Starting phenix.real_space_refine on Tue Aug 26 14:16:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wyj_37930/08_2025/8wyj_37930_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wyj_37930/08_2025/8wyj_37930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wyj_37930/08_2025/8wyj_37930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wyj_37930/08_2025/8wyj_37930.map" model { file = "/net/cci-nas-00/data/ceres_data/8wyj_37930/08_2025/8wyj_37930_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wyj_37930/08_2025/8wyj_37930_neut.cif" } resolution = 3.1 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4444 atoms to isotropic. 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 153 5.16 5 C 22035 2.51 5 N 5796 2.21 5 O 6507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 175 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34491 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8083 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8083 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8083 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 924 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 118} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "S" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 956 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 796 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 738 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 97} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 924 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 118} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 956 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 796 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 738 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 97} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 924 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 118} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 956 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 796 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 738 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 97} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 8.24, per 1000 atoms: 0.24 Number of scatterers: 34491 At special positions: 0 Unit cell: (185.92, 166.83, 211.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 153 16.00 O 6507 8.00 N 5796 7.00 C 22035 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.06 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 487 " distance=2.04 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 589 " distance=2.04 Simple disulfide: pdb=" SG CYS A 616 " - pdb=" SG CYS A 648 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 670 " distance=1.98 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.08 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 524 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 487 " distance=2.04 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 589 " distance=2.04 Simple disulfide: pdb=" SG CYS B 616 " - pdb=" SG CYS B 648 " distance=2.02 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 670 " distance=2.01 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.06 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 524 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 487 " distance=2.03 Simple disulfide: pdb=" SG CYS C 537 " - pdb=" SG CYS C 589 " distance=2.03 Simple disulfide: pdb=" SG CYS C 616 " - pdb=" SG CYS C 648 " distance=2.01 Simple disulfide: pdb=" SG CYS C 661 " - pdb=" SG CYS C 670 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 89 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 89 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 89 " distance=2.05 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS J 24 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.4 microseconds 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8268 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 68 sheets defined 12.9% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'A' and resid 615 through 625 removed outlier: 3.791A pdb=" N ILE A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 625 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.537A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 767 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 773 through 781 removed outlier: 3.707A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 824 removed outlier: 3.841A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 921 through 941 removed outlier: 3.586A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 992 through 1011 removed outlier: 3.771A pdb=" N ILE A 997 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1031 Processing helix chain 'A' and resid 1139 through 1146 removed outlier: 3.556A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.583A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 541 through 545 Processing helix chain 'B' and resid 749 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 768 Processing helix chain 'B' and resid 777 through 782 removed outlier: 3.748A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 777 through 782' Processing helix chain 'B' and resid 849 through 855 removed outlier: 3.582A pdb=" N ALA B 852 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 removed outlier: 4.147A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.808A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 926 Processing helix chain 'B' and resid 932 through 939 removed outlier: 4.693A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 962 removed outlier: 3.682A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 967 Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 990 Processing helix chain 'B' and resid 992 through 1000 Processing helix chain 'B' and resid 1000 through 1015 removed outlier: 3.565A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1023 Processing helix chain 'B' and resid 1026 through 1033 Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.686A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.743A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 439 through 441 No H-bonds generated for 'chain 'C' and resid 439 through 441' Processing helix chain 'C' and resid 621 through 625 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 750 through 755 removed outlier: 4.335A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 765 removed outlier: 3.746A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 774 removed outlier: 3.566A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 824 Processing helix chain 'C' and resid 873 through 878 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.747A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 890' Processing helix chain 'C' and resid 897 through 901 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.035A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 929 removed outlier: 3.568A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 932 No H-bonds generated for 'chain 'C' and resid 930 through 932' Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 945 through 950 Processing helix chain 'C' and resid 950 through 955 Processing helix chain 'C' and resid 962 through 966 Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1001 removed outlier: 3.503A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1012 removed outlier: 3.737A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1014 through 1023 Processing helix chain 'C' and resid 1026 through 1031 Processing helix chain 'C' and resid 1143 through 1147 Processing helix chain 'Q' and resid 73 through 76 removed outlier: 4.182A pdb=" N THR Q 76 " --> pdb=" O ASP Q 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 73 through 76' Processing helix chain 'S' and resid 64 through 68 Processing helix chain 'R' and resid 80 through 84 Processing helix chain 'T' and resid 49 through 53 removed outlier: 3.534A pdb=" N ALA T 52 " --> pdb=" O ILE T 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 43 removed outlier: 4.080A pdb=" N GLY D 42 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 68 Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'H' and resid 59 through 63 removed outlier: 4.218A pdb=" N GLN H 62 " --> pdb=" O ILE H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 76 Processing helix chain 'I' and resid 64 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.917A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 312 removed outlier: 4.406A pdb=" N GLY A 311 " --> pdb=" O THR A 598 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR A 598 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 394 through 396 removed outlier: 3.742A pdb=" N SER A 513 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 394 through 396 removed outlier: 3.742A pdb=" N SER A 513 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 512 " --> pdb=" O CYS A 432 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 540 Processing sheet with id=AA9, first strand: chain 'A' and resid 564 through 565 removed outlier: 6.839A pdb=" N PHE A 564 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 672 through 674 removed outlier: 3.615A pdb=" N SER A 691 " --> pdb=" O GLN A 674 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 720 through 728 removed outlier: 5.861A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.456A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.589A pdb=" N ASN C 703 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1077 through 1078 removed outlier: 4.716A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 48 removed outlier: 4.140A pdb=" N TYR B 279 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC2, first strand: chain 'B' and resid 189 through 195 removed outlier: 3.623A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.847A pdb=" N GLY B 593 " --> pdb=" O GLN B 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 394 through 403 removed outlier: 3.603A pdb=" N VAL B 509 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 552 through 553 removed outlier: 3.698A pdb=" N THR B 552 " --> pdb=" O ASP B 585 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 575 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 641 through 644 Processing sheet with id=AC7, first strand: chain 'B' and resid 663 through 666 removed outlier: 6.641A pdb=" N VAL B 669 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.694A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 713 removed outlier: 3.604A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 728 removed outlier: 4.095A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B1070 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.507A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AD5, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.716A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AD7, first strand: chain 'C' and resid 276 through 279 removed outlier: 4.230A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.141A pdb=" N VAL C 594 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 593 " --> pdb=" O GLN C 612 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR C 611 " --> pdb=" O CYS C 648 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 396 through 397 Processing sheet with id=AE1, first strand: chain 'C' and resid 400 through 402 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 653 through 654 removed outlier: 5.566A pdb=" N GLU C 653 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 674 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 712 through 721 removed outlier: 6.462A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA C1070 " --> pdb=" O ASN C 717 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 721 removed outlier: 6.462A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA C1070 " --> pdb=" O ASN C 717 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1086 through 1090 removed outlier: 5.612A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE8, first strand: