 749 MET cc_start: 0.7577 (mtt) cc_final: 0.7043 (mtm) REVERT: B 1029 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 1090 ILE cc_start: 0.8652 (mt) cc_final: 0.8399 (mt) REVERT: B 1091 ASN cc_start: 0.7988 (t0) cc_final: 0.7367 (t0) REVERT: E 111 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7664 (tmm) REVERT: E 117 MET cc_start: 0.8420 (tmm) cc_final: 0.7850 (tmm) REVERT: E 124 MET cc_start: 0.7326 (tmm) cc_final: 0.6866 (tmm) REVERT: C 134 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6746 (p90) REVERT: C 184 PRO cc_start: 0.8595 (Cg_exo) cc_final: 0.8312 (Cg_endo) REVERT: C 637 ARG cc_start: 0.7115 (ptt180) cc_final: 0.5722 (ptp-170) REVERT: C 643 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7509 (m-70) REVERT: C 735 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7964 (pp) REVERT: C 748 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6740 (tm-30) REVERT: C 814 MET cc_start: 0.8840 (mmp) cc_final: 0.8520 (tpp) REVERT: C 940 TRP cc_start: 0.6311 (t-100) cc_final: 0.6002 (t-100) REVERT: C 998 ILE cc_start: 0.9373 (mt) cc_final: 0.9048 (tt) REVERT: C 1091 ASN cc_start: 0.8095 (t0) cc_final: 0.7334 (t0) REVERT: C 1111 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8550 (p90) REVERT: F 36 VAL cc_start: 0.7114 (m) cc_final: 0.6909 (m) REVERT: F 110 GLN cc_start: 0.7299 (mt0) cc_final: 0.7077 (mt0) REVERT: F 111 MET cc_start: 0.7971 (tmm) cc_final: 0.7634 (tmm) REVERT: F 124 MET cc_start: 0.7477 (tmm) cc_final: 0.7049 (tmm) outliers start: 152 outliers final: 110 residues processed: 383 average time/residue: 0.1768 time to fit residues: 112.6249 Evaluate side-chains 364 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 243 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 63 LEU 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 153 CYS 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 372 CYS Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 466 VAL 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 643 HIS Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 759 HIS 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 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 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 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 321 ARG 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 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 779 VAL Chi-restraints excluded: chain B residue 791 VAL 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 956 ILE 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 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 53 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 125 THR 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 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 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 779 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 826 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 336 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 214 optimal weight: 0.9980 chunk 354 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 351 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 316 optimal weight: 0.0030 chunk 304 optimal weight: 0.8980 chunk 5 optimal weight: 0.0570 chunk 252 optimal weight: 0.0980 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 HIS A 688 ASN ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 688 ASN B 765 GLN ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN C 688 ASN C1018 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.089711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.073001 restraints weight = 87535.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075347 restraints weight = 51577.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.077000 restraints weight = 35772.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078158 restraints weight = 27503.