Starting phenix.real_space_refine on Sat Aug 8 13:22:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lzh_63524/08_2026/9lzh_63524.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lzh_63524/08_2026/9lzh_63524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lzh_63524/08_2026/9lzh_63524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lzh_63524/08_2026/9lzh_63524.map" model { file = "/net/cci-nas-00/data/ceres_data/9lzh_63524/08_2026/9lzh_63524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lzh_63524/08_2026/9lzh_63524.cif" } resolution = 3.16 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= 0.003 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 17531 2.51 5 N 4501 2.21 5 O 5462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27644 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 9021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 9021 Classifications: {'peptide': 1165} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1108} Chain breaks: 6 Chain: "B" Number of atoms: 9021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 9021 Classifications: {'peptide': 1165} Link IDs: {'PTRANS': 56, 'TRANS': 1108} Chain breaks: 6 Chain: "C" Number of atoms: 9021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 9021 Classifications: {'peptide': 1165} Link IDs: {'PTRANS': 56, 'TRANS': 1108} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.49, per 1000 atoms: 0.20 Number of scatterers: 27644 At special positions: 0 Unit cell: (152.608, 144.923, 162.489, 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 150 16.00 O 5462 8.00 N 4501 7.00 C 17531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 242 " distance=2.02 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 442 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 659 " distance=2.02 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 655 " distance=2.03 Simple disulfide: pdb=" SG CYS A 684 " - pdb=" SG CYS A 717 " distance=2.03 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 740 " distance=2.03 Simple disulfide: pdb=" SG CYS A 805 " - pdb=" SG CYS A 827 " distance=2.03 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 816 " distance=2.03 Simple disulfide: pdb=" SG CYS A 911 " - pdb=" SG CYS A 924 " distance=2.03 Simple disulfide: pdb=" SG CYS A1105 " - pdb=" SG CYS A1116 " distance=2.02 Simple disulfide: pdb=" SG CYS A1155 " - pdb=" SG CYS A1163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 442 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 659 " distance=2.03 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 655 " distance=2.02 Simple disulfide: pdb=" SG CYS B 684 " - pdb=" SG CYS B 717 " distance=2.03 Simple disulfide: pdb=" SG CYS B 731 " - pdb=" SG CYS B 740 " distance=2.03 Simple disulfide: pdb=" SG CYS B 805 " - pdb=" SG CYS B 827 " distance=2.03 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 816 " distance=2.03 Simple disulfide: pdb=" SG CYS B 911 " - pdb=" SG CYS B 924 " distance=2.03 Simple disulfide: pdb=" SG CYS B1105 " - pdb=" SG CYS B1116 " distance=2.03 Simple disulfide: pdb=" SG CYS B1155 " - pdb=" SG CYS B1163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 242 " distance=2.04 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 354 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 412 " distance=2.02 Simple disulfide: pdb=" SG CYS C 430 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 442 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 507 " - pdb=" SG CYS C 531 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 659 " distance=2.04 Simple disulfide: pdb=" SG CYS C 625 " - pdb=" SG CYS C 655 " distance=2.03 Simple disulfide: pdb=" SG CYS C 684 " - pdb=" SG CYS C 717 " distance=2.03 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 740 " distance=2.03 Simple disulfide: pdb=" SG CYS C 805 " - pdb=" SG CYS C 827 " distance=2.03 Simple disulfide: pdb=" SG CYS C 810 " - pdb=" SG CYS C 816 " distance=2.03 Simple disulfide: pdb=" SG CYS C 911 " - pdb=" SG CYS C 924 " distance=2.03 Simple disulfide: pdb=" SG CYS C1105 " - pdb=" SG CYS C1116 " distance=2.03 Simple disulfide: pdb=" SG CYS C1155 " - pdb=" SG CYS C1163 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " NAG I 3 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " NAG M 3 " BETA1-6 " NAG K 1 " - " FUC K 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 30 " " NAG A1302 " - " ASN A 111 " " NAG A1303 " - " ASN A 172 " " NAG A1304 " - " ASN A 415 " " NAG A1305 " - " ASN A 784 " " NAG A1306 " - " ASN A1144 " " NAG A1307 " - " ASN A 71 " " NAG A1308 " - " ASN A 162 " " NAG B1301 " - " ASN B 162 " " NAG B1302 " - " ASN B 172 " " NAG B1303 " - " ASN B 71 " " NAG B1304 " - " ASN B 723 " " NAG B1305 " - " ASN B 869 " " NAG C1301 " - " ASN C 71 " " NAG C1302 " - " ASN C 162 " " NAG C1303 " - " ASN C 172 " " NAG C1304 " - " ASN C 241 " " NAG C1305 " - " ASN C 723 " " NAG C1306 " - " ASN C 784 " " NAG C1307 " - " ASN C 869 " " NAG D 1 " - " ASN A 227 " " NAG E 1 " - " ASN A 241 " " NAG F 1 " - " ASN A 869 " " NAG G 1 " - " ASN B 241 " " NAG H 1 " - " ASN B 111 " " NAG I 1 " - " ASN B 227 " " NAG J 1 " - " ASN B 415 " " NAG K 1 " - " ASN C 227 " " NAG L 1 " - " ASN C 111 " " NAG M 1 " - " ASN C 415 " Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6498 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 51 sheets defined 25.8% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 40 through 47 removed outlier: 3.705A pdb=" N PHE A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 removed outlier: 4.459A pdb=" N SER A 113 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 removed outlier: 3.572A pdb=" N SER A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.615A pdb=" N LEU A 278 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 415 through 422 removed outlier: 3.863A pdb=" N LEU A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.527A pdb=" N ALA A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 473 removed outlier: 4.315A pdb=" N LEU A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 683 through 691 removed outlier: 3.640A pdb=" N VAL A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR A 688 " --> pdb=" O CYS A 684 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 Processing helix chain 'A' and resid 804 through 811 Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 822 through 824 No H-bonds generated for 'chain 'A' and resid 822 through 824' Processing helix chain 'A' and resid 825 through 852 Processing helix chain 'A' and resid 870 through 874 removed outlier: 3.603A pdb=" N GLN A 874 " --> pdb=" O THR A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 897 Processing helix chain 'A' and resid 906 through 915 Processing helix chain 'A' and resid 922 through 924 No H-bonds generated for 'chain 'A' and resid 922 through 924' Processing helix chain 'A' and resid 925 through 930 removed outlier: 3.501A pdb=" N GLY A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 956 removed outlier: 3.669A pdb=" N THR A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 950 " --> pdb=" O TYR A 946 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 951 " --> pdb=" O THR A 947 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY A 952 " --> pdb=" O SER A 948 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 955 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY A 956 " --> pdb=" O GLY A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 979 removed outlier: 3.710A pdb=" N PHE A 976 " --> pdb=" O ALA A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1006 Processing helix chain 'A' and resid 1007 through 1010 Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 3.517A pdb=" N VAL A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1041 removed outlier: 3.701A pdb=" N GLN A1030 " --> pdb=" O ASN A1026 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A1031 " --> pdb=" O ALA A1027 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A1039 " --> pdb=" O LEU A1035 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER A1040 " --> pdb=" O ALA A1036 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1057 Processing helix chain 'A' and resid 1058 through 1105 removed outlier: 4.256A pdb=" N ASP A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ALA A1064 " --> pdb=" O PRO A1060 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN A1065 " --> pdb=" O GLU A1061 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A1078 " --> pdb=" O LEU A1074 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A1088 " --> pdb=" O GLN A1084 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A1090 " --> pdb=" O VAL A1086 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A1091 " --> pdb=" O ARG A1087 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A1094 " --> pdb=" O THR A1090 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.757A pdb=" N PHE B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 removed outlier: 4.552A pdb=" N SER B 113 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 236 removed outlier: 