chain 'Q' and resid 21 through 23 removed outlier: 3.874A pdb=" N MET Q 69 " --> pdb=" O GLU Q 82 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 37 through 39 removed outlier: 3.878A pdb=" N VAL Q 93 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR Q 119 " --> pdb=" O TYR Q 94 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AF2, first strand: chain 'S' and resid 46 through 50 removed outlier: 6.527A pdb=" N TRP S 36 " --> pdb=" O MET S 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 69 through 71 removed outlier: 3.516A pdb=" N THR S 69 " --> pdb=" O GLU S 82 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU S 82 " --> pdb=" O THR S 69 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 18 through 22 removed outlier: 6.398A pdb=" N VAL R 20 " --> pdb=" O SER R 77 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N SER R 77 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE R 22 " --> pdb=" O THR R 75 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N THR R 75 " --> pdb=" O ILE R 22 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 35 through 36 removed outlier: 3.681A pdb=" N ASN R 35 " --> pdb=" O GLN R 90 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'T' and resid 37 through 38 Processing sheet with id=AF7, first strand: chain 'D' and resid 68 through 69 Processing sheet with id=AF8, first strand: chain 'D' and resid 93 through 94 removed outlier: 3.955A pdb=" N TYR D 94 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D 119 " --> pdb=" O TYR D 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AG1, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AG2, first strand: chain 'E' and resid 45 through 50 removed outlier: 6.457A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 69 through 71 Processing sheet with id=AG4, first strand: chain 'F' and resid 18 through 22 removed outlier: 5.913A pdb=" N ASP F 18 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER F 78 " --> pdb=" O ASP F 18 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL F 20 " --> pdb=" O ILE F 76 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AG6, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AG7, first strand: chain 'H' and resid 21 through 23 removed outlier: 3.875A pdb=" N MET H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 35 through 39 Processing sheet with id=AG9, first strand: chain 'I' and resid 37 through 38 Processing sheet with id=AH1, first strand: chain 'I' and resid 69 through 71 removed outlier: 3.609A pdb=" N THR I 69 " --> pdb=" O GLU I 82 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU I 82 " --> pdb=" O THR I 69 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 18 through 22 removed outlier: 5.626A pdb=" N ASP J 18 " --> pdb=" O SER J 78 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 37 through 38 Processing sheet with id=AH4, first strand: chain 'J' and resid 49 through 50 removed outlier: 3.801A pdb=" N HIS J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 64 through 67 538 hydrogen bonds defined for protein. 1278 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: 7.34 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5586 1.29 - 1.43: 9630 1.43 - 1.56: 19901 1.56 - 1.69: 1 1.69 - 1.82: 198 Bond restraints: 35316 Sorted by residual: bond pdb=" C PRO B 715 " pdb=" O PRO B 715 " ideal model delta sigma weight residual 1.234 1.162 0.071 1.14e-02 7.69e+03 3.91e+01 bond pdb=" C PRO C1053 " pdb=" O PRO C1053 " ideal model delta sigma weight residual 1.233 1.178 0.055 1.06e-02 8.90e+03 2.74e+01 bond pdb=" CA SER A1030 " pdb=" CB SER A1030 " ideal model delta sigma weight residual 1.532 1.452 0.080 1.53e-02 4.27e+03 2.74e+01 bond pdb=" CA SER A 595 " pdb=" CB SER A 595 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.35e-02 5.49e+03 2.59e+01 bond pdb=" CA ALA C1080 " pdb=" CB ALA C1080 " ideal model delta sigma weight residual 1.539 1.470 0.069 1.36e-02 5.41e+03 2.55e+01 ... (remaining 35311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 41563 2.75 - 5.49: 5832 5.49 - 8.24: 543 8.24 - 10.98: 93 10.98 - 13.73: 11 Bond angle restraints: 48042 Sorted by residual: angle pdb=" N VAL A 502 " pdb=" CA VAL A 502 " pdb=" C VAL A 502 " ideal model delta sigma weight residual 113.53 103.33 10.20 9.80e-01 1.04e+00 1.08e+02 angle pdb=" N ILE A 882 " pdb=" CA ILE A 882 " pdb=" C ILE A 882 " ideal model delta sigma weight residual 113.47 103.99 9.48 1.01e+00 9.80e-01 8.80e+01 angle pdb=" N PRO A 498 " pdb=" CA PRO A 498 " pdb=" C PRO A 498 " ideal model delta sigma weight residual 113.75 100.02 13.73 1.49e+00 4.50e-01 8.49e+01 angle pdb=" C THR A 286 " pdb=" CA THR A 286 " pdb=" CB THR A 286 " ideal model delta sigma weight residual 111.22 100.42 10.80 1.23e+00 6.61e-01 7.71e+01 angle pdb=" N LYS H 12 " pdb=" CA LYS H 12 " pdb=" C LYS H 12 " ideal model delta sigma weight residual 109.81 122.57 -12.76 1.53e+00 4.27e-01 6.95e+01 ... (remaining 48037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16491 17.98 - 35.96: 2277 35.96 - 53.94: 1507 53.94 - 71.93: 493 71.93 - 89.91: 115 Dihedral angle restraints: 20883 sinusoidal: 7974 harmonic: 12909 Sorted by residual: dihedral pdb=" CD ARG I 85 " pdb=" NE ARG I 85 " pdb=" CZ ARG I 85 " pdb=" NH1 ARG I 85 " ideal model delta sinusoidal sigma weight residual 0.00 89.83 -89.83 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CD ARG A1091 " pdb=" NE ARG A1091 " pdb=" CZ ARG A1091 " pdb=" NH1 ARG A1091 " ideal model delta sinusoidal sigma weight residual 0.00 -89.70 89.70 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CD ARG I 38 " pdb=" NE ARG I 38 " pdb=" CZ ARG I 38 " pdb=" NH1 ARG I 38 " ideal model delta sinusoidal sigma weight residual 0.00 89.46 -89.46 1 1.00e+01 1.00e-02 9.51e+01 ... (remaining 20880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 3725 0.124 - 0.247: 1559 0.247 - 0.371: 106 0.371 - 0.495: 0 0.495 - 0.619: 1 Chirality restraints: 5391 Sorted by residual: chirality pdb=" CB VAL Q 33 " pdb=" CA VAL Q 33 " pdb=" CG1 VAL Q 33 " pdb=" CG2 VAL Q 33 " both_signs ideal model delta sigma weight residual False -2.63 -2.01 -0.62 2.00e-01 2.50e+01 9.56e+00 chirality pdb=" CA PHE B 329 " pdb=" N PHE B 329 " pdb=" C PHE B 329 " pdb=" CB PHE B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA PHE B 540 " pdb=" N PHE B 540 " pdb=" C PHE B 540 " pdb=" CB PHE B 540 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 5388 not shown) Planarity restraints: 6198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 46 " -1.107 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG K 46 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG K 46 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG K 46 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG K 46 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 85 " 1.103 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG I 85 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG I 85 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG I 85 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG I 85 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1091 " -1.103 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG A1091 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A1091 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A1091 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A1091 " -0.015 2.00e-02 2.50e+03 ... (remaining 6195 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 11071 2.78 - 3.31: 36993 3.31 - 3.84: 62763 3.84 - 4.37: 78866 4.37 - 4.90: 120828 Nonbonded interactions: 310521 Sorted by model distance: nonbonded pdb=" O THR R 6 " pdb=" N SER R 8 " model vdw 2.252 3.120 nonbonded pdb=" O THR J 86 " pdb=" N THR J 102 " model vdw 2.254 3.120 nonbonded pdb=" O VAL A 705 " pdb=" N TYR A 707 " model vdw 2.261 3.120 nonbonded pdb=" O MET B 869 " pdb=" N ALA B 871 " model vdw 2.269 3.120 nonbonded pdb=" O ASN B1125 " pdb=" N ASP B1127 " model vdw 2.270 3.120 ... (remaining 310516 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'T' } 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 individual isotropic 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: 10.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 33.210 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5221 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 : 0.013 0.080 35364 Z= 0.954 Angle : 1.919 13.725 48138 Z= 1.329 Chirality : 0.116 0.619 5391 Planarity : 0.054 0.496 6198 Dihedral : 24.253 89.908 12471 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 69.37 Ramachandran Plot: Outliers : 17.67 % Allowed : 28.17 % Favored : 54.16 % Rotamer: Outliers : 41.03 % Allowed : 16.52 % Favored : 42.45 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.86 (0.08), residues: 4398 helix: -5.34 (0.06), residues: 613 sheet: -4.13 (0.15), residues: 820 loop : -5.98 (0.07), residues: 2965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 457 TYR 0.031 0.003 TYR A 917 PHE 0.032 0.003 PHE C 318 TRP 0.018 0.002 TRP C 64 HIS 0.009 0.002 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.01314 (35316) covalent geometry : angle 1.91736 (48042) SS BOND : bond 0.01625 ( 48) SS BOND : angle 2.53020 ( 96) hydrogen bonds : bond 0.27996 ( 530) hydrogen bonds : angle 12.83387 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1910 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1530 poor density : 380 time to evaluate : 1.409 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: 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: 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: 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 63 THR cc_start: 0.8021 (OUTLIER) cc_final: 0.7785 (m) REVERT: A 90 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8152 (p) REVERT: A 102 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6688 (mmt-90) REVERT: A 202 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6761 (mtmt) REVERT: A 223 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7859 (mm-30) REVERT: A 266 TYR cc_start: 0.6443 (m-80) cc_final: 0.5448 (m-10) REVERT: A 282 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7845 (m-40) REVERT: A 346 ARG cc_start: 0.3167 (OUTLIER) cc_final: 0.2444 (mmt90) REVERT: A 392 PHE cc_start: 0.1030 (OUTLIER) cc_final: -0.1163 (m-80) REVERT: A 401 VAL cc_start: 0.2454 (OUTLIER) cc_final: 0.2231 (t) REVERT: A 460 LYS cc_start: 0.4368 (OUTLIER) cc_final: 0.2060 (ptpt) REVERT: A 462 LYS cc_start: 0.0914 (OUTLIER) cc_final: -0.1341 (mttt) REVERT: A 471 GLU cc_start: 0.1106 (OUTLIER) cc_final: 0.0296 (tp30) REVERT: A 474 GLN cc_start: 0.2557 (OUTLIER) cc_final: 0.1931 (pp30) REVERT: A 478 LYS cc_start: 0.1564 (OUTLIER) cc_final: 0.0178 (mmtt) REVERT: A 518 HIS cc_start: 0.1923 (OUTLIER) cc_final: -0.1197 (t70) REVERT: A 576 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7904 (mmt-90) REVERT: A 633 ARG cc_start: 0.7293 (mmp-170) cc_final: 0.7082 (mmp-170) REVERT: A 643 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7215 (tm130) REVERT: A 654 TYR cc_start: 0.8400 (t80) cc_final: 0.8076 (t80) REVERT: A 733 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8287 (mtpt) REVERT: A 740 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7798 (tmm) REVERT: A 787 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8104 (mt0) REVERT: A 847 ARG cc_start: 0.4037 (OUTLIER) cc_final: 0.2073 (mtt90) REVERT: A 985 ASP cc_start: 0.7360 (p0) cc_final: 0.6752 (t0) REVERT: A 1000 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7927 (mtm180) REVERT: A 1028 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8631 (mtpp) REVERT: A 1071 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8868 (mt0) REVERT: A 1100 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8232 (m) REVERT: A 1111 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: B 41 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7097 (mtpp) REVERT: B 128 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7423 (mm) REVERT: B 129 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6040 (tptp) REVERT: B 169 