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.078929 restraints weight = 22706.879| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 29451 Z= 0.114 Angle : 0.615 10.323 40155 Z= 0.325 Chirality : 0.044 0.182 4536 Planarity : 0.004 0.054 5208 Dihedral : 5.518 51.257 4019 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.59 % Allowed : 20.67 % Favored : 75.75 % 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: -2.24 (0.13), residues: 3663 helix: 0.02 (0.20), residues: 744 sheet: -1.88 (0.19), residues: 609 loop : -1.98 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1019 TYR 0.021 0.001 TYR A1111 PHE 0.021 0.001 PHE E 90 TRP 0.019 0.001 TRP B 940 HIS 0.008 0.001 HIS C1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (29394) covalent geometry : angle 0.60510 / 0.32 (40032) SS BOND : bond 0.00469 / 0.28 ( 48) SS BOND : angle 2.28524 / 1.38 ( 96) hydrogen bonds : bond 0.03759 / 2.48 ( 774) hydrogen bonds : angle 5.22891 / 3.65 ( 2079) link_NAG-ASN : bond 0.00415 / 0.18 ( 9) link_NAG-ASN : angle 1.31514 / 0.81 ( 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 410 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 297 time to evaluate : 1.165 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: A 137 TYR cc_start: 0.8670 (m-80) cc_final: 0.8329 (m-10) REVERT: A 385 PHE cc_start: 0.8528 (m-10) cc_final: 0.8279 (m-10) REVERT: A 431 LEU cc_start: 0.8890 (mt) cc_final: 0.8677 (tp) REVERT: A 544 ASN cc_start: 0.8476 (t0) cc_final: 0.8266 (t0) REVERT: A 643 HIS cc_start: 0.8026 (OUTLIER) cc_final: 0.7389 (m-70) REVERT: A 735 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7730 (pp) REVERT: A 749 MET cc_start: 0.7322 (mtt) cc_final: 0.6878 (mtt) REVERT: A 940 TRP cc_start: 0.6737 (t-100) cc_final: 0.6391 (t-100) REVERT: A 963 MET cc_start: 0.8315 (ttt) cc_final: 0.8076 (tmm) REVERT: A 1029 GLU cc_start: 0.8811 (tp30) cc_final: 0.8483 (tp30) REVERT: A 1068 ILE cc_start: 0.9417 (mt) cc_final: 0.9152 (tp) REVERT: A 1091 ASN cc_start: 0.7564 (t0) cc_final: 0.7044 (t0) REVERT: D 54 LEU cc_start: 0.7212 (pt) cc_final: 0.6900 (tp) REVERT: D 75 ILE cc_start: 0.8038 (mt) cc_final: 0.7758 (mm) REVERT: D 88 MET cc_start: 0.8725 (ttp) cc_final: 0.8032 (ppp) REVERT: D 110 GLN cc_start: 0.7303 (mt0) cc_final: 0.6789 (mm-40) REVERT: D 111 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7808 (tmm) REVERT: D 124 MET cc_start: 0.7494 (tmm) cc_final: 0.6935 (tmm) REVERT: B 26 ASN cc_start: 0.8448 (t0) cc_final: 0.7712 (t0) REVERT: B 184 PRO cc_start: 0.8609 (Cg_exo) cc_final: 0.8380 (Cg_endo) REVERT: B 385 PHE cc_start: 0.8669 (m-10) cc_final: 0.8378 (m-10) REVERT: B 637 ARG cc_start: 0.7472 (ptt180) cc_final: 0.7175 (ptt180) REVERT: B 643 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7519 (m-70) REVERT: B 749 MET cc_start: 0.7533 (mtt) cc_final: 0.6972 (mtm) REVERT: B 1029 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7973 (tm-30) REVERT: B 1090 ILE cc_start: 0.8523 (mt) cc_final: 0.8273 (mt) REVERT: B 1091 ASN cc_start: 0.7858 (t0) cc_final: 0.7309 (t0) REVERT: B 1099 ILE cc_start: 0.8558 (mm) cc_final: 0.8306 (mm) REVERT: E 90 PHE cc_start: 0.7999 (m-80) cc_final: 0.7374 (m-80) REVERT: E 91 THR cc_start: 0.8378 (p) cc_final: 0.7975 (p) REVERT: E 110 GLN cc_start: 0.6946 (mt0) cc_final: 0.6268 (mm-40) REVERT: E 111 MET cc_start: 0.8037 (tmm) cc_final: 0.7691 (tmm) REVERT: E 117 MET cc_start: 0.8353 (tmm) cc_final: 0.7844 (tmm) REVERT: C 26 ASN cc_start: 0.8585 (t0) cc_final: 0.8005 (t0) REVERT: C 184 PRO cc_start: 0.8579 (Cg_exo) cc_final: 0.8279 (Cg_endo) REVERT: C 748 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6794 (tm-30) REVERT: C 940 TRP cc_start: 0.6268 (t-100) cc_final: 0.5925 (t-100) REVERT: C 998 ILE cc_start: 0.9273 (mt) cc_final: 0.9048 (tt) REVERT: C 1091 ASN cc_start: 0.7912 (t0) cc_final: 0.7188 (t0) REVERT: C 1099 ILE cc_start: 0.8476 (mm) cc_final: 0.8221 (mm) REVERT: C 1111 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.8493 (p90) REVERT: F 111 MET cc_start: 0.7996 (tmm) cc_final: 0.7645 (tmm) REVERT: F 124 MET cc_start: 0.7412 (tmm) cc_final: 0.7202 (tmm) outliers start: 113 outliers final: 86 residues processed: 374 average time/residue: 0.1735 time to fit residues: 108.9481 Evaluate side-chains 355 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 264 