4.188A pdb=" N PHE B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 356 Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.996A pdb=" N THR B 395 " --> pdb=" O PRO B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 removed outlier: 3.816A pdb=" N LEU B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.502A pdb=" N ALA B 439 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.697A pdb=" N ILE B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 683 through 690 removed outlier: 3.685A pdb=" N VAL B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR B 688 " --> pdb=" O CYS B 684 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 804 through 811 Processing helix chain 'B' and resid 813 through 821 Processing helix chain 'B' and resid 822 through 824 No H-bonds generated for 'chain 'B' and resid 822 through 824' Processing helix chain 'B' and resid 825 through 852 Processing helix chain 'B' and resid 887 through 897 removed outlier: 3.506A pdb=" N VAL B 897 " --> pdb=" O LEU B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 915 removed outlier: 3.630A pdb=" N MET B 912 " --> pdb=" O TYR B 908 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY B 915 " --> pdb=" O CYS B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 925 Processing helix chain 'B' and resid 925 through 930 removed outlier: 3.507A pdb=" N GLY B 930 " --> pdb=" O GLN B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 957 removed outlier: 3.584A pdb=" N THR B 947 " --> pdb=" O GLU B 943 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 950 " --> pdb=" O TYR B 946 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 951 " --> pdb=" O THR B 947 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY B 952 " --> pdb=" O SER B 948 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 955 " --> pdb=" O LEU B 951 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 956 " --> pdb=" O GLY B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 983 removed outlier: 3.642A pdb=" N PHE B 976 " --> pdb=" O ALA B 972 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 982 " --> pdb=" O ARG B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1006 Processing helix chain 'B' and resid 1015 through 1041 removed outlier: 3.516A pdb=" N VAL B1021 " --> pdb=" O ALA B1017 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B1032 " --> pdb=" O ASN B1028 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B1039 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B1040 " --> pdb=" O ALA B1036 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN B1041 " --> pdb=" O SER B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1057 Processing helix chain 'B' and resid 1058 through 1105 removed outlier: 4.047A pdb=" N ASP B1063 " --> pdb=" O PRO B1059 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA B1064 " --> pdb=" O PRO B1060 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B1065 " --> pdb=" O GLU B1061 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B1077 " --> pdb=" O ARG B1073 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B1078 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B1089 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B1090 " --> pdb=" O VAL B1086 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B1091 " --> pdb=" O ARG B1087 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B1092 " --> pdb=" O SER B1088 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B1095 " --> pdb=" O ALA B1091 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 47 removed outlier: 3.680A pdb=" N PHE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 4.541A pdb=" N SER C 113 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.722A pdb=" N SER C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 removed outlier: 3.523A pdb=" N TYR C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 removed outlier: 3.760A pdb=" N LEU C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 439 removed outlier: 3.502A pdb=" N ALA C 439 " --> pdb=" O PRO C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 456 No H-bonds generated for 'chain 'C' and resid 454 through 456' Processing helix chain 'C' and resid 457 through 462 removed outlier: 3.711A pdb=" N ILE C 461 " --> pdb=" O MET C 457 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 457 through 462' Processing helix chain 'C' and resid 468 through 473 Processing helix chain 'C' and resid 531 through 535 removed outlier: 3.797A pdb=" N SER C 535 " --> pdb=" O ARG C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 600 removed outlier: 3.872A pdb=" N SER C 598 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 599 " --> pdb=" O GLY C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 690 removed outlier: 3.506A pdb=" N VAL C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 705 Processing helix chain 'C' and resid 804 through 811 Processing helix chain 'C' and resid 813 through 822 removed outlier: 4.314A pdb=" N GLU C 822 " --> pdb=" O LYS C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 852 Processing helix chain 'C' and resid 870 through 874 Processing helix chain 'C' and resid 887 through 897 Processing helix chain 'C' and resid 906 through 914 removed outlier: 3.580A pdb=" N MET C 912 " --> pdb=" O TYR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 930 Processing helix chain 'C' and resid 939 through 956 removed outlier: 3.601A pdb=" N THR C 947 " --> pdb=" O GLU C 943 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY C 952 " --> pdb=" O SER C 948 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C 953 " --> pdb=" O SER C 949 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 955 " --> pdb=" O LEU C 951 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY C 956 " --> pdb=" O GLY C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 981 removed outlier: 3.600A pdb=" N PHE C 976 " --> pdb=" O ALA C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 990 Processing helix chain 'C' and resid 992 through 1006 Processing helix chain 'C' and resid 1007 through 1010 Processing helix chain 'C' and resid 1015 through 1038 removed outlier: 3.508A pdb=" N VAL C1021 " --> pdb=" O ALA C1017 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C1032 " --> pdb=" O ASN C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1049 through 1057 Processing helix chain 'C' and resid 1058 through 1105 removed outlier: 4.062A pdb=" N ASP C1063 " --> pdb=" O PRO C1059 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ALA C1064 " --> pdb=" O PRO C1060 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN C1065 " --> pdb=" O GLU C1061 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU C1089 " --> pdb=" O LEU C1085 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR C1090 " --> pdb=" O VAL C1086 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C1091 " --> pdb=" O ARG C1087 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C1092 " --> pdb=" O SER C1088 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA C1095 " --> pdb=" O ALA C1091 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 removed outlier: 6.327A pdb=" N ILE A 61 " --> pdb=" O MET A 283 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ARG A 285 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 270 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR A 288 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL A 268 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLY A 122 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 323 " --> pdb=" O GLY A 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 81 removed outlier: 7.830A pdb=" N THR A 327 " --> pdb=" O ASP A 343 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP A 343 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 329 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 341 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP A 331 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 237 through 249 removed outlier: 6.960A pdb=" N VAL A 240 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS A 194 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N CYS A 242 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE A 192 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 244 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS A 191 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 159 through 162 removed outlier: 4.039A pdb=" N SER A 159 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 212 through 214 removed outlier: 6.577A pdb=" N ILE A 212 " --> pdb=" O SER A 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 364 through 367 removed outlier: 3.564A pdb=" N CYS A 717 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 381 removed outlier: 6.758A pdb=" N PHE A 379 " --> pdb=" O SER A 612 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 644 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 636 " --> pdb=" O VAL A 644 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 405 through 409 removed outlier: 6.682A pdb=" N