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.3722 (mm-30) REVERT: B 201 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7666 (p90) REVERT: B 204 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: B 206 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7301 (tptt) REVERT: B 234 ILE cc_start: 0.7271 (mt) cc_final: 0.6477 (mp) REVERT: B 306 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: B 319 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7304 (ttp80) REVERT: B 357 ARG cc_start: 0.5620 (OUTLIER) cc_final: 0.5218 (ptt90) REVERT: B 462 LYS cc_start: 0.1378 (OUTLIER) cc_final: 0.0225 (pttp) REVERT: B 488 TYR cc_start: 0.1693 (OUTLIER) cc_final: 0.1020 (m-10) REVERT: B 559 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8431 (mp) REVERT: B 566 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7739 (mtt180) REVERT: B 602 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8149 (t0) REVERT: B 709 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7925 (m110) REVERT: B 733 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8491 (mtpt) REVERT: B 811 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7626 (mtmm) REVERT: B 849 LEU cc_start: 0.1459 (OUTLIER) cc_final: 0.1237 (tt) REVERT: B 854 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6639 (tttm) REVERT: B 933 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8019 (mtmt) REVERT: B 986 PRO cc_start: 0.6494 (Cg_exo) cc_final: 0.5459 (Cg_endo) REVERT: B 1028 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8790 (mtpp) REVERT: B 1142 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8337 (mm-40) REVERT: C 44 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.7665 (mtm180) REVERT: C 86 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.4361 (t80) REVERT: C 87 ASN cc_start: 0.5984 (OUTLIER) cc_final: 0.5746 (p0) REVERT: C 187 LYS cc_start: 0.6740 (OUTLIER) cc_final: 0.5888 (tttm) REVERT: C 200 TYR cc_start: 0.7993 (m-10) cc_final: 0.7793 (m-10) REVERT: C 211 ILE cc_start: 0.5591 (OUTLIER) cc_final: 0.5288 (mt) REVERT: C 237 PHE cc_start: 0.7706 (p90) cc_final: 0.7435 (p90) REVERT: C 265 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6931 (t80) REVERT: C 346 ARG cc_start: 0.0089 (OUTLIER) cc_final: -0.0393 (tmt170) REVERT: C 377 PHE cc_start: 0.0631 (OUTLIER) cc_final: 0.0344 (m-80) REVERT: C 398 ASP cc_start: 0.4139 (OUTLIER) cc_final: 0.3505 (m-30) REVERT: C 406 GLU cc_start: 0.2151 (OUTLIER) cc_final: 0.0982 (mm-30) REVERT: C 424 LYS cc_start: 0.1238 (OUTLIER) cc_final: 0.0443 (tptt) REVERT: C 445 HIS cc_start: 0.2808 (OUTLIER) cc_final: 0.2116 (m90) REVERT: C 467 ASP cc_start: 0.2574 (OUTLIER) cc_final: 0.2151 (p0) REVERT: C 473 TYR cc_start: -0.1513 (OUTLIER) cc_final: -0.2462 (t80) REVERT: C 479 PRO cc_start: 0.4356 (OUTLIER) cc_final: 0.3880 (Cg_endo) REVERT: C 643 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: C 659 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8825 (m-80) REVERT: C 674 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.6567 (mp-120) REVERT: C 725 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: C 787 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8296 (mt0) REVERT: C 830 ASP cc_start: 0.5492 (OUTLIER) cc_final: 0.5224 (t0) REVERT: C 853 GLN cc_start: 0.4972 (OUTLIER) cc_final: 0.4284 (pm20) REVERT: C 854 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6317 (tttm) REVERT: C 914 ASN cc_start: 0.7758 (t0) cc_final: 0.6811 (t0) REVERT: C 918 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: C 997 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8577 (mp) REVERT: C 1000 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.7580 (mtp180) REVERT: C 1074 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7600 (p0) REVERT: Q 87 ARG cc_start: 0.4632 (OUTLIER) cc_final: 0.4282 (mmt-90) REVERT: S 70 MET cc_start: 0.2250 (OUTLIER) cc_final: -0.0203 (mpp) REVERT: S 114 PHE cc_start: 0.1344 (OUTLIER) cc_final: 0.0774 (p90) REVERT: R 103 LYS cc_start: 0.3138 (OUTLIER) cc_final: 0.1855 (ttpp) REVERT: D 12 LYS cc_start: 0.0306 (OUTLIER) cc_final: -0.0388 (ptmm) REVERT: D 46 GLU cc_start: 0.3801 (OUTLIER) cc_final: 0.3292 (mm-30) REVERT: E 50 TRP cc_start: 0.0062 (OUTLIER) cc_final: -0.1508 (t60) REVERT: E 51 ILE cc_start: -0.1443 (OUTLIER) cc_final: -0.1652 (mt) REVERT: F 28 GLN cc_start: 0.0447 (OUTLIER) cc_final: -0.1275 (pp30) REVERT: F 80 GLN cc_start: 0.0054 (OUTLIER) cc_final: -0.0383 (pp30) REVERT: F 96 TYR cc_start: 0.1846 (OUTLIER) cc_final: 0.1631 (m-80) REVERT: H 46 GLU cc_start: 0.2206 (OUTLIER) cc_final: 0.1920 (mm-30) REVERT: H 52 ILE cc_start: 0.0560 (OUTLIER) cc_final: 0.0109 (pt) REVERT: I 81 MET cc_start: 0.1386 (OUTLIER) cc_final: -0.0179 (ptt) REVERT: J 96 TYR cc_start: -0.0122 (OUTLIER) cc_final: -0.1301 (m-10) REVERT: K 62 ARG cc_start: 0.2862 (OUTLIER) cc_final: 0.1477 (tmm-80) outliers start: 1530 outliers final: 570 residues processed: 1736 average time/residue: 0.2343 time to fit residues: 645.1226 Evaluate side-chains 933 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 662 poor density : 271 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 463 PRO Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 643 GLN Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 676 GLN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1000 ARG Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 322 PRO Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 479 PRO Chi-restraints excluded: chain B residue 488 TYR Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 564 PHE Chi-restraints excluded: chain B residue 566 ARG Chi-restraints excluded: chain B residue 576 ARG Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 ARG Chi-restraints excluded: chain B residue 674 GLN Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 807 PRO Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 445 HIS Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 479 PRO Chi-restraints excluded: chain C residue 483 LYS Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 513 SER Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 560 PRO Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 564 PHE Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 582 GLU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 586 ILE Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 606 GLN Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 623 ILE Chi-restraints excluded: chain C residue 630 PRO Chi-restraints excluded: chain C residue 633 ARG Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 643 GLN Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 659 TYR Chi-restraints excluded: chain C residue 674 GLN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1138 TYR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 51 PHE Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain Q residue 64 PHE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 87 ARG Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 112 PHE Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 48 MET Chi-restraints excluded: chain S residue 50 TRP Chi-restraints excluded: chain S residue 70 MET Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 102 ARG Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 114 PHE Chi-restraints excluded: chain S residue 115 ASP Chi-restraints excluded: chain S residue 123 VAL Chi-restraints excluded: chain R residue 3 ILE Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 33 TYR Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 56 GLU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 103 LYS Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 30 SER Chi-restraints excluded: chain T residue 39 GLN Chi-restraints excluded: chain T residue 62 ARG Chi-restraints excluded: chain T residue 72 PHE Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain T residue 81 PRO Chi-restraints excluded: chain T residue 83 ASP Chi-restraints excluded: chain T residue 84 PHE Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain T residue 94 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 41 PRO Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 14 PRO Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 50 TRP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 85 ARG Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 96 TYR Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 88 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 41 PRO Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 96 TYR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 46 ARG Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 81 PRO Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 89 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 271 GLN A 317 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 414 GLN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 ASN ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 GLN A 901 GLN A 955 ASN A 992 GLN A1011 GLN A1048 HIS A1098 ASN A1142 GLN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 217 GLN B 271 GLN B 334 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 445 HIS ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 640 ASN B 774 GLN B 784 GLN B 872 GLN B 907 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN B1142 GLN C 122 ASN C 165 ASN C 188 ASN C 196 ASN C 233 ASN C 343 ASN C 405 ASN C 414 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 562 GLN C 602 ASN C 612 GLN C 615 ASN C 657 ASN C 674 GLN C 755 GLN C 779 GLN C 804 GLN C 914 ASN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C 978 ASN C1023 ASN C1054 GLN C1058 HIS C1064 HIS C1088 HIS C1113 GLN C1125 ASN C1135 ASN Q 102 ASN S 59 ASN ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 90 GLN T 92 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN E 57 ASN E 59 ASN F 28 GLN F 80 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 102 ASN I 57 ASN I 59 ASN ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.209430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.142667 restraints weight = 65730.878| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 4.25 r_work: 0.3375 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 35364 Z= 0.251 Angle : 1.101 15.594 48138 Z= 0.565 Chirality : 0.057 0.434 5391 Planarity : 0.009 0.156 6198 Dihedral : 17.391 88.280 6222 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 28.88 Ramachandran Plot: Outliers : 2.71 % Allowed : 23.28 % Favored : 74.01 % Rotamer: Outliers : 17.54 % Allowed : 23.22 % Favored : 59.