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 153 CYS 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 473 THR Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 759 HIS 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 954 TYR Chi-restraints excluded: chain A residue 1005 ASN 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 B residue 21 CYS Chi-restraints excluded: chain B residue 42 VAL 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 804 LEU 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 954 TYR 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 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 53 VAL Chi-restraints excluded: chain C residue 63 LEU 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 370 LEU 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 645 ASP 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 827 THR 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 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 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: 10.0000 chunk 319 optimal weight: 0.7980 chunk 267 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 328 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 163 optimal weight: 0.6980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 688 ASN A 765 GLN A1018 ASN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN B 688 ASN ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 ASN C 688 ASN C 750 GLN ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 ASN F 110 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.086787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.070019 restraints weight = 88810.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.072301 restraints weight = 52286.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.073867 restraints weight = 36260.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.075000 restraints weight = 28095.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.075796 restraints weight = 23256.736| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3212 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= 0.212 Angle : 0.676 12.603 40155 Z= 0.354 Chirality : 0.045 0.180 4536 Planarity : 0.004 0.058 5208 Dihedral : 5.625 55.902 4019 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 4.00 % Allowed : 20.86 % Favored : 75.14 % 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: -2.27 (0.13), residues: 3663 helix: 0.15 (0.20), residues: 717 sheet: -1.90 (0.19), residues: 639 loop : -2.02 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1019 TYR 0.024 0.002 TYR F 120 PHE 0.033 0.002 PHE D 90 TRP 0.049 0.002 TRP D 67 HIS 0.006 0.001 HIS C1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (29394) covalent geometry : angle 0.66450 / 0.35 (40032) SS BOND : bond 0.00492 / 0.28 ( 48) SS BOND : angle 2.60012 / 1.55 ( 96) hydrogen bonds : bond 0.04079 / 2.73 ( 774) hydrogen bonds : angle 5.28653 / 3.69 ( 2079) link_NAG-ASN : bond 0.00341 / 0.16 ( 9) link_NAG-ASN : angle 1.29937 / 0.79 ( 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: 126 poor density : 257 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6628 (p90) REVERT: A 137 TYR cc_start: 0.8774 (m-80) cc_final: 0.8372 (m-10) REVERT: A 385 PHE cc_start: 0.8554 (m-10) cc_final: 0.8340 (m-10) REVERT: A 544 ASN cc_start: 0.8566 (t0) cc_final: 0.8337 (t0) REVERT: A 643 HIS cc_start: 0.8252 (OUTLIER) cc_final: 0.7672 (m-70) REVERT: A 701 MET cc_start: 0.7738 (ttp) cc_final: 0.7531 (ptp) REVERT: A 735 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7976 (pp) REVERT: A 749 MET cc_start: 0.7513 (mtt) cc_final: 0.7070 (mtt) REVERT: A 940 TRP cc_start: 0.6873 (t-100) cc_final: 0.6497 (t-100) REVERT: A 963 MET cc_start: 0.8371 (ttt) cc_final: 0.8064 (tmm) REVERT: A 1029 GLU cc_start: 0.8865 (tp30) cc_final: 0.8492 (tp30) REVERT: A 1068 ILE cc_start: 0.9464 (mt) cc_final: 0.9242 (mm) REVERT: A 1091 ASN cc_start: 0.7878 (t0) cc_final: 0.7252 (t0) REVERT: D 54 LEU cc_start: 0.7322 (pt) cc_final: 0.6982 (tp) REVERT: D 88 MET cc_start: 0.8876 (ttp) cc_final: 0.8320 (ppp) REVERT: D 110 GLN cc_start: 