SER A 488 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL A 425 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 413 through 414 Processing sheet with id=AB2, first strand: chain 'A' and resid 517 through 520 removed outlier: 6.346A pdb=" N VAL A 562 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS A 507 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A 560 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG A 509 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU A 558 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 722 through 728 removed outlier: 6.415A pdb=" N SER A 722 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL A 760 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 10.725A pdb=" N ASN A 724 " --> pdb=" O VAL A 760 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 767 through 769 removed outlier: 5.861A pdb=" N ILE A 767 " --> pdb=" O THR B 857 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1195 through 1196 removed outlier: 4.643A pdb=" N PHE A1171 " --> pdb=" O ALA A1151 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR A 778 " --> pdb=" O ALA B 968 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 786 through 795 removed outlier: 3.855A pdb=" N VAL A1123 " --> pdb=" O VAL A1138 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TYR A1140 " --> pdb=" O HIS A1121 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N HIS A1121 " --> pdb=" O TYR A1140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 801 through 803 Processing sheet with id=AB8, first strand: chain 'A' and resid 856 through 858 Processing sheet with id=AB9, first strand: chain 'A' and resid 966 through 968 removed outlier: 3.539A pdb=" N PHE A 966 " --> pdb=" O ALA C 780 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR C 778 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C 778 " --> pdb=" O THR C1149 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR C1149 " --> pdb=" O THR C 778 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA C 780 " --> pdb=" O ASN C1147 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN C1147 " --> pdb=" O ALA C 780 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR C1145 " --> pdb=" O PRO C 782 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN C 784 " --> pdb=" O THR C1143 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLY C1132 " --> pdb=" O ASN C1128 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASN C1128 " --> pdb=" O GLY C1132 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR C1134 " --> pdb=" O VAL C1126 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL C1126 " --> pdb=" O TYR C1134 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE C1136 " --> pdb=" O SER C1124 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER C1124 " --> pdb=" O PHE C1136 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C1138 " --> pdb=" O ILE C1122 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1203 through 1206 removed outlier: 3.855A pdb=" N CYS A1163 " --> pdb=" O VAL A1206 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS A1155 " --> pdb=" O LEU A1215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 37 through 39 Processing sheet with id=AC3, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.486A pdb=" N ILE B 61 " --> pdb=" O MET B 283 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ARG B 285 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 270 " --> pdb=" O PHE B 286 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B 288 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 268 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLY B 122 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 323 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 73 through 81 removed outlier: 7.947A pdb=" N THR B 327 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASP B 343 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 329 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA B 341 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASP B 331 " --> pdb=" O ARG B 339 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 117 through 118 removed outlier: 3.664A pdb=" N TYR B 298 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 186 " --> pdb=" O ASN B 246 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN B 246 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA B 188 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE B 244 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR B 190 " --> pdb=" O CYS B 242 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N CYS B 242 " --> pdb=" O TYR B 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.988A pdb=" N SER B 159 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 364 through 367 removed outlier: 3.500A pdb=" N CYS B 717 " --> pdb=" O PHE B 679 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 380 through 381 Processing sheet with id=AC9, first strand: chain 'B' and resid 405 through 409 removed outlier: 6.705A pdb=" N SER B 488 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL B 425 " --> pdb=" O SER B 488 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 412 through 414 removed outlier: 6.643A pdb=" N CYS B 412 " --> pdb=" O CYS B 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 517 through 520 removed outlier: 6.402A pdb=" N VAL B 562 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N CYS B 507 " --> pdb=" O ILE B 560 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 560 " --> pdb=" O CYS B 507 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG B 509 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU B 558 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 727 through 728 Processing sheet with id=AD4, first strand: chain 'B' and resid 767 through 769 removed outlier: 5.926A pdb=" N ILE B 767 " --> pdb=" O THR C 857 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1129 removed outlier: 6.085A pdb=" N HIS B1121 " --> pdb=" O TYR B1140 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR B1140 " --> pdb=" O HIS B1121 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B1123 " --> pdb=" O VAL B1138 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N THR B1149 " --> pdb=" O THR B1173 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B1173 " --> pdb=" O THR B1149 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1129 removed outlier: 6.085A pdb=" N HIS B1121 " --> pdb=" O TYR B1140 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR B1140 " --> pdb=" O HIS B1121 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B1123 " --> pdb=" O VAL B1138 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN B 784 " --> pdb=" O THR B1143 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TYR B1145 " --> pdb=" O PRO B 782 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN B1147 " --> pdb=" O ALA B 780 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA B 780 " --> pdb=" O ASN B1147 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR B1149 " --> pdb=" O THR B 778 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B 778 " --> pdb=" O THR B1149 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR B 778 " --> pdb=" O ALA C 968 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 801 through 803 Processing sheet with id=AD8, first strand: chain 'B' and resid 864 through 865 Processing sheet with id=AD9, first strand: chain 'B' and resid 1203 through 1206 removed outlier: 3.653A pdb=" N CYS B1163 " --> pdb=" O VAL B1206 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 37 through 39 Processing sheet with id=AE2, first strand: chain 'C' and resid 61 through 62 removed outlier: 6.448A pdb=" N ILE C 61 " --> pdb=" O MET C 283 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ARG C 285 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU C 270 " --> pdb=" O PHE C 286 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR C 288 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL C 268 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLY C 122 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 323 " --> pdb=" O GLY C 122 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 73 through 81 removed outlier: 7.913A pdb=" N THR C 327 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASP C 343 " --> pdb=" O THR C 327 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU C 329 " --> pdb=" O ALA C 341 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 341 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP C 331 " --> pdb=" O ARG C 339 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 237 through 249 removed outlier: 7.195A pdb=" N VAL C 240 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS C 194 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N CYS C 242 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE C 192 " --> pdb=" O CYS C 242 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE C 244 " --> pdb=" O TYR C 190 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 159 through 162 removed