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -6.69 (0.09), residues: 4398 helix: -4.49 (0.11), residues: 660 sheet: -3.63 (0.14), residues: 951 loop : -5.05 (0.08), residues: 2787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 355 TYR 0.031 0.003 TYR B 200 PHE 0.039 0.003 PHE B 540 TRP 0.029 0.003 TRP C 353 HIS 0.015 0.002 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00557 (35316) covalent geometry : angle 1.09524 (48042) SS BOND : bond 0.00769 ( 48) SS BOND : angle 2.78537 ( 96) hydrogen bonds : bond 0.04514 ( 530) hydrogen bonds : angle 8.06190 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 654 poor density : 309 time to evaluate : 1.211 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7374 (OUTLIER) cc_final: 0.7146 (m) REVERT: A 102 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.6141 (mmt90) REVERT: A 202 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7063 (mtmt) REVERT: A 223 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7913 (mm-30) REVERT: A 346 ARG cc_start: 0.2584 (OUTLIER) cc_final: 0.2165 (mtt180) REVERT: A 401 VAL cc_start: 0.1970 (OUTLIER) cc_final: 0.1556 (t) REVERT: A 474 GLN cc_start: 0.1604 (OUTLIER) cc_final: 0.1101 (pp30) REVERT: A 573 ASP cc_start: 0.7964 (t0) cc_final: 0.7753 (t0) REVERT: A 576 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8246 (tpp-160) REVERT: A 643 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.7688 (tm130) REVERT: A 660 GLU cc_start: 0.7934 (tt0) cc_final: 0.7726 (tp30) REVERT: A 733 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8526 (mtmt) REVERT: A 740 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8874 (tpt) REVERT: A 787 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8431 (mt0) REVERT: A 847 ARG cc_start: 0.3585 (OUTLIER) cc_final: 0.1762 (mpt180) REVERT: A 939 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6295 (p90) REVERT: A 957 GLN cc_start: 0.8443 (tt0) cc_final: 0.8068 (tt0) REVERT: A 960 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.7994 (m110) REVERT: A 995 ARG cc_start: 0.8867 (ttm170) cc_final: 0.8542 (ttt90) REVERT: A 1000 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7453 (mtm180) REVERT: A 1071 GLN cc_start: 0.9369 (OUTLIER) cc_final: 0.9124 (mt0) REVERT: B 129 LYS cc_start: 0.6514 (OUTLIER) cc_final: 0.5747 (tptp) REVERT: B 204 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7204 (m-80) REVERT: B 206 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6701 (tptt) REVERT: B 220 SER cc_start: 0.8726 (m) cc_final: 0.8243 (p) REVERT: B 319 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7740 (ttp80) REVERT: B 396 TYR cc_start: 0.5779 (OUTLIER) cc_final: 0.4606 (p90) REVERT: B 428 ASP cc_start: 0.0885 (OUTLIER) cc_final: 0.0664 (t70) REVERT: B 462 LYS cc_start: 0.1522 (OUTLIER) cc_final: 0.1204 (pttp) REVERT: B 605 ASN cc_start: 0.8857 (m-40) cc_final: 0.8528 (t0) REVERT: B 733 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8702 (mtpt) REVERT: B 811 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7061 (mtmm) REVERT: B 849 LEU cc_start: 0.0446 (OUTLIER) cc_final: 0.0170 (tt) REVERT: B 854 LYS cc_start: 0.5598 (OUTLIER) cc_final: 0.5296 (tttm) REVERT: B 912 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8584 (p) REVERT: B 957 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8219 (mt0) REVERT: C 34 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7896 (mtp-110) REVERT: C 53 ASP cc_start: 0.8179 (t0) cc_final: 0.7884 (t0) REVERT: C 64 TRP cc_start: 0.6964 (OUTLIER) cc_final: 0.6514 (t60) REVERT: C 87 ASN cc_start: 0.5988 (OUTLIER) cc_final: 0.4978 (p0) REVERT: C 187 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6470 (tttm) REVERT: C 269 TYR cc_start: 0.8081 (m-80) cc_final: 0.7734 (m-80) REVERT: C 395 VAL cc_start: 0.0336 (OUTLIER) cc_final: 0.0089 (t) REVERT: C 398 ASP cc_start: 0.1876 (OUTLIER) cc_final: 0.0671 (m-30) REVERT: C 473 TYR cc_start: -0.3534 (OUTLIER) cc_final: -0.3773 (t80) REVERT: C 513 SER cc_start: 0.2674 (OUTLIER) cc_final: 0.2232 (p) REVERT: C 536 LYS cc_start: 0.7959 (tptt) cc_final: 0.7434 (tppp) REVERT: C 540 PHE cc_start: 0.5696 (t80) cc_final: 0.5384 (t80) REVERT: C 557 LYS cc_start: 0.8055 (mptt) cc_final: 0.7836 (mmtm) REVERT: C 674 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.6877 (mp10) REVERT: C 725 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8524 (tt0) REVERT: C 787 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8502 (mt0) REVERT: C 851 CYS cc_start: 0.5167 (OUTLIER) cc_final: 0.4320 (t) REVERT: C 914 ASN cc_start: 0.8049 (t0) cc_final: 0.6904 (t0) REVERT: C 918 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: C 966 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.7926 (mt) REVERT: C 1000 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7249 (mtp85) REVERT: C 1074 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.8161 (p0) REVERT: C 1113 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8479 (mt0) REVERT: Q 23 LYS cc_start: 0.6293 (mmpt) cc_final: 0.5447 (tptp) REVERT: Q 102 ASN cc_start: 0.1888 (OUTLIER) cc_final: 0.1335 (m-40) REVERT: Q 112 PHE cc_start: 0.0743 (OUTLIER) cc_final: 0.0172 (m-80) REVERT: S 70 MET cc_start: 0.0915 (OUTLIER) cc_final: -0.0483 (mpp) REVERT: S 78 THR cc_start: 0.5046 (m) cc_final: 0.4608 (m) REVERT: R 34 LEU cc_start: 0.6891 (tt) cc_final: 0.6609 (pp) REVERT: R 55 LEU cc_start: 0.4908 (OUTLIER) cc_final: 0.4487 (mt) REVERT: R 103 LYS cc_start: 0.4373 (OUTLIER) cc_final: 0.3911 (mmmt) REVERT: D 12 LYS cc_start: -0.2501 (OUTLIER) cc_final: -0.3313 (ptmm) REVERT: D 54 LEU cc_start: 0.2108 (OUTLIER) cc_final: 0.1846 (pp) REVERT: E 19 LYS cc_start: 0.2185 (OUTLIER) cc_final: 0.1503 (mmmt) REVERT: E 50 TRP cc_start: -0.2363 (OUTLIER) cc_final: -0.3051 (t60) REVERT: E 71 THR cc_start: 0.3893 (OUTLIER) cc_final: 0.3545 (p) REVERT: F 35 ASN cc_start: 0.0975 (OUTLIER) cc_final: -0.1011 (t0) REVERT: H 13 LYS cc_start: 0.1327 (OUTLIER) cc_final: 0.0889 (tttt) REVERT: H 52 ILE cc_start: -0.0083 (OUTLIER) cc_final: -0.0465 (pt) REVERT: I 48 MET cc_start: 0.3205 (mtp) cc_final: 0.2202 (tpp) REVERT: I 81 MET cc_start: -0.1392 (OUTLIER) cc_final: -0.1740 (ptt) REVERT: J 4 GLN cc_start: 0.4123 (OUTLIER) cc_final: 0.2487 (tt0) outliers start: 654 outliers final: 350 residues processed: 899 average time/residue: 0.2306 time to fit residues: 333.8048 Evaluate side-chains 652 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 411 poor density : 241 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 643 GLN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1000 ARG Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 674 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 513 SER Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 633 ARG Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 674 GLN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 51 PHE Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain Q residue 64 PHE Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 99 LEU Chi-restraints excluded: chain Q residue 102 ASN Chi-restraints excluded: chain Q residue 112 PHE Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 50 TRP Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 70 MET Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 102 ARG Chi-restraints excluded: chain S residue 115 ASP Chi-restraints excluded: chain S residue 123 VAL Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 103 LYS Chi-restraints excluded: chain T residue 62 ARG Chi-restraints excluded: chain T residue 84 PHE Chi-restraints excluded: chain T residue 94 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 50 TRP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 85 ARG Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 89 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 200 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 343 optimal weight: 0.0870 chunk 139 optimal weight: 10.0000 chunk 373 optimal weight: 7.9990 chunk 331 optimal weight: 20.0000 chunk 306 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 367 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 chunk 308 optimal weight: 0.4980 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 134 GLN A 331 ASN A1071 GLN B 26 GLN B 49 HIS B 354 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 657 ASN B 955 ASN B 965 GLN B1011 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN C 615 ASN C 624 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 GLN ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN G 38 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** K 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.204226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.137836 restraints weight = 65640.667| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 4.81 r_work: 0.3340 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 35364 Z= 0.210 Angle : 0.924 14.155 48138 Z= 0.471 Chirality : 0.051 0.365 5391 Planarity : 0.007 0.095 6198 Dihedral : 14.115 89.735 5513 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 2.07 % Allowed : 22.01 % Favored : 75.92 % Rotamer: Outliers : 12.95 % Allowed : 25.42 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.12 % 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 aren not related in a simple way. whole: -5.94 (0.10), residues: 4398 helix: -3.48 (0.15), residues: 650 sheet: -3.43 (0.15), residues: 931 loop : -4.53 (0.09), residues: 2817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 55 TYR 0.037 0.002 TYR B 200 PHE 0.069 0.002 PHE B 540 TRP 0.025 0.002 TRP J 36 HIS 0.011 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00472 (35316) covalent geometry : angle 0.92092 (48042) SS BOND : bond 0.00762 ( 48) SS BOND : angle 1.98611 ( 96) hydrogen bonds : bond 0.03998 ( 530) hydrogen bonds : angle 7.09242 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 483 poor density : 275 time to evaluate : 1.382 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7676 (OUTLIER) cc_final: 0.7367 (m) REVERT: A 65 PHE cc_start: 0.8565 (m-80) cc_final: 0.7846 (m-80) REVERT: A 111 ASP cc_start: 0.6946 (t0) cc_final: 0.6746 (t0) REVERT: A 202 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7354 (mtmt) REVERT: A 346 ARG cc_start: 0.2578 (OUTLIER) cc_final: 0.2331 (mtp85) REVERT: A 464 PHE cc_start: -0.1114 (OUTLIER) cc_final: -0.1499 (m-10) REVERT: A 474 GLN cc_start: 0.1435 (OUTLIER) cc_final: 0.1195 (pp30) REVERT: A 573 ASP cc_start: 0.7936 (t0) cc_final: 0.7531 (t0) REVERT: A 576 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8213 (tpp-160) REVERT: A 643 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.7866 (tm130) REVERT: A 660 GLU cc_start: 0.8200 (tt0) cc_final: 0.7895 (tp30) REVERT: A 733 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8521 (mtpt) REVERT: A 847 ARG cc_start: 0.3182 (OUTLIER) cc_final: 0.1702 (mtt90) REVERT: A 939 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6546 (p90) REVERT: A 957 GLN cc_start: 0.8733 (tt0) cc_final: 0.8372 (tt0) REVERT: A 1000 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8284 (mtm180) REVERT: B 41 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.6625 (mtpp) REVERT: B 65 PHE cc_start: 0.7716 (m-10) cc_final: 0.7088 (m-10) REVERT: B 83 VAL cc_start: 0.6799 (OUTLIER) cc_final: 0.6518 (t) REVERT: B 129 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.5548 (tmtt) REVERT: B 191 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7944 (mm-30) REVERT: B 204 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7420 (m-80) REVERT: B 219 PHE cc_start: 0.6828 (t80) cc_final: 0.6445 (t80) REVERT: B 220 SER cc_start: 0.8759 (m) cc_final: 0.8335 (p) REVERT: B 309 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: B 319 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7973 (ttp80) REVERT: B 380 TYR cc_start: 0.6451 (OUTLIER) cc_final: 0.5504 (m-10) REVERT: B 396 TYR cc_start: 0.5825 (OUTLIER) cc_final: 0.4656 (p90) REVERT: B 462 LYS cc_start: 0.1651 (OUTLIER) cc_final: 0.1399 (ptmm) REVERT: B 538 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8426 (m) REVERT: B 605 ASN cc_start: 0.9011 (m-40) cc_final: 0.8751 (t0) REVERT: B 632 TRP cc_start: 0.7273 (t60) cc_final: 0.7001 (t60) REVERT: B 733 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8772 (mtpt) REVERT: B 849 LEU cc_start: -0.0185 (OUTLIER) cc_final: -0.0528 (tt) REVERT: B 854 LYS cc_start: 0.5871 (OUTLIER) cc_final: 0.5635 (tttm) REVERT: B 878 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8748 (tt) REVERT: C 53 ASP cc_start: 0.8449 (t0) cc_final: 0.7961 (t0) REVERT: C 54 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8578 (mp) REVERT: C 187 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6344 (tmtt) REVERT: C 236 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7734 (mtm110) REVERT: C 269 TYR cc_start: 0.8255 (m-80) cc_final: 0.7750 (m-80) REVERT: C 371 PHE cc_start: -0.0648 (OUTLIER) cc_final: -0.1542 (m-80) REVERT: C 409 GLN cc_start: 0.0693 (OUTLIER) cc_final: 0.0426 (tp40) REVERT: C 457 ARG cc_start: 0.4262 (OUTLIER) cc_final: 0.2231 (ptp90) REVERT: C 458 LYS cc_start: 0.2929 (OUTLIER) cc_final: 0.2412 (mtmm) REVERT: C 513 SER cc_start: 0.2865 (OUTLIER) cc_final: 0.2037 (p) REVERT: C 674 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: C 725 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8820 (tt0) REVERT: C 853 GLN cc_start: 0.4422 (OUTLIER) cc_final: 0.3575 (pm20) REVERT: C 902 MET cc_start: 0.9194 (tpp) cc_final: 0.8965 (mmt) REVERT: C 918 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: C 966 