0.7264 (mt0) cc_final: 0.6678 (mm-40) REVERT: D 111 MET cc_start: 0.8099 (tmm) cc_final: 0.7826 (tmm) REVERT: D 124 MET cc_start: 0.7654 (tmm) cc_final: 0.6961 (tmm) REVERT: B 26 ASN cc_start: 0.8587 (t0) cc_final: 0.7871 (t0) REVERT: B 134 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.7439 (p90) REVERT: B 184 PRO cc_start: 0.8498 (Cg_exo) cc_final: 0.8276 (Cg_endo) REVERT: B 637 ARG cc_start: 0.7684 (ptt180) cc_final: 0.7197 (ptt180) REVERT: B 643 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.7803 (m-70) REVERT: B 652 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8284 (tp) REVERT: B 749 MET cc_start: 0.7530 (mtt) cc_final: 0.6994 (mtm) REVERT: B 1029 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8032 (tm-30) REVERT: B 1090 ILE cc_start: 0.8669 (mt) cc_final: 0.8409 (mt) REVERT: B 1091 ASN cc_start: 0.8052 (t0) cc_final: 0.7460 (t0) REVERT: B 1099 ILE cc_start: 0.8541 (mm) cc_final: 0.8215 (mm) REVERT: E 90 PHE cc_start: 0.8290 (m-80) cc_final: 0.7668 (m-80) REVERT: E 91 THR cc_start: 0.8545 (p) cc_final: 0.8194 (p) REVERT: E 111 MET cc_start: 0.8067 (tmm) cc_final: 0.7692 (tmm) REVERT: E 117 MET cc_start: 0.8402 (tmm) cc_final: 0.7883 (tmm) REVERT: C 184 PRO cc_start: 0.8574 (Cg_exo) cc_final: 0.8290 (Cg_endo) REVERT: C 429 TYR cc_start: 0.8711 (p90) cc_final: 0.8316 (p90) REVERT: C 633 CYS cc_start: 0.4709 (m) cc_final: 0.4480 (m) REVERT: C 643 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7460 (m-70) REVERT: C 748 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6737 (tm-30) REVERT: C 940 TRP cc_start: 0.6463 (t-100) cc_final: 0.6086 (t-100) REVERT: C 1091 ASN cc_start: 0.8131 (t0) cc_final: 0.7346 (t0) REVERT: C 1111 TYR cc_start: 0.8870 (OUTLIER) cc_final: 0.8490 (p90) REVERT: F 111 MET cc_start: 0.7983 (tmm) cc_final: 0.7633 (tmm) REVERT: F 124 MET cc_start: 0.7604 (tmm) cc_final: 0.7044 (tmm) outliers start: 126 outliers final: 110 residues processed: 355 average time/residue: 0.1720 time to fit residues: 103.4772 Evaluate side-chains 360 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 242 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 153 CYS 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 264 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 371 PHE 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 466 VAL 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 643 HIS Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 759 HIS 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 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 1111 TYR Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain D residue 78 GLU 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 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 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 388 ILE 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 652 LEU 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 804 LEU 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 954 TYR 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 1082 CYS 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 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 438 ILE Chi-restraints excluded: chain C residue 466 VAL 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 643 HIS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 731 TYR 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 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 C residue 1128 SER Chi-restraints excluded: chain F residue 78 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 109 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 330 optimal weight: 0.4980 chunk 47 optimal weight: 0.0670 chunk 218 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 246 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 126 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 337 optimal weight: 0.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 688 ASN A 964 ASN A1018 ASN B 523 HIS B 544 ASN B 688 ASN ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN C 688 ASN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 ASN F 110 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.088974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072195 restraints weight = 87610.