outlier: 4.050A pdb=" N SER C 159 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 364 through 367 removed outlier: 3.523A pdb=" N CYS C 717 " --> pdb=" O PHE C 679 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 378 through 381 removed outlier: 6.631A pdb=" N PHE C 379 " --> pdb=" O SER C 612 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL C 644 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL C 636 " --> pdb=" O VAL C 644 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 396 through 397 removed outlier: 6.402A pdb=" N GLY C 396 " --> pdb=" O THR C 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 405 through 409 removed outlier: 6.861A pdb=" N SER C 488 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL C 425 " --> pdb=" O SER C 488 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 413 through 414 Processing sheet with id=AF2, first strand: chain 'C' and resid 517 through 520 removed outlier: 5.308A pdb=" N GLY C 502 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL C 566 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE C 504 " --> pdb=" O THR C 564 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR C 564 " --> pdb=" O ILE C 504 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 506 " --> pdb=" O VAL C 562 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 727 through 728 removed outlier: 4.436A pdb=" N LEU C 733 " --> pdb=" O ALA C 741 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 801 through 803 Processing sheet with id=AF5, first strand: chain 'C' and resid 1203 through 1206 removed outlier: 3.767A pdb=" N CYS C1163 " --> pdb=" O VAL C1206 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N CYS C1155 " --> pdb=" O LEU C1215 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1169 through 1172 986 hydrogen bonds defined for protein. 2679 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: 7.11 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.55: 28064 1.55 - 1.90: 201 1.90 - 2.25: 0 2.25 - 2.60: 0 2.60 - 2.96: 3 Bond restraints: 28268 Sorted by residual: bond pdb=" C PHE C 694 " pdb=" N SER C 695 " ideal model delta sigma weight residual 1.331 2.955 -1.625 1.26e-02 6.30e+03 1.66e+04 bond pdb=" C PHE B 694 " pdb=" N SER B 695 " ideal model delta sigma weight residual 1.332 2.926 -1.594 1.40e-02 5.10e+03 1.30e+04 bond pdb=" C PHE A 694 " pdb=" N SER A 695 " ideal model delta sigma weight residual 1.333 2.954 -1.621 1.56e-02 4.11e+03 1.08e+04 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.525 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" N THR C 251 " pdb=" CA THR C 251 " ideal model delta sigma weight residual 1.457 1.490 -0.034 6.40e-03 2.44e+04 2.80e+01 ... (remaining 28263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.58: 38448 10.58 - 21.17: 6 21.17 - 31.75: 4 31.75 - 42.34: 0 42.34 - 52.92: 2 Bond angle restraints: 38460 Sorted by residual: angle pdb=" O PHE B 694 " pdb=" C PHE B 694 " pdb=" N SER B 695 " ideal model delta sigma weight residual 122.86 69.94 52.92 1.18e+00 7.18e-01 2.01e+03 angle pdb=" O PHE A 694 " pdb=" C PHE A 694 " pdb=" N SER A 695 " ideal model delta sigma weight residual 122.59 75.11 47.48 1.33e+00 5.65e-01 1.27e+03 angle pdb=" CA PHE B 694 " pdb=" C PHE B 694 " pdb=" N SER B 695 " ideal model delta sigma weight residual 115.51 90.96 24.55 1.27e+00 6.20e-01 3.74e+02 angle pdb=" O PHE C 694 " pdb=" C PHE C 694 " pdb=" N SER C 695 " ideal model delta sigma weight residual 121.83 98.34 23.49 1.28e+00 6.10e-01 3.37e+02 angle pdb=" C PHE C 694 " pdb=" N SER C 695 " pdb=" CA SER C 695 " ideal model delta sigma weight residual 121.29 89.55 31.74 1.74e+00 3.30e-01 3.33e+02 ... (remaining 38455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.68: 16466 22.68 - 45.36: 794 45.36 - 68.04: 105 68.04 - 90.72: 17 90.72 - 113.40: 9 Dihedral angle restraints: 17391 sinusoidal: 7203 harmonic: 10188 Sorted by residual: dihedral pdb=" C ASN A 241 " pdb=" N ASN A 241 " pdb=" CA ASN A 241 " pdb=" CB ASN A 241 " ideal model delta harmonic sigma weight residual -122.60 -143.34 20.74 0 2.50e+00 1.60e-01 6.88e+01 dihedral pdb=" CA ASN B1159 " pdb=" C ASN B1159 " pdb=" N PRO B1160 " pdb=" CA PRO B1160 " ideal model delta harmonic sigma weight residual -180.00 -141.98 -38.02 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA LYS C 57 " pdb=" C LYS C 57 " pdb=" N VAL C 58 " pdb=" CA VAL C 58 " ideal model delta harmonic sigma weight residual -180.00 -143.85 -36.15 0 5.00e+00 4.00e-02 5.23e+01 ... (remaining 17388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 4365 0.173 - 0.345: 58 0.345 - 0.518: 5 0.518 - 0.691: 1 0.691 - 0.864: 2 Chirality restraints: 4431 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 227 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.86e+01 chirality pdb=" CA ASN A 241 " pdb=" N ASN A 241 " pdb=" C ASN A 241 " pdb=" CB ASN A 241 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CA ASN B 241 " pdb=" N ASN B 241 " pdb=" C ASN B 241 " pdb=" CB ASN B 241 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.54 2.00e-01 2.50e+01 7.16e+00 ... (remaining 4428 not shown) Planarity restraints: 4957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 694 " -0.184 2.00e-02 2.50e+03 2.67e-01 7.10e+02 pdb=" C PHE B 694 " 0.424 2.00e-02 2.50e+03 pdb=" O PHE B 694 " -0.264 2.00e-02 2.50e+03 pdb=" N SER B 695 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 694 " -0.164 2.00e-02 2.50e+03 2.54e-01 6.44e+02 pdb=" C PHE C 694 " 0.423 2.00e-02 2.50e+03 pdb=" O PHE C 694 " -0.226 2.00e-02 2.50e+03 pdb=" N SER C 695 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 694 " -0.176 2.00e-02 2.50e+03 2.24e-01 5.03e+02 pdb=" C PHE A 694 " 0.380 2.00e-02 2.50e+03 pdb=" O PHE A 694 " -0.151 2.00e-02 2.50e+03 pdb=" N SER A 695 " -0.052 2.00e-02 2.50e+03 ... (remaining 4954 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 213 2.59 - 3.17: 23009 3.17 - 3.74: 40024 3.74 - 4.32: 59821 4.32 - 4.90: 99407 Nonbonded interactions: 222474 Sorted by model distance: nonbonded pdb=" O PRO A 81 " pdb=" OH TYR A 328 " model vdw 2.012 3.040 nonbonded pdb=" O PRO B 81 " pdb=" OH TYR B 328 " model vdw 2.022 3.040 nonbonded pdb=" OG1 THR B1090 " pdb=" OE2 GLU C1089 " model vdw 2.041 3.040 nonbonded pdb=" O PRO C 81 " pdb=" OH TYR C 328 " model vdw 2.053 3.040 nonbonded pdb=" OG SER C 113 " pdb=" OG SER C 209 " model vdw 2.084 3.040 ... (remaining 222469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 21 through 1305) selection = chain 'B' selection = (chain 'C' and resid 21 through 1305) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'E' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'L' and resid 1) } ncs_group { reference = chain 'I' selection = chain 'M' } 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.040 Process input model: 26.910 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.060 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 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 : 0.018 1.625 28360 Z= 1.232 Angle : 1.028 52.925 38686 Z= 0.645 Chirality : 0.060 0.864 4431 Planarity : 0.008 0.267 4927 Dihedral : 13.058 113.398 10743 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.90 % Favored : 94.89 % Rotamer: Outliers : 0.76 % Allowed : 1.33 % Favored : 97.91 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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 are not related in a simple way. whole: -0.91 (0.13), residues: 3447 helix: 0.38 (0.20), residues: 684 sheet: 0.05 (0.18), residues: 768 loop : -1.25 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 696 TYR 0.052 0.002 TYR B 328 PHE 0.021 0.002 PHE A1043 TRP 0.033 0.003 TRP C 49 HIS 0.007 0.001 HIS C1137 Details of bonding type rmsd/Z covalent geometry : bond 0.01756 / 1.23 (28268) covalent geometry : angle 0.99573 / 0.64 (38460) SS BOND : bond 0.00487 / 0.32 ( 50) SS BOND : angle 2.00130 / 1.46 ( 100) hydrogen bonds : bond 0.20852 / 14.12 ( 979) hydrogen bonds : angle 7.80375 / 5.40 ( 2679) link_BETA1-4 : bond 0.00861 / 0.56 ( 11) link_BETA1-4 : angle 3.66272 / 2.13 ( 33) link_BETA1-6 : bond 0.00413 / 0.22 ( 1) link_BETA1-6 : angle 1.20936 / 0.67 ( 3) link_NAG-ASN : bond 0.00758 / 0.44 ( 30) link_NAG-ASN : angle 4.57595 / 3.10 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 401 time to evaluate : 1.014 Fit side-chains REVERT: A 45 SER cc_start: 0.8908 (t) cc_final: 0.8617 (m) REVERT: A 339 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7743 (ttm110) REVERT: A 588 SER cc_start: 0.7328 (m) cc_final: 0.7023 (t) REVERT: A 637 TYR cc_start: 0.9021 (m-80) cc_final: 0.8444 (m-80) REVERT: A 701 ASN cc_start: 0.7150 (OUTLIER) cc_final: 0.6947 (m-40) REVERT: A 792 GLU cc_start: 0.8195 (tt0) cc_final: 0.7675 (tt0) REVERT: A 1168 ASP cc_start: 0.7321 (t70) cc_final: 0.7111 (t0) REVERT: B 631 LYS cc_start: 0.7036 (tmtt) cc_final: 0.6657 (tptt) REVERT: B 637 TYR cc_start: 0.9035 (m-80) cc_final: 0.8799 (m-80) REVERT: B 686 HIS cc_start: 0.5352 (t-90) cc_final: 0.4920 (t-90) REVERT: B 1034 LYS cc_start: 0.8242 (tttt) cc_final: 0.7582 (ttpp) REVERT: B 1168 ASP