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8232 (mt) REVERT: C 1000 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7472 (mtp85) REVERT: Q 23 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6105 (tptp) REVERT: Q 38 ARG cc_start: 0.6018 (ptm160) cc_final: 0.5576 (ptm160) REVERT: Q 48 MET cc_start: 0.2971 (ptp) cc_final: 0.2051 (mmt) REVERT: S 70 MET cc_start: 0.1856 (OUTLIER) cc_final: -0.0692 (mpp) REVERT: R 34 LEU cc_start: 0.7125 (tt) cc_final: 0.6843 (pp) REVERT: R 92 TYR cc_start: 0.0251 (m-10) cc_final: 0.0021 (m-10) REVERT: T 63 PHE cc_start: -0.0508 (OUTLIER) cc_final: -0.0810 (m-10) REVERT: D 12 LYS cc_start: -0.2379 (OUTLIER) cc_final: -0.3259 (ptmm) REVERT: D 81 MET cc_start: 0.2971 (ttp) cc_final: 0.2174 (ttp) REVERT: E 70 MET cc_start: 0.0718 (mtt) cc_final: 0.0311 (mtm) REVERT: F 3 ILE cc_start: -0.1465 (OUTLIER) cc_final: -0.1681 (tp) REVERT: F 34 LEU cc_start: 0.4086 (OUTLIER) cc_final: 0.3475 (tp) REVERT: G 59 ILE cc_start: -0.4278 (OUTLIER) cc_final: -0.4662 (pt) REVERT: H 13 LYS cc_start: 0.1468 (OUTLIER) cc_final: 0.1266 (tttm) REVERT: H 52 ILE cc_start: -0.0674 (OUTLIER) cc_final: -0.0959 (pt) REVERT: I 20 VAL cc_start: 0.1050 (OUTLIER) cc_final: 0.0837 (p) REVERT: I 81 MET cc_start: -0.1118 (OUTLIER) cc_final: -0.1470 (ptt) REVERT: J 4 GLN cc_start: 0.4192 (OUTLIER) cc_final: 0.2965 (tt0) REVERT: J 56 GLU cc_start: 0.2551 (OUTLIER) cc_final: 0.1476 (mp0) REVERT: K 22 SER cc_start: 0.0915 (OUTLIER) cc_final: 0.0465 (t) outliers start: 483 outliers final: 281 residues processed: 708 average time/residue: 0.2233 time to fit residues: 259.1860 Evaluate side-chains 581 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 334 poor density : 247 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 643 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1000 ARG Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 674 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 236 ARG Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 513 SER Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 537 CYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 674 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain Q residue 23 LYS Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 51 PHE Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain Q residue 64 PHE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 50 TRP Chi-restraints excluded: chain S residue 55 ASN Chi-restraints excluded: chain S residue 70 MET Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 115 ASP Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain T residue 30 SER Chi-restraints excluded: chain T residue 48 LEU Chi-restraints excluded: chain T residue 63 PHE Chi-restraints excluded: chain T residue 84 PHE Chi-restraints excluded: chain T residue 94 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 63 PHE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 89 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 226 optimal weight: 0.5980 chunk 308 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 275 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 282 optimal weight: 0.9980 chunk 290 optimal weight: 0.9980 chunk 336 optimal weight: 0.8980 chunk 245 optimal weight: 0.0570 chunk 402 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 196 ASN B 271 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN B 762 GLN B1054 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 ASN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.205794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.142882 restraints weight = 64873.506| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 4.64 r_work: 0.3333 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 35364 Z= 0.168 Angle : 0.850 12.719 48138 Z= 0.430 Chirality : 0.049 0.425 5391 Planarity : 0.006 0.097 6198 Dihedral : 12.012 85.449 5287 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 1.68 % Allowed : 18.76 % Favored : 79.56 % Rotamer: Outliers : 10.46 % Allowed : 26.39 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -5.38 (0.10), residues: 4398 helix: -2.80 (0.18), residues: 648 sheet: -3.20 (0.15), residues: 942 loop : -4.16 (0.10), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 102 TYR 0.034 0.002 TYR B 265 PHE 0.059 0.002 PHE B 540 TRP 0.039 0.002 TRP B 353 HIS 0.008 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00363 (35316) covalent geometry : angle 0.84724 (48042) SS BOND : bond 0.00461 ( 48) SS BOND : angle 1.76320 ( 96) hydrogen bonds : bond 0.03426 ( 530) hydrogen bonds : angle 6.62264 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 390 poor density : 283 time to evaluate : 1.380 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.6811 (t0) cc_final: 0.6569 (t0) REVERT: A 236 ARG cc_start: 0.7972 (ptt-90) cc_final: 0.7560 (ptp-170) REVERT: A 304 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8188 (mtmt) REVERT: A 321 GLN cc_start: 0.8614 (tp40) cc_final: 0.8246 (tp40) REVERT: A 474 GLN cc_start: 0.1829 (OUTLIER) cc_final: 0.1400 (pp30) REVERT: A 480 CYS cc_start: 0.4328 (OUTLIER) cc_final: 0.3926 (t) REVERT: A 573 ASP cc_start: 0.7563 (t0) cc_final: 0.7260 (t0) REVERT: A 643 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.7803 (tm130) REVERT: A 733 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8406 (ptpp) REVERT: A 847 ARG cc_start: 0.3108 (OUTLIER) cc_final: 0.1547 (mtt90) REVERT: A 939 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6405 (p90) REVERT: A 957 GLN cc_start: 0.8557 (tt0) cc_final: 0.8172 (tt0) REVERT: A 977 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8030 (mp) REVERT: A 1000 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8168 (mtm180) REVERT: B 83 VAL cc_start: 0.6952 (OUTLIER) cc_final: 0.6748 (t) REVERT: B 129 LYS cc_start: 0.6526 (OUTLIER) cc_final: 0.5382 (tmtt) REVERT: B 192 PHE cc_start: 0.7941 (m-80) cc_final: 0.7675 (m-80) REVERT: B 206 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6934 (tptt) REVERT: B 219 PHE cc_start: 0.6595 (t80) cc_final: 0.6154 (t80) REVERT: B 220 SER cc_start: 0.8716 (m) cc_final: 0.8355 (p) REVERT: B 396 TYR cc_start: 0.5920 (OUTLIER) cc_final: 0.4664 (p90) REVERT: B 462 LYS cc_start: 0.2181 (OUTLIER) cc_final: 0.1878 (ptmt) REVERT: B 507 TYR cc_start: 0.6163 (OUTLIER) cc_final: 0.5146 (m-80) REVERT: B 605 ASN cc_start: 0.8929 (m-40) cc_final: 0.8695 (t0) REVERT: B 632 TRP cc_start: 0.7092 (t60) cc_final: 0.6824 (t60) REVERT: B 849 LEU cc_start: -0.0512 (OUTLIER) cc_final: -0.0775 (tt) REVERT: C 53 ASP cc_start: 0.8263 (t0) cc_final: 0.7866 (t0) REVERT: C 54 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8600 (mp) REVERT: C 102 ARG cc_start: 0.5420 (OUTLIER) cc_final: 0.4277 (ptp90) REVERT: C 187 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6252 (tmtt) REVERT: C 236 ARG cc_start: 0.8009 (ptp90) cc_final: 0.7741 (mtm110) REVERT: C 269 TYR cc_start: 0.8224 (m-80) cc_final: 0.7708 (m-80) REVERT: C 409 GLN cc_start: 0.0714 (OUTLIER) cc_final: 0.0421 (tp40) REVERT: C 445 HIS cc_start: 0.2069 (OUTLIER) cc_final: 0.1694 (m90) REVERT: C 674 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7052 (mp10) REVERT: C 725 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8603 (tt0) REVERT: C 853 GLN cc_start: 0.4305 (OUTLIER) cc_final: 0.3554 (pm20) REVERT: C 914 ASN cc_start: 0.8150 (t0) cc_final: 0.7209 (t0) REVERT: C 918 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: C 1000 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8048 (mtp85) REVERT: Q 23 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6711 (tptp) REVERT: Q 69 MET cc_start: 0.3217 (ptp) cc_final: 0.3006 (ptt) REVERT: S 70 MET cc_start: 0.1589 (OUTLIER) cc_final: 0.0015 (mpp) REVERT: S 115 ASP cc_start: 0.0716 (OUTLIER) cc_final: -0.0266 (p0) REVERT: R 5 MET cc_start: 0.0196 (pmm) cc_final: -0.0099 (pmm) REVERT: R 50 TYR cc_start: 0.4018 (m-10) cc_final: 0.3636 (m-10) REVERT: R 80 GLN cc_start: 0.3805 (OUTLIER) cc_final: 0.2594 (tm-30) REVERT: T 32 THR cc_start: 0.4755 (p) cc_final: 0.4529 (p) REVERT: T 47 LEU cc_start: 0.1740 (OUTLIER) cc_final: 0.1335 (mt) REVERT: D 12 LYS cc_start: -0.2442 (OUTLIER) cc_final: -0.3104 (ptmm) REVERT: D 48 MET cc_start: 0.0653 (tmm) cc_final: 0.0420 (tmm) REVERT: D 54 LEU cc_start: 0.1867 (OUTLIER) cc_final: 0.1619 (pp) REVERT: F 3 ILE cc_start: -0.1587 (OUTLIER) cc_final: -0.1941 (tp) REVERT: F 34 LEU cc_start: 0.4250 (OUTLIER) cc_final: 0.3658 (tp) REVERT: G 14 SER cc_start: 0.1225 (OUTLIER) cc_final: 0.0766 (t) REVERT: H 69 MET cc_start: 0.3835 (mpp) cc_final: 0.0859 (ppp) REVERT: I 48 MET cc_start: 0.4868 (tpp) cc_final: 0.4610 (tpt) REVERT: I 81 MET cc_start: -0.0202 (OUTLIER) cc_final: -0.0534 (ptt) REVERT: J 4 GLN cc_start: 0.3696 (OUTLIER) cc_final: 0.2355 (tt0) REVERT: K 54 SER cc_start: -0.1296 (t) cc_final: -0.1633 (m) outliers start: 390 outliers final: 235 residues processed: 628 average time/residue: 0.2203 time to fit residues: 227.9289 Evaluate side-chains 509 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 273 poor density : 236 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 643 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1000 ARG Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 238 GLN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 488 TYR Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 445 HIS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 674 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain Q residue 23 LYS Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 51 PHE Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain Q residue 64 PHE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 112 PHE Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 55 ASN Chi-restraints excluded: chain S residue 70 MET Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 115 ASP Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 32 ASN Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 80 GLN Chi-restraints excluded: chain T residue 30 SER Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 84 PHE Chi-restraints excluded: chain T residue 94 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 89 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 436 optimal weight: 50.0000 chunk 348 optimal weight: 9.9990 chunk 208 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 278 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 387 optimal weight: 20.0000 chunk 286 optimal weight: 0.8980 chunk 318 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 562 GLN ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 919 ASN A 955 ASN B 314 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1054 GLN C 66 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.205087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.136543 restraints weight = 64840.488| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 5.25 r_work: 0.3241 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 35364 Z= 0.264 Angle : 0.864 14.046 48138 Z= 0.437 Chirality : 0.050 0.302 5391 Planarity : 0.006 0.100 6198 Dihedral : 11.125 81.622 5177 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 1.61 % Allowed : 19.69 % Favored : 78.69 % Rotamer: Outliers : 10.30 % Allowed : 26.63 % Favored : 63.