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074599 restraints weight = 50248.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076297 restraints weight = 34321.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.077483 restraints weight = 26144.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.078253 restraints weight = 21482.585| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29451 Z= 0.113 Angle : 0.629 12.419 40155 Z= 0.328 Chirality : 0.044 0.182 4536 Planarity : 0.004 0.067 5208 Dihedral : 5.415 50.670 4019 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.08 % Allowed : 22.16 % Favored : 74.76 % 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: -2.03 (0.13), residues: 3663 helix: 0.26 (0.20), residues: 720 sheet: -1.64 (0.20), residues: 621 loop : -1.88 (0.12), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 637 TYR 0.022 0.001 TYR A1111 PHE 0.026 0.001 PHE D 90 TRP 0.041 0.002 TRP D 67 HIS 0.007 0.001 HIS C1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (29394) covalent geometry : angle 0.61917 / 0.32 (40032) SS BOND : bond 0.00418 / 0.24 ( 48) SS BOND : angle 2.21817 / 1.33 ( 96) hydrogen bonds : bond 0.03620 / 2.40 ( 774) hydrogen bonds : angle 5.06638 / 3.54 ( 2079) link_NAG-ASN : bond 0.00404 / 0.18 ( 9) link_NAG-ASN : angle 1.26110 / 0.77 ( 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 371 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 274 time to evaluate : 1.157 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: 0.7303 (OUTLIER) cc_final: 0.6637 (p90) REVERT: A 137 TYR cc_start: 0.8769 (m-80) cc_final: 0.8344 (m-10) REVERT: A 385 PHE cc_start: 0.8467 (m-10) cc_final: 0.8232 (m-10) REVERT: A 431 LEU cc_start: 0.8912 (mt) cc_final: 0.8654 (tp) REVERT: A 643 HIS cc_start: 0.8001 (OUTLIER) cc_final: 0.7348 (m-70) REVERT: A 735 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7722 (pp) REVERT: A 749 MET cc_start: 0.7355 (mtt) cc_final: 0.6870 (mtt) REVERT: A 823 MET cc_start: 0.7071 (tmm) cc_final: 0.6801 (tmm) REVERT: A 867 ARG cc_start: 0.7472 (mtp-110) cc_final: 0.7163 (ptm160) REVERT: A 963 MET cc_start: 0.8405 (ttt) cc_final: 0.8091 (tmm) REVERT: A 1029 GLU cc_start: 0.8814 (tp30) cc_final: 0.8385 (tp30) REVERT: A 1068 ILE cc_start: 0.9422 (mt) cc_final: 0.9173 (tp) REVERT: A 1091 ASN cc_start: 0.7623 (t0) cc_final: 0.7046 (t0) REVERT: D 54 LEU cc_start: 0.7265 (pt) cc_final: 0.6972 (tp) REVERT: D 75 ILE cc_start: 0.8003 (mt) cc_final: 0.7720 (mm) REVERT: D 88 MET cc_start: 0.8961 (ttp) cc_final: 0.8515 (ppp) REVERT: D 110 GLN cc_start: 0.7271 (mt0) cc_final: 0.6651 (mm-40) REVERT: D 111 MET cc_start: 0.8013 (tmm) cc_final: 0.7789 (tmm) REVERT: D 124 MET cc_start: 0.7523 (tmm) cc_final: 0.6895 (tmm) REVERT: B 26 ASN cc_start: 0.8594 (t0) cc_final: 0.7902 (t0) REVERT: B 149 MET cc_start: 0.8002 (pmm) cc_final: 0.7623 (pmm) REVERT: B 184 PRO cc_start: 0.8618 (Cg_exo) cc_final: 0.8386 (Cg_endo) REVERT: B 385 PHE cc_start: 0.8540 (m-10) cc_final: 0.8279 (m-10) REVERT: B 637 ARG cc_start: 0.7531 (ptt180) cc_final: 0.7110 (ptt180) REVERT: B 643 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7508 (m-70) REVERT: B 668 ARG cc_start: 0.7615 (ptt180) cc_final: 0.7278 (ttt180) REVERT: B 1029 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 1090 ILE cc_start: 0.8525 (mt) cc_final: 0.8277 (mt) REVERT: B 1091 ASN cc_start: 0.7986 (t0) cc_final: 0.7433 (t0) REVERT: B 1099 ILE cc_start: 0.8480 (mm) cc_final: 0.8108 (mm) REVERT: E 90 PHE cc_start: 0.8220 (m-80) cc_final: 0.7641 (m-80) REVERT: E 91 THR cc_start: 0.8448 (p) cc_final: 0.8093 (p) REVERT: E 110 GLN cc_start: 0.7313 (mt0) cc_final: 0.7066 (mt0) REVERT: E 111 MET cc_start: 0.8033 (tmm) cc_final: 0.7817 (tmm) REVERT: E 117 MET cc_start: 0.8354 (tmm) cc_final: 0.7894 (tmm) REVERT: C 26 ASN cc_start: 0.8650 (t0) cc_final: 0.8064 (t0) REVERT: C 184 PRO cc_start: 0.8602 (Cg_exo) cc_final: 0.8306 (Cg_endo) REVERT: C 633 CYS cc_start: 0.4860 (m) cc_final: 0.4640 (m) REVERT: C 643 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7217 (m-70) REVERT: C 748 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6584 (tm-30) REVERT: C 940 TRP cc_start: 0.6291 (t-100) cc_final: 0.5873 (t-100) REVERT: C 1091 ASN cc_start: 0.8022 (t0) cc_final: 0.7339 (t0) REVERT: C 1111 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8506 (p90) REVERT: F 88 MET cc_start: 0.8707 (ttp) cc_final: 0.7821 (ppp) REVERT: F 90 PHE cc_start: 0.8420 (m-80) cc_final: 0.7709 (m-10) REVERT: F 111 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7605 (tmm) REVERT: F 124 MET cc_start: 0.7427 (tmm) cc_final: 0.7089 (tmm) outliers start: 97 outliers final: 80 residues processed: 343 average time/residue: 0.1730 time to fit residues: 100.3273 Evaluate side-chains 349 residues out of total 3159 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 262 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 153 CYS 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 264 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 371 PHE 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 473 THR Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain A residue 643 HIS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 779 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 954 TYR 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 78 GLU 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 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 370 LEU 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 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 804 LEU Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 936 MET 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 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 53 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 217 TYR 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 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 731 TYR 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 941 SER Chi-restraints excluded: chain C residue 954 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 353 optimal weight: 5.9990 chunk 185 optimal weight: 0.7980 chunk 54 optimal weight: 0.0050 chunk 327 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 310 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 215 optimal weight: 0.2980 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 GLN A 688 ASN A1018 ASN ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN C 765 GLN C 789 GLN C1018 ASN F 110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.087918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.071174 restraints weight = 88739.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073496 restraints weight = 51575.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.075135 restraints weight = 35603.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.076273 restraints weight = 27340.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.077035 restraints weight = 22610.969| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29451 Z= 0.142 Angle : 0.631 11.967 40155 Z= 0.329 Chirality : 0.044 0.264 4536 Planarity : 0.004 0.051 5208 Dihedral : 5.375 53.892 4019 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.14 % Allowed : 22.41 % Favored : 74.44 % 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: -2.02 (0.13), residues: 3663 helix: 0.56 (0.20), residues: 699 sheet: -1.80 (0.19), residues: 636 loop : -1.90 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 637 TYR 0.025 0.001 TYR B 429 PHE 0.024 0.001 PHE C 105 TRP 0.036 0.002 TRP D 67 HIS 0.006 0.001 HIS C1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (29394) covalent geometry : angle 0.61997 / 0.32 (40032) SS BOND : bond 0.00420 / 0.24 ( 48) SS BOND : angle 2.34266 / 1.41 ( 96) hydrogen bonds : bond 0.03681 / 2.45 ( 774) hydrogen bonds : angle 4.99971 / 3.49 ( 2079) link_NAG-ASN : bond 0.00323 / 0.14 ( 9) link_NAG-ASN : angle 1.36004 / 0.84 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4680.54 seconds wall clock time: 82 minutes 13.76 seconds (4933.76 seconds total)