cc_start: 0.7575 (m-30) cc_final: 0.7288 (t70) REVERT: C 45 SER cc_start: 0.8977 (t) cc_final: 0.8651 (m) REVERT: C 69 TYR cc_start: 0.7662 (m-80) cc_final: 0.7309 (m-80) REVERT: C 465 SER cc_start: 0.9110 (t) cc_final: 0.8546 (p) REVERT: C 581 GLN cc_start: 0.8108 (tt0) cc_final: 0.7890 (tt0) REVERT: C 631 LYS cc_start: 0.7171 (tmtt) cc_final: 0.6895 (tttp) outliers start: 23 outliers final: 10 residues processed: 417 average time/residue: 0.1750 time to fit residues: 119.3522 Evaluate side-chains 275 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 264 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 659 CYS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain C residue 659 CYS Chi-restraints excluded: chain C residue 875 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 633 GLN A 701 ASN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN B 693 GLN B 941 ASN B1131 ASN C 310 ASN C 874 GLN C 980 ASN C1200 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.131799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.101345 restraints weight = 38302.038| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.58 r_work: 0.3066 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28360 Z= 0.164 Angle : 0.694 16.846 38686 Z= 0.352 Chirality : 0.047 0.603 4431 Planarity : 0.005 0.064 4927 Dihedral : 8.126 66.562 4700 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.04 % Favored : 94.79 % Rotamer: Outliers : 1.33 % Allowed : 8.20 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.14), residues: 3453 helix: 0.80 (0.20), residues: 708 sheet: 0.07 (0.18), residues: 765 loop : -1.24 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 634 TYR 0.027 0.002 TYR B 328 PHE 0.020 0.002 PHE A 244 TRP 0.015 0.002 TRP C 49 HIS 0.005 0.001 HIS B 686 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (28268) covalent geometry : angle 0.65590 / 0.34 (38460) SS BOND : bond 0.00488 / 0.29 ( 50) SS BOND : angle 1.22067 / 0.83 ( 100) hydrogen bonds : bond 0.05316 / 3.50 ( 979) hydrogen bonds : angle 5.75407 / 4.01 ( 2679) link_BETA1-4 : bond 0.00795 / 0.46 ( 11) link_BETA1-4 : angle 2.83068 / 1.67 ( 33) link_BETA1-6 : bond 0.00051 / 0.03 ( 1) link_BETA1-6 : angle 1.22901 / 0.69 ( 3) link_NAG-ASN : bond 0.00680 / 0.38 ( 30) link_NAG-ASN : angle 4.28171 / 2.87 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 296 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8975 (t) cc_final: 0.8533 (m) REVERT: A 274 ARG cc_start: 0.7490 (mtt90) cc_final: 0.6912 (mtm110) REVERT: A 339 ARG cc_start: 0.8518 (ttp80) cc_final: 0.8140 (ttp80) REVERT: A 588 SER cc_start: 0.7602 (m) cc_final: 0.7009 (t) REVERT: A 637 TYR cc_start: 0.9198 (m-80) cc_final: 0.8546 (m-80) REVERT: A 792 GLU cc_start: 0.9044 (tt0) cc_final: 0.8765 (tt0) REVERT: A 913 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8440 (ttpt) REVERT: A 977 TYR cc_start: 0.8459 (m-10) cc_final: 0.8182 (m-10) REVERT: A 1168 ASP cc_start: 0.7818 (t70) cc_final: 0.7565 (t0) REVERT: B 331 ASP cc_start: 0.7854 (t0) cc_final: 0.7553 (t0) REVERT: B 631 LYS cc_start: 0.6921 (tmtt) cc_final: 0.6434 (tptm) REVERT: B 686 HIS cc_start: 0.6424 (t-90) cc_final: 0.5628 (t-90) REVERT: B 825 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: B 1034 LYS cc_start: 0.8706 (tttt) cc_final: 0.8223 (ttpp) REVERT: B 1168 ASP cc_start: 0.8164 (m-30) cc_final: 0.7392 (t70) REVERT: B 1190 SER cc_start: 0.9250 (t) cc_final: 0.9023 (m) REVERT: C 45 SER cc_start: 0.8959 (t) cc_final: 0.8619 (m) REVERT: C 69 TYR cc_start: 0.7939 (m-80) cc_final: 0.7404 (m-80) REVERT: C 339 ARG cc_start: 0.8197 (mtm110) cc_final: 0.7884 (mtm110) REVERT: C 465 SER cc_start: 0.9356 (t) cc_final: 0.9019 (p) REVERT: C 541 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8033 (mp0) REVERT: C 631 LYS cc_start: 0.6950 (tmtt) cc_final: 0.6690 (tttp) REVERT: C 691 MET cc_start: 0.7275 (ptp) cc_final: 0.6841 (ptt) REVERT: C 826 PHE cc_start: 0.8333 (t80) cc_final: 0.8055 (t80) REVERT: C 912 MET cc_start: 0.7709 (mtm) cc_final: 0.7171 (mtt) REVERT: C 920 ARG cc_start: 0.7013 (ttt180) cc_final: 0.6586 (ttp80) outliers start: 40 outliers final: 25 residues processed: 327 average time/residue: 0.1713 time to fit residues: 90.9242 Evaluate side-chains 284 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1083 GLN Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 659 CYS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 659 CYS Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 991 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 191 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 284 optimal weight: 5.9990 chunk 339 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 302 optimal weight: 0.0570 chunk 174 optimal weight: 0.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.101619 restraints weight = 38663.338| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.72 r_work: 0.3067 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28360 Z= 0.136 Angle : 0.626 16.501 38686 Z= 0.317 Chirality : 0.045 0.592 4431 Planarity : 0.004 0.053 4927 Dihedral : 6.924 59.335 4691 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.04 % Favored : 94.87 % Rotamer: Outliers : 1.49 % Allowed : 9.73 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3453 helix: 1.02 (0.20), residues: 726 sheet: 0.02 (0.18), residues: 807 loop : -1.22 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 509 TYR 0.018 0.001 TYR A 328 PHE 0.019 0.001 PHE C 119 TRP 0.011 0.001 TRP C 49 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (28268) covalent geometry : angle 0.58627 / 0.31 (38460) SS BOND : bond 0.00648 / 0.35 ( 50) SS BOND : angle 1.73789 / 1.11 ( 100) hydrogen bonds : bond 0.04540 / 2.99 ( 979) hydrogen bonds : angle 5.27537 / 3.68 ( 2679) link_BETA1-4 : bond 0.00923 / 0.59 ( 11) link_BETA1-4 : angle 2.47049 / 1.41 ( 33) link_BETA1-6 : bond 0.00272 / 0.14 ( 1) link_BETA1-6 : angle 1.19016 / 0.66 ( 3) link_NAG-ASN : bond 0.00655 / 0.37 ( 30) link_NAG-ASN : angle 3.98091 / 2.65 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8935 (t) cc_final: 0.8433 (m) REVERT: A 220 CYS cc_start: 0.4185 (OUTLIER) cc_final: 0.3835 (m) REVERT: A 274 ARG cc_start: 0.7466 (mtt90) cc_final: 0.6966 (mtm110) REVERT: A 339 ARG cc_start: 0.8426 (ttp80) cc_final: 0.8140 (ttp80) REVERT: A 631 LYS cc_start: 0.7357 (mtpt) cc_final: 0.6522 (tmtt) REVERT: A 637 TYR cc_start: 0.9160 (m-80) cc_final: 0.8523 (m-80) REVERT: A 792 GLU cc_start: 0.9010 (tt0) cc_final: 0.8744 (tt0) REVERT: A 826 PHE cc_start: 0.8208 (t80) cc_final: 0.7999 (t80) REVERT: A 913 LYS cc_start: 0.8619 (ttpp) cc_final: 0.8408 (ttpt) REVERT: A 1168 ASP cc_start: 0.7674 (t70) cc_final: 0.7425 (t0) REVERT: B 331 ASP cc_start: 0.7775 (t0) cc_final: 0.7524 (t0) REVERT: B 443 TYR cc_start: 0.8986 (m-80) cc_final: 0.8403 (m-80) REVERT: B 465 SER cc_start: 0.9104 (t) cc_final: 0.8871 (p) REVERT: B 631 LYS cc_start: 0.6760 (tmtt) cc_final: 0.6264 (tptm) REVERT: B 686 HIS cc_start: 0.6464 (OUTLIER) cc_final: 0.5721 (t-90) REVERT: B 825 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8019 (mt0) REVERT: B 1034 LYS cc_start: 0.8482 (tttt) cc_final: 0.8013 (ttpp) REVERT: B 1168 ASP cc_start: 0.8057 (m-30) cc_final: 0.7371 (t70) REVERT: C 45 SER cc_start: 0.8934 (t) cc_final: 0.8548 (m) REVERT: C 69 TYR cc_start: 0.7589 (m-80) cc_final: 0.7231 (m-80) REVERT: C 339 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7786 (mtm110) REVERT: C 465 SER cc_start: 0.9326 (t) cc_final: 0.8962 (p) REVERT: C 541 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7600 (pt0) REVERT: C 691 MET cc_start: 0.7013 (ptp) cc_final: 0.6571 (ptt) REVERT: C 912 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6753 (mtp) REVERT: C 920 ARG cc_start: 0.7029 (ttt180) cc_final: 0.6694 (ttp80) REVERT: C 1089 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7749 (mm-30) outliers start: 45 outliers final: 33 residues processed: 316 average time/residue: 0.1599 time to fit residues: 82.8401 Evaluate side-chains 297 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 260 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1083 GLN Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 659 CYS Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 659 CYS Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1167 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 292 optimal weight: 6.9990 chunk 222 optimal weight: 0.0050 chunk 179 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 278 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 30 optimal weight: 0.0970 overall best weight: 2.