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -5.16 (0.11), residues: 4398 helix: -2.63 (0.18), residues: 648 sheet: -3.05 (0.15), residues: 941 loop : -4.01 (0.10), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 55 TYR 0.029 0.002 TYR C 170 PHE 0.044 0.002 PHE B 540 TRP 0.023 0.002 TRP B 353 HIS 0.006 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00609 (35316) covalent geometry : angle 0.86108 (48042) SS BOND : bond 0.00648 ( 48) SS BOND : angle 1.79667 ( 96) hydrogen bonds : bond 0.03875 ( 530) hydrogen bonds : angle 6.62958 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 384 poor density : 236 time to evaluate : 1.416 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: A 118 LEU cc_start: 0.7518 (mt) cc_final: 0.7297 (mp) REVERT: A 228 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7916 (pp) REVERT: A 236 ARG cc_start: 0.8010 (ptt-90) cc_final: 0.7558 (ptp-170) REVERT: A 304 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8501 (mtmt) REVERT: A 573 ASP cc_start: 0.8006 (t0) cc_final: 0.7710 (t0) REVERT: A 633 ARG cc_start: 0.7541 (mmm160) cc_final: 0.6924 (mmm160) REVERT: A 643 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.7676 (tm130) REVERT: A 733 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8608 (mtpt) REVERT: A 847 ARG cc_start: 0.3292 (OUTLIER) cc_final: 0.1412 (mpt180) REVERT: A 939 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6537 (p90) REVERT: A 957 GLN cc_start: 0.8832 (tt0) cc_final: 0.8493 (tt0) REVERT: A 1000 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7347 (mtm180) REVERT: B 41 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.6817 (mtpp) REVERT: B 83 VAL cc_start: 0.7027 (OUTLIER) cc_final: 0.6820 (t) REVERT: B 206 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7258 (tptt) REVERT: B 220 SER cc_start: 0.8820 (m) cc_final: 0.8424 (p) REVERT: B 309 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: B 326 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7714 (mm) REVERT: B 396 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.5011 (p90) REVERT: B 462 LYS cc_start: 0.1886 (OUTLIER) cc_final: 0.1669 (ptmt) REVERT: B 507 TYR cc_start: 0.6270 (OUTLIER) cc_final: 0.5495 (m-80) REVERT: B 564 PHE cc_start: 0.8630 (p90) cc_final: 0.8204 (p90) REVERT: B 605 ASN cc_start: 0.9066 (m-40) cc_final: 0.8861 (t0) REVERT: B 632 TRP cc_start: 0.7450 (t60) cc_final: 0.7132 (t60) REVERT: B 811 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.6977 (mtmm) REVERT: C 187 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6454 (tmtt) REVERT: C 236 ARG cc_start: 0.8064 (ptp90) cc_final: 0.7843 (mtm110) REVERT: C 445 HIS cc_start: 0.2153 (OUTLIER) cc_final: 0.1862 (m90) REVERT: C 539 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.7995 (m110) REVERT: C 674 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: C 725 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8765 (tt0) REVERT: C 853 GLN cc_start: 0.4373 (OUTLIER) cc_final: 0.3492 (pm20) REVERT: C 918 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: C 997 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8887 (mp) REVERT: C 1000 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.7944 (mtp180) REVERT: Q 23 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6897 (tptp) REVERT: S 70 MET cc_start: 0.3496 (OUTLIER) cc_final: 0.1942 (mpp) REVERT: S 115 ASP cc_start: 0.0424 (OUTLIER) cc_final: -0.0069 (p0) REVERT: R 5 MET cc_start: 0.0159 (pmm) cc_final: -0.0110 (pmm) REVERT: R 80 GLN cc_start: 0.3717 (OUTLIER) cc_final: 0.2553 (tm-30) REVERT: T 32 THR cc_start: 0.4891 (p) cc_final: 0.4688 (p) REVERT: T 47 LEU cc_start: 0.2087 (OUTLIER) cc_final: 0.1476 (mt) REVERT: D 12 LYS cc_start: -0.2436 (OUTLIER) cc_final: -0.3195 (ptmm) REVERT: D 48 MET cc_start: -0.0225 (tmm) cc_final: -0.0452 (tmm) REVERT: D 54 LEU cc_start: 0.2030 (OUTLIER) cc_final: 0.1745 (pp) REVERT: F 3 ILE cc_start: -0.0789 (OUTLIER) cc_final: -0.1045 (tp) REVERT: F 19 ARG cc_start: 0.1499 (OUTLIER) cc_final: 0.0995 (tpp-160) REVERT: F 34 LEU cc_start: 0.3925 (OUTLIER) cc_final: 0.3046 (tp) REVERT: F 35 ASN cc_start: 0.0304 (OUTLIER) cc_final: -0.2251 (t0) REVERT: G 14 SER cc_start: 0.1374 (OUTLIER) cc_final: 0.1053 (t) REVERT: H 30 ARG cc_start: 0.2511 (OUTLIER) cc_final: 0.1823 (ptp-170) REVERT: H 69 MET cc_start: 0.3007 (mpp) cc_final: 0.0879 (ppp) REVERT: I 48 MET cc_start: 0.4322 (tpp) cc_final: 0.3891 (tpt) REVERT: I 81 MET cc_start: -0.0344 (OUTLIER) cc_final: -0.0682 (ptt) REVERT: J 5 MET cc_start: 0.2863 (ptt) cc_final: 0.1339 (mmt) REVERT: K 2 ILE cc_start: 0.1771 (OUTLIER) cc_final: 0.1059 (mp) REVERT: K 54 SER cc_start: -0.1265 (t) cc_final: -0.1558 (m) outliers start: 384 outliers final: 258 residues processed: 579 average time/residue: 0.2191 time to fit residues: 210.1245 Evaluate side-chains 522 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 298 poor density : 224 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 643 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1000 ARG Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 445 HIS Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 539 ASN Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 674 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain Q residue 23 LYS Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 51 PHE Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain Q residue 64 PHE Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 55 ASN Chi-restraints excluded: chain S residue 70 MET Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 115 ASP Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 80 GLN Chi-restraints excluded: chain T residue 30 SER Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 84 PHE Chi-restraints excluded: chain T residue 94 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 33 TYR Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 89 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 43 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 347 optimal weight: 9.9990 chunk 345 optimal weight: 10.0000 chunk 424 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 348 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 265 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 505 GLN B 762 GLN C 535 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.203987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.137485 restraints weight = 65376.743| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 4.91 r_work: 0.3284 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 35364 Z= 0.185 Angle : 0.802 15.594 48138 Z= 0.406 Chirality : 0.048 0.372 5391 Planarity : 0.006 0.101 6198 Dihedral : 10.289 83.432 5122 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 1.43 % Allowed : 17.67 % Favored : 80.90 % Rotamer: Outliers : 8.72 % Allowed : 27.67 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -4.92 (0.11), residues: 4398 helix: -2.41 (0.18), residues: 656 sheet: -2.91 (0.15), residues: 957 loop : -3.85 (0.10), residues: 2785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 30 TYR 0.024 0.002 TYR B 265 PHE 0.037 0.002 PHE A 759 TRP 0.020 0.002 TRP C 632 HIS 0.006 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00419 (35316) covalent geometry : angle 0.79912 (48042) SS BOND : bond 0.00383 ( 48) SS BOND : angle 1.82392 ( 96) hydrogen bonds : bond 0.03323 ( 530) hydrogen bonds : angle 6.37475 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 325 poor density : 240 time to evaluate : 1.367 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7865 (pp) REVERT: A 236 ARG cc_start: 0.7987 (ptt-90) cc_final: 0.7548 (ptp-170) REVERT: A 304 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8342 (mtmt) REVERT: A 338 PHE cc_start: 0.2963 (OUTLIER) cc_final: 0.2278 (m-10) REVERT: A 573 ASP cc_start: 0.7846 (t0) cc_final: 0.7501 (t0) REVERT: A 643 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.7660 (tm130) REVERT: A 733 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8415 (ptpp) REVERT: A 847 ARG cc_start: 0.3222 (OUTLIER) cc_final: 0.1223 (mpt180) REVERT: A 939 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.6498 (p90) REVERT: A 957 GLN cc_start: 0.8796 (tt0) cc_final: 0.8511 (tt0) REVERT: A 983 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.8214 (ttm110) REVERT: A 1000 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8432 (mtm180) REVERT: A 1142 GLN cc_start: 0.7495 (mp10) cc_final: 0.7259 (mp10) REVERT: B 54 LEU cc_start: 0.8993 (mt) cc_final: 0.8688 (mt) REVERT: B 206 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7225 (tptt) REVERT: B 220 SER cc_start: 0.8806 (m) cc_final: 0.8427 (p) REVERT: B 309 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: B 353 TRP cc_start: 0.1127 (m100) cc_final: 0.0654 (m100) REVERT: B 396 TYR cc_start: 0.5906 (OUTLIER) cc_final: 0.4632 (p90) REVERT: B 467 ASP cc_start: 0.1700 (OUTLIER) cc_final: 0.0829 (t70) REVERT: B 507 TYR cc_start: 0.6202 (OUTLIER) cc_final: 0.5243 (m-80) REVERT: B 632 TRP cc_start: 0.7347 (t60) cc_final: 0.7050 (t60) REVERT: B 811 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7620 (mtmm) REVERT: C 64 TRP cc_start: 0.6967 (OUTLIER) cc_final: 0.6235 (t60) REVERT: C 96 GLU cc_start: 0.3660 (OUTLIER) cc_final: 0.3280 (pt0) REVERT: C 102 ARG cc_start: 0.5714 (OUTLIER) cc_final: 0.4599 (ptp90) REVERT: C 725 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8741 (tt0) REVERT: C 918 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: C 997 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8894 (mp) REVERT: C 1000 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7697 (mtp85) REVERT: Q 23 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.6889 (tptp) REVERT: Q 38 ARG cc_start: 0.5970 (ptm160) cc_final: 0.5693 (ptm160) REVERT: S 70 MET cc_start: 0.2728 (OUTLIER) cc_final: 0.1233 (mpp) REVERT: S 115 ASP cc_start: -0.0231 (OUTLIER) cc_final: -0.0628 (p0) REVERT: R 5 MET cc_start: 0.0200 (pmm) cc_final: -0.0002 (pmm) REVERT: R 80 GLN cc_start: 0.3805 (OUTLIER) cc_final: 0.2555 (tm-30) REVERT: T 47 LEU cc_start: 0.1845 (OUTLIER) cc_final: 0.1270 (mp) REVERT: D 54 LEU cc_start: 0.1788 (OUTLIER) cc_final: 0.1564 (pp) REVERT: F 35 ASN cc_start: 0.0358 (OUTLIER) cc_final: -0.1065 (t0) REVERT: G 14 SER cc_start: 0.2048 (OUTLIER) cc_final: 0.1623 (t) REVERT: G 93 ASP cc_start: -0.1924 (OUTLIER) cc_final: -0.2173 (t0) REVERT: H 69 MET cc_start: 0.3028 (mpp) cc_final: 0.1024 (ppp) REVERT: I 48 MET cc_start: 0.4714 (tpp) cc_final: 0.4322 (tpt) REVERT: I 81 MET cc_start: -0.0160 (OUTLIER) cc_final: -0.0654 (ptt) REVERT: K 37 TYR cc_start: -0.3061 (OUTLIER) cc_final: -0.3475 (t80) REVERT: K 54 SER cc_start: -0.1064 (t) cc_final: -0.1353 (m) outliers start: 325 outliers final: 236 residues processed: 529 average time/residue: 0.2182 time to fit residues: 191.8297 Evaluate side-chains 491 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 268 poor density : 223 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 643 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1000 ARG Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 488 TYR Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain Q residue 23 LYS Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 51 PHE Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain Q residue 64 PHE Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 55 ASN Chi-restraints excluded: chain S residue 70 MET Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 115 ASP Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 80 GLN Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 84 PHE Chi-restraints excluded: chain T residue 94 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 112 PHE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 89 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 37 optimal weight: 5.9990 chunk 43 optimal weight: 0.0670 chunk 177 optimal weight: 0.9980 chunk 311 optimal weight: 20.0000 chunk 207 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 314 optimal weight: 0.8980 chunk 319 optimal weight: 30.0000 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 GLN B 52 GLN B 196 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B1142 GLN C 343 ASN C 445 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 ASN I 116 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.202662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.136816 restraints weight = 65669.917| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 5.06 r_work: 0.3275 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.6594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35364 Z= 0.174 Angle : 0.790 16.892 48138 Z= 0.397 Chirality : 0.047 0.341 5391 Planarity : 0.006 0.100 6198 Dihedral : 9.842 82.234 5087 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 1.36 % Allowed : 18.14 % Favored : 80.49 % Rotamer: Outliers : 8.15 % Allowed : 27.89 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -4.74 (0.11), residues: 4398 helix: -2.18 (0.19), residues: 656 sheet: -2.86 (0.15), residues: 960 loop : -3.71 (0.10), residues: 2782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 55 TYR 0.022 0.002 TYR B 204 PHE 0.032 0.002 PHE A 759 TRP 0.020 0.002 TRP C 632 HIS 0.005 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00397 (35316) covalent geometry : angle 0.78784 (48042) SS BOND : bond 0.00409 ( 48) SS BOND : angle 1.64123 ( 96) hydrogen bonds : bond 0.03263 ( 530) hydrogen bonds : angle 6.26021 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 304 poor density : 235 time to evaluate : 1.172 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 118 LEU cc_start: 0.7441 (mt) cc_final: 0.7190 (mp) REVERT: A 228 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7883 (pp) REVERT: A 236 ARG cc_start: 0.7966 (ptt-90) cc_final: 0.7544 (ptp-170) REVERT: A 304 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8298 (mtmt) REVERT: A 321 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8212 (mm-40) REVERT: A 338 PHE cc_start: 0.3040 (OUTLIER) cc_final: 0.2380 (m-10) REVERT: A 573 ASP cc_start: 0.7849 (t0) cc_final: 0.7499 (t0) REVERT: A 643 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.7696 (tm130) REVERT: A 733 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8271 (ptpt) REVERT: A 748 GLU cc_start: 0.8346 (mp0) cc_final: 0.8108 (mp0) REVERT: A 847 ARG cc_start: 0.3299 (OUTLIER) cc_final: 0.1234 (mpt180) REVERT: A 939 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6576 (p90) REVERT: A 957 GLN cc_start: 0.8835 (tt0) cc_final: 0.8553 (tt0) REVERT: A 983 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.8153 (ttm110) REVERT: A 1142 GLN cc_start: 0.7565 (mp10) cc_final: 0.7324 (mp10) REVERT: B 127 PHE cc_start: 0.8297 (t80) cc_final: 0.8097 (t80) REVERT: B 206 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7263 (tptt) REVERT: B 220 SER cc_start: 0.8864 (m) cc_final: 0.8488 (p) REVERT: B 309 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: B 391 CYS cc_start: 0.2778 (OUTLIER) cc_final: 0.2105 (p) REVERT: B 507 TYR cc_start: 0.6244 (OUTLIER) cc_final: 0.5294 (m-80) REVERT: B 632 TRP cc_start: 0.7342 (t60) cc_final: 0.7080 (t60) REVERT: B 653 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8061 (pm20) REVERT: B 746 SER cc_start: 0.8502 (OUTLIER) cc_final: 0.7999 (t) REVERT: B 811 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7631 (mtmm) REVERT: C 53 ASP cc_start: 0.8454 (t0) cc_final: 0.7993 (t0) REVERT: C 64 TRP cc_start: 0.7036 (OUTLIER) cc_final: 0.6261 (t60) REVERT: C 96 GLU cc_start: 0.3619 (OUTLIER) cc_final: 0.3177 (pt0) REVERT: C 102 ARG cc_start: 0.5731 (OUTLIER) cc_final: 0.4543 (ptp90) REVERT: C 187 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.6376 (tmtt) REVERT: C 539 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8160 (m-40) REVERT: C 725 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8763 (tt0) REVERT: C 918 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: C 997 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8862 (mp) REVERT: C 1000 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.7717 (mtp85) REVERT: Q 23 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7138 (tptp) REVERT: Q 38 ARG cc_start: 0.5824 (ptm160) cc_final: 0.5576 (ptm160) REVERT: Q 99 LEU cc_start: 0.1552 (tt) cc_final: 0.1317 (tp) REVERT: S 70 MET cc_start: 0.2642 (OUTLIER) cc_final: 0.1696 (mpp) REVERT: R 80 GLN cc_start: 0.3824 (OUTLIER) cc_final: 0.2594 (tm-30) REVERT: T 47 LEU cc_start: 0.1967 (OUTLIER) cc_final: 0.1438 (mt) REVERT: D 54 LEU cc_start: 0.1753 (OUTLIER) cc_final: 0.1476 (pp) REVERT: D 60 TYR cc_start: 0.3928 (OUTLIER) cc_final: 0.2817 (p90) REVERT: F 34 LEU cc_start: 0.4132 (OUTLIER) cc_final: 0.3221 (tp) REVERT: F 35 ASN cc_start: 0.0506 (OUTLIER) cc_final: -0.1830 (t0) REVERT: F 106 ILE cc_start: 0.2161 (OUTLIER) cc_final: 0.1887 (tp) REVERT: G 14 SER cc_start: 0.2074 (OUTLIER) cc_final: 0.1776 (t) REVERT: G 93 ASP cc_start: -0.1868 (OUTLIER) cc_final: -0.2103 (t0) REVERT: H 69 MET cc_start: 0.2946 (mpp) cc_final: 0.1091 (ppp) REVERT: I 48 MET cc_start: 0.4852 (tpp) cc_final: 0.4301 (tpt) REVERT: I 81 MET cc_start: -0.0167 (ttt) cc_final: -0.0759 (ptt) REVERT: J 5 MET cc_start: 0.2234 (ptt) cc_final: 0.0671 (tmm) REVERT: K 2 ILE cc_start: 0.0880 (OUTLIER) cc_final: -0.0010 (mp) outliers start: 304 outliers final: 227 residues processed: 510 average time/residue: 0.2061 time to fit residues: 175.1210 Evaluate side-chains 481 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 263 poor density : 218 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 643 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 488 TYR Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 64 TRP Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 539 ASN Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain Q residue 23 LYS Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 51 PHE Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain Q residue 64 PHE Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 55 ASN Chi-restraints excluded: chain S residue 70 MET Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 80 GLN Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 84 PHE Chi-restraints excluded: chain T residue 94 THR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 13 LYS Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 89 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 28 optimal weight: 7.9990 chunk 251 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 406 optimal weight: 30.0000 chunk 329 optimal weight: 9.9990 chunk 291 optimal weight: 0.0270 chunk 306 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 380 optimal weight: 30.0000 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN B 52 GLN B 196 ASN B 360 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 955 ASN C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.201273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.136642 restraints weight = 65648.005| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 4.43 r_work: 0.3239 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.6767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 35364 Z= 0.215 Angle : 0.796 15.938 48138 Z= 0.401 Chirality : 0.048 0.411 5391 Planarity : 0.006 0.102 6198 Dihedral : 9.447 80.922 5051 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 1.18 % Allowed : 17.74 % Favored : 81.08 % Rotamer: Outliers : 7.88 % Allowed : 28.00 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -4.67 (0.11), residues: 4398 helix: -2.07 (0.19), residues: 649 sheet: -2.88 (0.15), residues: 985 loop : -3.65 (0.10), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 30 TYR 0.023 0.002 TYR Q 80 PHE 0.035 0.002 PHE B 927 TRP 0.017 0.002 TRP C 632 HIS 0.004 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00503 (35316) covalent geometry : angle 0.79367 (48042) SS BOND : bond 0.00424 ( 48) SS BOND : angle 1.58944 ( 96) hydrogen bonds : bond 0.03430 ( 530) hydrogen bonds : angle 6.29129 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 294 poor density : 214 time to evaluate : 1.458 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 118 LEU cc_start: 0.7464 (mt) cc_final: 0.7206 (mp) REVERT: A 228 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7847 (pp) REVERT: A 236 ARG cc_start: 0.7955 (ptt-90) cc_final: 0.7551 (ptp-170) REVERT: A 304 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8189 (mtmt) REVERT: A 338 PHE cc_start: 0.3082 (OUTLIER) cc_final: 0.2406 (m-10) REVERT: A 573 ASP cc_start: 0.7629 (t0) cc_final: 0.7300 (t0) REVERT: A 643 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.7652 (tm130) REVERT: A 733 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8338 (mtpt) REVERT: A 847 ARG cc_start: 0.3186 (OUTLIER) cc_final: 0.1120 (mpt180) REVERT: A 939 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6624 (p90) REVERT: A 983 ARG cc_start: 0.8369 (ttp-110) cc_final: 0.8033 (ttm110) REVERT: A 1142 GLN cc_start: 0.7584 (mp10) cc_final: 0.7330 (mp10) REVERT: B 206 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7129 (tptt) REVERT: B 220 SER cc_start: 0.8761 (m) cc_final: 0.8410 (p) REVERT: B 309 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: B 507 TYR cc_start: 0.6259 (OUTLIER) cc_final: 0.5389 (m-80) REVERT: B 632 TRP cc_start: 0.7066 (t60) cc_final: 0.6863 (t60) REVERT: B 653 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: B 811 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7003 (mtmm) REVERT: C 102 ARG cc_start: 0.5635 (OUTLIER) cc_final: 0.4313 (ptp90) REVERT: C 187 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6188 (tmtt) REVERT: C 539 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.8090 (m-40) REVERT: C 725 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8533 (tt0) REVERT: C 918 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: C 997 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8772 (mp) REVERT: C 1000 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7617 (mtp85) REVERT: Q 23 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7342 (tptp) REVERT: Q 38 ARG cc_start: 0.5719 (ptm160) cc_final: 0.5252 (ptm160) REVERT: S 81 MET cc_start: 0.0338 (ttp) cc_final: -0.0760 (ptp) REVERT: T 47 LEU cc_start: 0.1842 (OUTLIER) cc_final: 0.1477 (mt) REVERT: D 54 LEU cc_start: 0.1805 (OUTLIER) cc_final: 0.1564 (pp) REVERT: F 34 LEU cc_start: 0.4061 (OUTLIER) cc_final: 0.3243 (tp) REVERT: F 35 ASN cc_start: 0.0539 (OUTLIER) cc_final: -0.2011 (t0) REVERT: G 14 SER cc_start: 0.1946 (m) cc_final: 0.1667 (t) REVERT: G 93 ASP cc_start: -0.1508 (OUTLIER) cc_final: -0.1794 (t0) REVERT: H 69 MET cc_start: 0.2380 (mpp) cc_final: 0.0842 (ppp) REVERT: I 48 MET cc_start: 0.4414 (tpp) cc_final: 0.3837 (tpt) REVERT: I 81 MET cc_start: -0.0363 (ttt) cc_final: -0.0809 (ptt) REVERT: J 5 MET cc_start: 0.2677 (ptt) cc_final: 0.1362 (mtt) REVERT: K 2 ILE cc_start: 0.1263 (OUTLIER) cc_final: 0.0527 (mp) outliers start: 294 outliers final: 233 residues processed: 481 average time/residue: 0.2211 time to fit residues: 176.4383 Evaluate side-chains 462 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 259 poor density : 203 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 643 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 488 TYR Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 539 ASN Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain Q residue 23 LYS Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 51 PHE Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain Q residue 64 PHE Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 36 TRP Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 55 ASN Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 84 PHE Chi-restraints excluded: chain T residue 94 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 50 TRP Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 89 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 375 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 310 optimal weight: 0.0060 chunk 121 optimal weight: 0.9980 chunk 364 optimal weight: 9.9990 chunk 306 optimal weight: 0.7980 chunk 292 optimal weight: 0.9980 chunk 291 optimal weight: 0.8980 chunk 194 optimal weight: 0.5980 chunk 411 optimal weight: 3.9990 chunk 414 optimal weight: 8.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 762 GLN A 957 GLN B 20 ASN B 196 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 ASN B1010 GLN C 709 ASN C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.202648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.136849 restraints weight = 65576.535| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 5.23 r_work: 0.3323 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.7018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35364 Z= 0.148 Angle : 0.761 11.024 48138 Z= 0.384 Chirality : 0.047 0.399 5391 Planarity : 0.005 0.108 6198 Dihedral : 9.017 82.550 5032 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 1.14 % Allowed : 16.78 % Favored : 82.08 % Rotamer: Outliers : 6.87 % Allowed : 28.91 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -4.45 (0.11), residues: 4398 helix: -1.66 (0.20), residues: 646 sheet: -2.72 (0.15), residues: 980 loop : -3.58 (0.10), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 30 TYR 0.022 0.001 TYR B 204 PHE 0.025 0.002 PHE B 939 TRP 0.034 0.002 TRP Q 115 HIS 0.006 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00329 (35316) covalent geometry : angle 0.75946 (48042) SS BOND : bond 0.00333 ( 48) SS BOND : angle 1.34974 ( 96) hydrogen bonds : bond 0.03030 ( 530) hydrogen bonds : angle 6.09510 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 228 time to evaluate : 1.398 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: A 228 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7883 (pp) REVERT: A 236 ARG cc_start: 0.7925 (ptt-90) cc_final: 0.7524 (ptp-170) REVERT: A 304 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8437 (mtmt) REVERT: A 321 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8438 (mm-40) REVERT: A 338 PHE cc_start: 0.2848 (OUTLIER) cc_final: 0.2230 (m-10) REVERT: A 573 ASP cc_start: 0.7708 (t0) cc_final: 0.7381 (t0) REVERT: A 643 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.7786 (tm130) REVERT: A 733 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8365 (ptpt) REVERT: A 847 ARG cc_start: 0.3192 (OUTLIER) cc_final: 0.1089 (mpt180) REVERT: A 939 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6466 (p90) REVERT: A 983 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.8081 (ttm110) REVERT: A 1142 GLN cc_start: 0.7676 (mp10) cc_final: 0.7423 (mp10) REVERT: B 206 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7262 (tptt) REVERT: B 220 SER cc_start: 0.8802 (m) cc_final: 0.8468 (p) REVERT: B 309 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: B 507 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.4960 (m-80) REVERT: B 653 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8084 (pm20) REVERT: B 811 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7625 (mttt) REVERT: B 994 ASP cc_start: 0.8362 (m-30) cc_final: 0.7920 (t0) REVERT: C 53 ASP cc_start: 0.8427 (t0) cc_final: 0.8082 (t70) REVERT: C 96 GLU cc_start: 0.3537 (OUTLIER) cc_final: 0.2904 (pt0) REVERT: C 102 ARG cc_start: 0.5681 (OUTLIER) cc_final: 0.4253 (ptp90) REVERT: C 189 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7632 (tp) REVERT: C 539 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8119 (m-40) REVERT: C 725 GLU cc_start: 0.9084 (tp30) cc_final: 0.8736 (tt0) REVERT: C 918 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: C 997 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8834 (mp) REVERT: C 1000 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.7679 (mtp85) REVERT: Q 23 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.7001 (tptp) REVERT: Q 38 ARG cc_start: 0.5315 (ptm160) cc_final: 0.4978 (ptm160) REVERT: S 70 MET cc_start: 0.2762 (mtm) cc_final: 0.1702 (mtm) REVERT: S 81 MET cc_start: 0.0251 (ttp) cc_final: -0.0953 (ptp) REVERT: F 34 LEU cc_start: 0.4282 (OUTLIER) cc_final: 0.3465 (tp) REVERT: F 35 ASN cc_start: 0.0789 (OUTLIER) cc_final: -0.1066 (t0) REVERT: G 14 SER cc_start: 0.2053 (m) cc_final: 0.1787 (t) REVERT: G 93 ASP cc_start: -0.1616 (OUTLIER) cc_final: -0.1886 (t0) REVERT: H 30 ARG cc_start: 0.1301 (OUTLIER) cc_final: 0.0394 (mtp180) REVERT: H 69 MET cc_start: 0.2728 (mpp) cc_final: 0.1017 (ppp) REVERT: I 48 MET cc_start: 0.4795 (tpp) cc_final: 0.4267 (tpt) REVERT: I 81 MET cc_start: -0.0053 (ttt) cc_final: -0.0673 (ptt) REVERT: J 5 MET cc_start: 0.1933 (ptt) cc_final: 0.1038 (mtt) REVERT: K 2 ILE cc_start: 0.0677 (OUTLIER) cc_final: -0.0276 (mp) outliers start: 256 outliers final: 197 residues processed: 457 average time/residue: 0.2239 time to fit residues: 170.2600 Evaluate side-chains 441 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 219 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 643 GLN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 488 TYR Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 539 ASN Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain Q residue 23 LYS Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 51 PHE Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 64 PHE Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 36 TRP Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 55 ASN Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 84 PHE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 50 TRP Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 89 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 389 optimal weight: 6.9990 chunk 378 optimal weight: 30.0000 chunk 381 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 166 optimal weight: 0.0870 chunk 180 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 437 optimal weight: 50.0000 chunk 49 optimal weight: 0.5980 chunk 251 optimal weight: 10.0000 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 196 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 535 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.202070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.137241 restraints weight = 64929.027| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 4.83 r_work: 0.3316 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.7148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 35364 Z= 0.167 Angle : 0.775 11.115 48138 Z= 0.391 Chirality : 0.047 0.386 5391 Planarity : 0.006 0.109 6198 Dihedral : 8.726 80.904 5012 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 1.11 % Allowed : 16.76 % Favored : 82.13 % Rotamer: Outliers : 6.36 % Allowed : 29.34 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -4.34 (0.11), residues: 4398 helix: -1.55 (0.20), residues: 652 sheet: -2.66 (0.15), residues: 968 loop : -3.50 (0.10), residues: 2778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 98 TYR 0.034 0.002 TYR B 265 PHE 0.029 0.002 PHE Q 95 TRP 0.074 0.002 TRP Q 115 HIS 0.003 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00384 (35316) covalent geometry : angle 0.77315 (48042) SS BOND : bond 0.00307 ( 48) SS BOND : angle 1.31145 ( 96) hydrogen bonds : bond 0.03128 ( 530) hydrogen bonds : angle 6.07268 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 216 time to evaluate : 1.353 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: A 228 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7928 (pp) REVERT: A 236 ARG cc_start: 0.7848 (ptt-90) cc_final: 0.7460 (ptp-170) REVERT: A 338 PHE cc_start: 0.2811 (OUTLIER) cc_final: 0.2236 (m-10) REVERT: A 573 ASP cc_start: 0.7426 (t0) cc_final: 0.7130 (t0) REVERT: A 733 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8301 (ptpt) REVERT: A 847 ARG cc_start: 0.3066 (OUTLIER) cc_final: 0.1030 (mpt180) REVERT: A 939 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6313 (p90) REVERT: A 983 ARG cc_start: 0.8362 (ttp-110) cc_final: 0.8020 (ttm110) REVERT: A 1142 GLN cc_start: 0.7647 (mp10) cc_final: 0.7400 (mp10) REVERT: B 52 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 206 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7141 (tptt) REVERT: B 220 SER cc_start: 0.8759 (m) cc_final: 0.8435 (p) REVERT: B 309 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: B 507 TYR cc_start: 0.6022 (OUTLIER) cc_final: 0.4939 (m-80) REVERT: B 653 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7871 (pm20) REVERT: B 811 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7059 (mtmm) REVERT: B 994 ASP cc_start: 0.8096 (m-30) cc_final: 0.7726 (t0) REVERT: C 53 ASP cc_start: 0.8215 (t0) cc_final: 0.7904 (t70) REVERT: C 96 GLU cc_start: 0.3467 (OUTLIER) cc_final: 0.2779 (pt0) REVERT: C 102 ARG cc_start: 0.5562 (OUTLIER) cc_final: 0.4015 (ptp90) REVERT: C 189 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7589 (tp) REVERT: C 539 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8198 (m-40) REVERT: C 725 GLU cc_start: 0.8770 (tp30) cc_final: 0.8447 (tt0) REVERT: C 918 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: C 997 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8698 (mp) REVERT: C 1000 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7494 (mtp85) REVERT: Q 38 ARG cc_start: 0.5250 (ptm160) cc_final: 0.4924 (ptm160) REVERT: Q 115 TRP cc_start: 0.5469 (t-100) cc_final: 0.5180 (t-100) REVERT: S 70 MET cc_start: 0.1947 (mtm) cc_final: 0.1723 (mtm) REVERT: S 102 ARG cc_start: 0.2632 (tpp80) cc_final: 0.2431 (tpp80) REVERT: F 34 LEU cc_start: 0.4326 (OUTLIER) cc_final: 0.3521 (tp) REVERT: F 35 ASN cc_start: 0.0788 (OUTLIER) cc_final: -0.1043 (t0) REVERT: G 14 SER cc_start: 0.1595 (m) cc_final: 0.1383 (t) REVERT: G 93 ASP cc_start: -0.1516 (OUTLIER) cc_final: -0.1792 (t0) REVERT: H 30 ARG cc_start: 0.1442 (OUTLIER) cc_final: 0.0453 (mtp180) REVERT: H 69 MET cc_start: 0.2643 (mpp) cc_final: 0.1153 (ppp) REVERT: I 48 MET cc_start: 0.4872 (tpp) cc_final: 0.4310 (tpt) REVERT: I 81 MET cc_start: 0.0054 (ttt) cc_final: -0.0592 (ptt) REVERT: J 5 MET cc_start: 0.2434 (ptt) cc_final: 0.1306 (mtt) outliers start: 237 outliers final: 206 residues processed: 430 average time/residue: 0.2248 time to fit residues: 160.8046 Evaluate side-chains 433 residues out of total 3861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 206 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 847 ARG Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 954 HIS Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 488 TYR Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 616 CYS Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 539 ASN Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1000 ARG Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 51 PHE Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 64 PHE Chi-restraints excluded: chain S residue 11 VAL Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain S residue 36 TRP Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 55 ASN Chi-restraints excluded: chain S residue 85 ARG Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 84 PHE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 29 PHE Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain I residue 50 TRP Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 89 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 8 optimal weight: 8.9990 chunk 250 optimal weight: 7.9990 chunk 323 optimal weight: 8.9990 chunk 426 optimal weight: 0.9980 chunk 370 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 228 optimal weight: 0.7980 chunk 399 optimal weight: 3.9990 chunk 23 optimal weight: 0.0070 chunk 91 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS B 134 GLN B 165 ASN B 196 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.202743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.138109 restraints weight = 65419.814| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 5.11 r_work: 0.3290 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.7274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 35364 Z= 0.149 Angle : 0.760 14.490 48138 Z= 0.383 Chirality : 0.047 0.331 5391 Planarity : 0.006 0.110 6198 Dihedral : 8.504 81.193 5005 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 1.05 % Allowed : 16.58 % Favored : 82.38 % Rotamer: Outliers : 6.25 % Allowed : 29.63 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -4.21 (0.11), residues: 4398 helix: -1.32 (0.20), residues: 650 sheet: -2.60 (0.15), residues: 967 loop : -3.44 (0.10), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 91 TYR 0.028 0.001 TYR B 265 PHE 0.028 0.002 PHE B 939 TRP 0.073 0.002 TRP Q 36 HIS 0.020 0.001 HIS B 624 Details of bonding type rmsd covalent geometry : bond 0.00335 (35316) covalent geometry : angle 0.75888 (48042) SS BOND : bond 0.00323 ( 48) SS BOND : angle 1.25470 ( 96) hydrogen bonds : bond 0.03069 ( 530) hydrogen bonds : angle 6.00619 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18478.13 seconds wall clock time: 314 minutes 47.46 seconds (18887.46 seconds total)