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN C 324 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098152 restraints weight = 38768.994| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.72 r_work: 0.3015 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 28360 Z= 0.213 Angle : 0.671 16.722 38686 Z= 0.339 Chirality : 0.047 0.603 4431 Planarity : 0.004 0.061 4927 Dihedral : 6.793 59.863 4691 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.71 % Favored : 94.18 % Rotamer: Outliers : 2.19 % Allowed : 10.79 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3453 helix: 0.94 (0.20), residues: 726 sheet: -0.08 (0.18), residues: 768 loop : -1.36 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 509 TYR 0.025 0.002 TYR C 190 PHE 0.020 0.002 PHE C 119 TRP 0.014 0.002 TRP C 49 HIS 0.007 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 (28268) covalent geometry : angle 0.63569 / 0.33 (38460) SS BOND : bond 0.00733 / 0.39 ( 50) SS BOND : angle 1.53632 / 1.14 ( 100) hydrogen bonds : bond 0.04799 / 3.15 ( 979) hydrogen bonds : angle 5.30612 / 3.70 ( 2679) link_BETA1-4 : bond 0.00738 / 0.47 ( 11) link_BETA1-4 : angle 2.43242 / 1.38 ( 33) link_BETA1-6 : bond 0.00225 / 0.12 ( 1) link_BETA1-6 : angle 1.22670 / 0.68 ( 3) link_NAG-ASN : bond 0.00612 / 0.37 ( 30) link_NAG-ASN : angle 4.02445 / 2.65 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 256 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8981 (t) cc_final: 0.8447 (m) REVERT: A 220 CYS cc_start: 0.4336 (OUTLIER) cc_final: 0.4017 (m) REVERT: A 274 ARG cc_start: 0.7515 (mtt90) cc_final: 0.6960 (mtm110) REVERT: A 339 ARG cc_start: 0.8433 (ttp80) cc_final: 0.8135 (ttp80) REVERT: A 588 SER cc_start: 0.7952 (m) cc_final: 0.7338 (t) REVERT: A 631 LYS cc_start: 0.7390 (mtpt) cc_final: 0.6564 (tmtt) REVERT: A 637 TYR cc_start: 0.9209 (m-80) cc_final: 0.8568 (m-80) REVERT: A 792 GLU cc_start: 0.9049 (tt0) cc_final: 0.8802 (tt0) REVERT: A 913 LYS cc_start: 0.8641 (ttpp) cc_final: 0.8435 (ttpt) REVERT: A 1168 ASP cc_start: 0.7895 (t70) cc_final: 0.7599 (t0) REVERT: B 214 GLU cc_start: 0.7002 (tt0) cc_final: 0.6546 (pp20) REVERT: B 315 TRP cc_start: 0.7972 (OUTLIER) cc_final: 0.7063 (m-90) REVERT: B 331 ASP cc_start: 0.7837 (t0) cc_final: 0.7626 (t0) REVERT: B 443 TYR cc_start: 0.9128 (m-80) cc_final: 0.8620 (m-80) REVERT: B 592 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8265 (mtp) REVERT: B 631 LYS cc_start: 0.6813 (tmtt) cc_final: 0.6290 (tptm) REVERT: B 686 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.5903 (t-90) REVERT: B 755 GLN cc_start: 0.7570 (mt0) cc_final: 0.7146 (tt0) REVERT: B 825 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8257 (mt0) REVERT: B 1034 LYS cc_start: 0.8536 (tttt) cc_final: 0.8063 (ttpp) REVERT: B 1168 ASP cc_start: 0.8083 (m-30) cc_final: 0.7345 (t70) REVERT: B 1190 SER cc_start: 0.9318 (t) cc_final: 0.9062 (m) REVERT: C 45 SER cc_start: 0.8970 (t) cc_final: 0.8573 (m) REVERT: C 541 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7690 (pt0) REVERT: C 691 MET cc_start: 0.7129 (ptp) cc_final: 0.6727 (ptt) REVERT: C 912 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6824 (mtp) outliers start: 66 outliers final: 46 residues processed: 307 average time/residue: 0.1691 time to fit residues: 86.5932 Evaluate side-chains 296 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1083 GLN Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1149 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 315 TRP Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 592 MET Chi-restraints excluded: chain B residue 659 CYS Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 659 CYS Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1167 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 317 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 ASN B 673 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.098298 restraints weight = 38704.505| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.72 r_work: 0.3023 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 28360 Z= 0.202 Angle : 0.671 19.432 38686 Z= 0.339 Chirality : 0.047 0.619 4431 Planarity : 0.004 0.061 4927 Dihedral : 6.759 59.640 4691 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.47 % Favored : 94.41 % Rotamer: Outliers : 1.86 % Allowed : 12.32 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3453 helix: 0.93 (0.20), residues: 726 sheet: -0.30 (0.18), residues: 771 loop : -1.40 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.018 0.002 TYR C 210 PHE 0.021 0.002 PHE C 119 TRP 0.012 0.002 TRP C 49 HIS 0.005 0.001 HIS B1137 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (28268) covalent geometry : angle 0.63365 / 0.33 (38460) SS BOND : bond 0.00789 / 0.42 ( 50) SS BOND : angle 2.06543 / 1.51 ( 100) hydrogen bonds : bond 0.04623 / 3.03 ( 979) hydrogen bonds : angle 5.24710 / 3.66 ( 2679) link_BETA1-4 : bond 0.00750 / 0.46 ( 11) link_BETA1-4 : angle 2.34718 / 1.33 ( 33) link_BETA1-6 : bond 0.00269 / 0.14 ( 1) link_BETA1-6 : angle 1.18219 / 0.66 ( 3) link_NAG-ASN : bond 0.00602 / 0.36 ( 30) link_NAG-ASN : angle 3.88295 / 2.56 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 255 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8984 (t) cc_final: 0.8518 (m) REVERT: A 274 ARG cc_start: 0.7422 (mtt90) cc_final: 0.7076 (mtm110) REVERT: A 588 SER cc_start: 0.7932 (m) cc_final: 0.7318 (t) REVERT: A 631 LYS cc_start: 0.7493 (mtpt) cc_final: 0.6644 (tmtt) REVERT: A 637 TYR cc_start: 0.9223 (m-80) cc_final: 0.8652 (m-80) REVERT: A 792 GLU cc_start: 0.8997 (tt0) cc_final: 0.8782 (tt0) REVERT: A 913 LYS cc_start: 0.8658 (ttpp) cc_final: 0.8427 (ttpt) REVERT: A 977 TYR cc_start: 0.8523 (m-10) cc_final: 0.8268 (m-10) REVERT: A 1168 ASP cc_start: 0.7840 (t70) cc_final: 0.7559 (t0) REVERT: B 214 GLU cc_start: 0.6850 (tt0) cc_final: 0.6550 (pp20) REVERT: B 315 TRP cc_start: 0.7932 (OUTLIER) cc_final: 0.6918 (m-90) REVERT: B 331 ASP cc_start: 0.7973 (t0) cc_final: 0.7758 (t0) REVERT: B 592 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8396 (mtp) REVERT: B 631 LYS cc_start: 0.6962 (tmtt) cc_final: 0.6435 (tptm) REVERT: B 686 HIS cc_start: 0.7003 (OUTLIER) cc_final: 0.6270 (t-90) REVERT: B 755 GLN cc_start: 0.7622 (mt0) cc_final: 0.7243 (tt0) REVERT: B 825 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: B 1034 LYS cc_start: 0.8701 (tttt) cc_final: 0.8281 (ttpp) REVERT: B 1168 ASP cc_start: 0.8107 (m-30) cc_final: 0.7591 (t70) REVERT: C 45 SER cc_start: 0.9025 (t) cc_final: 0.8701 (m) REVERT: C 691 MET cc_start: 0.7243 (ptp) cc_final: 0.6829 (ptt) REVERT: C 912 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.6929 (mtp) REVERT: C 914 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7319 (tm-30) outliers start: 56 outliers final: 39 residues processed: 293 average time/residue: 0.1689 time to fit residues: 81.8713 Evaluate side-chains 283 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1083 GLN Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 315 TRP Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 592 MET Chi-restraints excluded: chain B residue 659 CYS Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 659 CYS Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1167 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 151 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 182 optimal weight: 10.0000 chunk 277 optimal weight: 0.0970 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 673 ASN B 980 ASN C1159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099765 restraints weight = 38609.896| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.81 r_work: 0.3041 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28360 Z= 0.136 Angle : 0.620 19.636 38686 Z= 0.312 Chirality : 0.045 0.615 4431 Planarity : 0.004 0.056 4927 Dihedral : 6.522 59.582 4691 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.36 % Favored : 94.50 % Rotamer: Outliers : 2.03 % Allowed : 12.55 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3453 helix: 1.18 (0.20), residues: 726 sheet: -0.19 (0.18), residues: 789 loop : -1.31 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.016 0.001 TYR A1140 PHE 0.020 0.001 PHE C 119 TRP 0.009 0.001 TRP A 315 HIS 0.004 0.001 HIS B1137 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (28268) covalent geometry : angle 0.58398 / 0.30 (38460) SS BOND : bond 0.00521 / 0.27 ( 50) SS BOND : angle 1.71488 / 1.22 ( 100) hydrogen bonds : bond 0.04065 / 2.67 ( 979) hydrogen bonds : angle 5.05901 / 3.53 ( 2679) link_BETA1-4 : bond 0.00751 / 0.46 ( 11) link_BETA1-4 : angle 2.30564 / 1.30 ( 33) link_BETA1-6 : bond 0.00266 / 0.14 ( 1) link_BETA1-6 : angle 1.21675 / 0.67 ( 3) link_NAG-ASN : bond 0.00588 / 0.33 ( 30) link_NAG-ASN : angle 3.74637 / 2.47 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 256 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8879 (t) cc_final: 0.8365 (m) REVERT: A 274 ARG cc_start: 0.7345 (mtt90) cc_final: 0.7001 (mtm110) REVERT: A 631 LYS cc_start: 0.7400 (mtpt) cc_final: 0.6650 (tptm) REVERT: A 637 TYR cc_start: 0.9194 (m-80) cc_final: 0.8594 (m-80) REVERT: A 792 GLU cc_start: 0.8966 (tt0) cc_final: 0.8740 (tt0) REVERT: A 913 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8424 (ttpt) REVERT: A 977 TYR cc_start: 0.8457 (m-10) cc_final: 0.8194 (m-10) REVERT: A 1168 ASP cc_start: 0.7823 (t70) cc_final: 0.7545 (t0) REVERT: B 214 GLU cc_start: 0.6849 (tt0) cc_final: 0.6527 (pp20) REVERT: B 315 TRP cc_start: 0.7859 (OUTLIER) cc_final: 0.6724 (m-90) REVERT: B 331 ASP cc_start: 0.7867 (t0) cc_final: 0.7629 (t0) REVERT: B 592 MET cc_start: 0.8587 (ttp) cc_final: 0.8372 (mtp) REVERT: B 631 LYS cc_start: 0.6921 (tmtt) cc_final: 0.6390 (tptm) REVERT: B 686 HIS cc_start: 0.6976 (OUTLIER) cc_final: 0.6215 (t-90) REVERT: B 755 GLN cc_start: 0.7530 (mt0) cc_final: 0.7144 (tt0) REVERT: B 825 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8216 (mt0) REVERT: B 1034 LYS cc_start: 0.8641 (tttt) cc_final: 0.8218 (ttpp) REVERT: B 1168 ASP cc_start: 0.8108 (m-30) cc_final: 0.7560 (t70) REVERT: C 45 SER cc_start: 0.8982 (t) cc_final: 0.8619 (m) REVERT: C 691 MET cc_start: 0.7194 (ptp) cc_final: 0.6763 (ptt) REVERT: C 912 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6941 (mtp) REVERT: C 914 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7274 (tm-30) REVERT: C 1089 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7664 (tp30) outliers start: 61 outliers final: 44 residues processed: 300 average time/residue: 0.1606 time to fit residues: 80.4953 Evaluate side-chains 291 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1083 GLN Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1149 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 315 TRP Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 659 CYS Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 659 CYS Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1167 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 277 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 167 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 295 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 411 ASN B 673 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.129600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.099128 restraints weight = 38663.563| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.77 r_work: 0.3035 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28360 Z= 0.167 Angle : 0.660 20.355 38686 Z= 0.331 Chirality : 0.046 0.611 4431 Planarity : 0.004 0.058 4927 Dihedral : 6.491 59.477 4691 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.42 % Favored : 94.41 % Rotamer: Outliers : 2.03 % Allowed : 13.31 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3453 helix: 1.14 (0.20), residues: 729 sheet: -0.27 (0.18), residues: 789 loop : -1.29 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 634 TYR 0.016 0.001 TYR A1140 PHE 0.020 0.001 PHE C 119 TRP 0.010 0.001 TRP C 49 HIS 0.004 0.001 HIS B1137 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (28268) covalent geometry : angle 0.62039 / 0.32 (38460) SS BOND : bond 0.00665 / 0.36 ( 50) SS BOND : angle 2.30377 / 1.71 ( 100) hydrogen bonds : bond 0.04223 / 2.77 ( 979) hydrogen bonds : angle 5.05154 / 3.52 ( 2679) link_BETA1-4 : bond 0.00731 / 0.45 ( 11) link_BETA1-4 : angle 2.33785 / 1.32 ( 33) link_BETA1-6 : bond 0.00265 / 0.14 ( 1) link_BETA1-6 : angle 1.21673 / 0.68 ( 3) link_NAG-ASN : bond 0.00637 / 0.42 ( 30) link_NAG-ASN : angle 3.86575 / 2.53 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 248 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ARG cc_start: 0.7408 (mtt90) cc_final: 0.7019 (mtm110) REVERT: A 631 LYS cc_start: 0.7420 (mtpt) cc_final: 0.6695 (tptm) REVERT: A 637 TYR cc_start: 0.9202 (m-80) cc_final: 0.8607 (m-80) REVERT: A 913 LYS cc_start: 0.8660 (ttpp) cc_final: 0.8431 (ttpt) REVERT: A 977 TYR cc_start: 0.8490 (m-10) cc_final: 0.8230 (m-10) REVERT: A 1168 ASP cc_start: 0.7871 (t70) cc_final: 0.7569 (t0) REVERT: B 214 GLU cc_start: 0.6859 (tt0) cc_final: 0.6545 (pp20) REVERT: B 315 TRP cc_start: 0.7902 (OUTLIER) cc_final: 0.6740 (m-90) REVERT: B 331 ASP cc_start: 0.7891 (t0) cc_final: 0.7656 (t0) REVERT: B 447 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8662 (m) REVERT: B 592 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8386 (mtp) REVERT: B 631 LYS cc_start: 0.7153 (tmtt) cc_final: 0.6589 (tptm) REVERT: B 686 HIS cc_start: 0.7044 (OUTLIER) cc_final: 0.6284 (t-90) REVERT: B 755 GLN cc_start: 0.7582 (mt0) cc_final: 0.7170 (tt0) REVERT: B 825 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: B 1034 LYS cc_start: 0.8678 (tttt) cc_final: 0.8264 (ttpp) REVERT: B 1168 ASP cc_start: 0.8122 (m-30) cc_final: 0.7608 (t70) REVERT: C 45 SER cc_start: 0.8992 (t) cc_final: 0.8637 (m) REVERT: C 691 MET cc_start: 0.7221 (ptp) cc_final: 0.6789 (ptt) REVERT: C 912 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7011 (mtp) REVERT: C 914 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7317 (tm-30) outliers start: 61 outliers final: 48 residues processed: 289 average time/residue: 0.1676 time to fit residues: 80.9348 Evaluate side-chains 293 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 239 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1075 ILE Chi-restraints excluded: chain A residue 1083 GLN Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1149 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 315 TRP Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 592 MET Chi-restraints excluded: chain B residue 659 CYS Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 659 CYS Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1167 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 230 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 chunk 333 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 0.0670 chunk 197 optimal weight: 5.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 411 ASN B 673 ASN B 693 GLN C 858 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.130062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099708 restraints weight = 38674.791| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.75 r_work: 0.3043 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28360 Z= 0.148 Angle : 0.629 18.363 38686 Z= 0.316 Chirality : 0.045 0.613 4431 Planarity : 0.004 0.057 4927 Dihedral : 6.363 59.717 4691 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.18 % Favored : 94.61 % Rotamer: Outliers : 2.06 % Allowed : 13.65 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3453 helix: 1.23 (0.20), residues: 729 sheet: -0.13 (0.18), residues: 753 loop : -1.30 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 634 TYR 0.015 0.001 TYR A1140 PHE 0.020 0.001 PHE C 119 TRP 0.009 0.001 TRP C 49 HIS 0.004 0.001 HIS B1137 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (28268) covalent geometry : angle 0.59238 / 0.31 (38460) SS BOND : bond 0.00706 / 0.37 ( 50) SS BOND : angle 1.87993 / 1.39 ( 100) hydrogen bonds : bond 0.04011 / 2.64 ( 979) hydrogen bonds : angle 4.98047 / 3.47 ( 2679) link_BETA1-4 : bond 0.00753 / 0.46 ( 11) link_BETA1-4 : angle 2.28426 / 1.29 ( 33) link_BETA1-6 : bond 0.00235 / 0.12 ( 1) link_BETA1-6 : angle 1.20553 / 0.67 ( 3) link_NAG-ASN : bond 0.00601 / 0.37 ( 30) link_NAG-ASN : angle 3.76406 / 2.47 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 247 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ARG cc_start: 0.7359 (mtt90) cc_final: 0.6962 (mtm110) REVERT: A 283 MET cc_start: 0.9204 (mtp) cc_final: 0.8999 (mtp) REVERT: A 631 LYS cc_start: 0.7438 (mtpt) cc_final: 0.6715 (tptm) REVERT: A 637 TYR cc_start: 0.9190 (m-80) cc_final: 0.8614 (m-80) REVERT: A 913 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8446 (ttpt) REVERT: A 977 TYR cc_start: 0.8466 (m-10) cc_final: 0.8204 (m-10) REVERT: A 1168 ASP cc_start: 0.7861 (t70) cc_final: 0.7548 (t0) REVERT: B 214 GLU cc_start: 0.6863 (tt0) cc_final: 0.6547 (pp20) REVERT: B 315 TRP cc_start: 0.7884 (OUTLIER) cc_final: 0.7449 (m100) REVERT: B 331 ASP cc_start: 0.7882 (t0) cc_final: 0.7641 (t0) REVERT: B 447 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8668 (m) REVERT: B 631 LYS cc_start: 0.7155 (tmtt) cc_final: 0.6594 (tptm) REVERT: B 686 HIS cc_start: 0.7046 (OUTLIER) cc_final: 0.6288 (t-90) REVERT: B 755 GLN cc_start: 0.7569 (mt0) cc_final: 0.7173 (tt0) REVERT: B 825 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: B 1034 LYS cc_start: 0.8668 (tttt) cc_final: 0.8264 (ttpp) REVERT: B 1168 ASP cc_start: 0.8115 (m-30) cc_final: 0.7615 (t70) REVERT: C 45 SER cc_start: 0.8980 (t) cc_final: 0.8617 (m) REVERT: C 438 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8512 (tt) REVERT: C 631 LYS cc_start: 0.6898 (tmtt) cc_final: 0.6656 (tttp) REVERT: C 691 MET cc_start: 0.7242 (ptp) cc_final: 0.6807 (ptt) REVERT: C 912 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6997 (mtp) REVERT: C 914 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7489 (tm-30) outliers start: 62 outliers final: 51 residues processed: 290 average time/residue: 0.1604 time to fit residues: 77.7503 Evaluate side-chains 294 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 237 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1083 GLN Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1149 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 315 TRP Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 659 CYS Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 659 CYS Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1167 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 204 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 302 optimal weight: 0.7980 chunk 206 optimal weight: 10.0000 chunk 330 optimal weight: 4.9990 chunk 296 optimal weight: 0.9990 chunk 54 optimal weight: 0.2980 chunk 342 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 673 ASN C 581 GLN C 858 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102254 restraints weight = 38432.532| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.55 r_work: 0.3074 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28360 Z= 0.106 Angle : 0.600 16.537 38686 Z= 0.302 Chirality : 0.044 0.620 4431 Planarity : 0.004 0.054 4927 Dihedral : 6.173 59.628 4691 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.78 % Favored : 95.02 % Rotamer: Outliers : 1.69 % Allowed : 14.04 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3453 helix: 1.31 (0.20), residues: 747 sheet: -0.04 (0.18), residues: 753 loop : -1.25 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.015 0.001 TYR A1140 PHE 0.024 0.001 PHE C 826 TRP 0.009 0.001 TRP A 315 HIS 0.003 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (28268) covalent geometry : angle 0.56313 / 0.29 (38460) SS BOND : bond 0.00572 / 0.30 ( 50) SS BOND : angle 1.61884 / 1.18 ( 100) hydrogen bonds : bond 0.03578 / 2.37 ( 979) hydrogen bonds : angle 4.80837 / 3.35 ( 2679) link_BETA1-4 : bond 0.00760 / 0.46 ( 11) link_BETA1-4 : angle 2.26294 / 1.28 ( 33) link_BETA1-6 : bond 0.00277 / 0.15 ( 1) link_BETA1-6 : angle 1.25912 / 0.70 ( 3) link_NAG-ASN : bond 0.00651 / 0.39 ( 30) link_NAG-ASN : angle 3.79674 / 2.52 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ARG cc_start: 0.7314 (mtt90) cc_final: 0.6844 (mtm110) REVERT: A 283 MET cc_start: 0.9194 (mtp) cc_final: 0.8992 (mtp) REVERT: A 631 LYS cc_start: 0.7637 (mtpt) cc_final: 0.6865 (tptm) REVERT: A 913 LYS cc_start: 0.8635 (ttpp) cc_final: 0.8411 (ttpt) REVERT: A 977 TYR cc_start: 0.8346 (m-10) cc_final: 0.8098 (m-10) REVERT: A 1168 ASP cc_start: 0.7810 (t70) cc_final: 0.7503 (t0) REVERT: B 214 GLU cc_start: 0.6940 (tt0) cc_final: 0.6541 (pp20) REVERT: B 315 TRP cc_start: 0.7805 (OUTLIER) cc_final: 0.7495 (m100) REVERT: B 331 ASP cc_start: 0.7780 (t0) cc_final: 0.7544 (t0) REVERT: B 631 LYS cc_start: 0.6997 (tmtt) cc_final: 0.6447 (tptm) REVERT: B 686 HIS cc_start: 0.6854 (OUTLIER) cc_final: 0.6025 (t-90) REVERT: B 755 GLN cc_start: 0.7535 (mt0) cc_final: 0.7075 (tt0) REVERT: B 875 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8189 (t) REVERT: B 1034 LYS cc_start: 0.8459 (tttt) cc_final: 0.8014 (ttpp) REVERT: B 1168 ASP cc_start: 0.8106 (m-30) cc_final: 0.7481 (t70) REVERT: C 45 SER cc_start: 0.8855 (t) cc_final: 0.8446 (m) REVERT: C 72 ILE cc_start: 0.7413 (tt) cc_final: 0.7049 (pt) REVERT: C 691 MET cc_start: 0.7023 (ptp) cc_final: 0.6582 (ptt) REVERT: C 826 PHE cc_start: 0.8191 (t80) cc_final: 0.7989 (t80) REVERT: C 914 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7604 (tm-30) outliers start: 51 outliers final: 39 residues processed: 285 average time/residue: 0.1542 time to fit residues: 73.8980 Evaluate side-chains 282 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1083 GLN Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1149 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 315 TRP Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 659 CYS Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 875 VAL Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 659 CYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 991 GLU Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1167 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 44 optimal weight: 6.9990 chunk 190 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 52 optimal weight: 0.0980 chunk 296 optimal weight: 0.0770 chunk 139 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 411 ASN B 673 ASN C 581 GLN C 858 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.133606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.103675 restraints weight = 38200.026| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.57 r_work: 0.3095 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28360 Z= 0.101 Angle : 0.584 16.259 38686 Z= 0.292 Chirality : 0.044 0.586 4431 Planarity : 0.004 0.053 4927 Dihedral : 5.985 59.868 4691 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.84 % Favored : 94.96 % Rotamer: Outliers : 1.43 % Allowed : 14.64 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3453 helix: 1.45 (0.20), residues: 747 sheet: 0.00 (0.18), residues: 756 loop : -1.18 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 634 TYR 0.015 0.001 TYR A1140 PHE 0.019 0.001 PHE C 826 TRP 0.010 0.001 TRP A 315 HIS 0.003 0.001 HIS C 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (28268) covalent geometry : angle 0.54832 / 0.28 (38460) SS BOND : bond 0.00642 / 0.34 ( 50) SS BOND : angle 1.51196 / 1.11 ( 100) hydrogen bonds : bond 0.03384 / 2.25 ( 979) hydrogen bonds : angle 4.66782 / 3.25 ( 2679) link_BETA1-4 : bond 0.00745 / 0.45 ( 11) link_BETA1-4 : angle 2.26728 / 1.28 ( 33) link_BETA1-6 : bond 0.00319 / 0.17 ( 1) link_BETA1-6 : angle 1.29684 / 0.72 ( 3) link_NAG-ASN : bond 0.00639 / 0.37 ( 30) link_NAG-ASN : angle 3.69696 / 2.44 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 263 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ARG cc_start: 0.7391 (mtt90) cc_final: 0.7058 (mtm110) REVERT: A 631 LYS cc_start: 0.7610 (mtpt) cc_final: 0.6933 (tptm) REVERT: A 913 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8457 (ttpt) REVERT: A 1168 ASP cc_start: 0.7738 (t70) cc_final: 0.7470 (t0) REVERT: B 214 GLU cc_start: 0.6790 (tt0) cc_final: 0.6577 (pp20) REVERT: B 315 TRP cc_start: 0.7788 (OUTLIER) cc_final: 0.7416 (m100) REVERT: B 331 ASP cc_start: 0.7831 (t0) cc_final: 0.7593 (t0) REVERT: B 631 LYS cc_start: 0.7129 (tmtt) cc_final: 0.6544 (tptm) REVERT: B 686 HIS cc_start: 0.6948 (OUTLIER) cc_final: 0.6160 (t-90) REVERT: B 755 GLN cc_start: 0.7589 (mt0) cc_final: 0.7260 (tt0) REVERT: B 1034 LYS cc_start: 0.8645 (tttt) cc_final: 0.8280 (ttpp) REVERT: B 1168 ASP cc_start: 0.8113 (m-30) cc_final: 0.7554 (t70) REVERT: C 45 SER cc_start: 0.8864 (t) cc_final: 0.8468 (m) REVERT: C 72 ILE cc_start: 0.7519 (tt) cc_final: 0.7256 (pt) REVERT: C 637 TYR cc_start: 0.8958 (m-80) cc_final: 0.8710 (m-80) REVERT: C 691 MET cc_start: 0.7147 (ptp) cc_final: 0.6727 (ptt) REVERT: C 914 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7634 (tm-30) outliers start: 43 outliers final: 35 residues processed: 290 average time/residue: 0.1566 time to fit residues: 76.1716 Evaluate side-chains 276 residues out of total 3012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 871 THR Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1083 GLN Chi-restraints excluded: chain A residue 1099 SER Chi-restraints excluded: chain A residue 1149 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 315 TRP Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 659 CYS Chi-restraints excluded: chain B residue 686 HIS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 659 CYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 977 TYR Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1167 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 67 optimal weight: 0.9990 chunk 343 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 328 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 274 optimal weight: 0.0000 chunk 40 optimal weight: 0.7980 chunk 315 optimal weight: 5.9990 chunk 165 optimal weight: 0.3980 chunk 249 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN C 858 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.133568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103159 restraints weight = 38137.898| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.63 r_work: 0.3084 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 28360 Z= 0.146 Angle : 0.729 59.199 38686 Z= 0.397 Chirality : 0.044 0.586 4431 Planarity : 0.004 0.052 4927 Dihedral : 5.968 59.910 4690 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.89 % Favored : 94.87 % Rotamer: Outliers : 1.23 % Allowed : 14.87 % Favored : 83.90 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3453 helix: 1.46 (0.20), residues: 747 sheet: -0.00 (0.18), residues: 756 loop : -1.17 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 634 TYR 0.015 0.001 TYR A1140 PHE 0.019 0.001 PHE C 826 TRP 0.009 0.001 TRP A 315 HIS 0.003 0.001 HIS C 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (28268) covalent geometry : angle 0.69568 / 0.39 (38460) SS BOND : bond 0.01986 / 0.69 ( 50) SS BOND : angle 2.37433 / 1.61 ( 100) hydrogen bonds : bond 0.03384 / 2.25 ( 979) hydrogen bonds : angle 4.66758 / 3.25 ( 2679) link_BETA1-4 : bond 0.00741 / 0.45 ( 11) link_BETA1-4 : angle 2.27054 / 1.28 ( 33) link_BETA1-6 : bond 0.00284 / 0.15 ( 1) link_BETA1-6 : angle 1.29617 / 0.72 ( 3) link_NAG-ASN : bond 0.00628 / 0.37 ( 30) link_NAG-ASN : angle 3.69683 / 2.45 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6617.05 seconds wall clock time: 114 minutes 4.02 seconds (6844.02 seconds total)