Starting phenix.real_space_refine on Mon Aug 25 13:18:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ug9_42218/08_2025/8ug9_42218.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ug9_42218/08_2025/8ug9_42218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ug9_42218/08_2025/8ug9_42218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ug9_42218/08_2025/8ug9_42218.map" model { file = "/net/cci-nas-00/data/ceres_data/8ug9_42218/08_2025/8ug9_42218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ug9_42218/08_2025/8ug9_42218.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.018 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 132 5.16 5 C 18024 2.51 5 N 4695 2.21 5 O 5532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28383 Number of models: 1 Model: "" Number of chains: 21 Chain: "M" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "N" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "O" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "A" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 56, 'TRANS': 1006} Chain breaks: 6 Chain: "B" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 56, 'TRANS': 1006} Chain breaks: 6 Chain: "C" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 56, 'TRANS': 1006} 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: 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: "I" 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: "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: 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: "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: "P" 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: "Q" 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: "R" 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.03, per 1000 atoms: 0.25 Number of scatterers: 28383 At special positions: 0 Unit cell: (158.4, 157.3, 165, 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 132 16.00 O 5532 8.00 N 4695 7.00 C 18024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 95 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 428 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 521 " distance=2.04 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 645 " distance=2.05 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 667 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 428 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 521 " distance=2.04 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B 836 " - pdb=" SG CYS B 847 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 375 " - pdb=" SG CYS C 428 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 521 " distance=2.04 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C 836 " - pdb=" SG CYS C 847 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " 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 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 119 " " NAG A1302 " - " ASN A 161 " " NAG A1303 " - " ASN A 230 " " NAG A1304 " - " ASN A 278 " " NAG A1305 " - " ASN A 327 " " NAG A1306 " - " ASN A 339 " " NAG A1307 " - " ASN A 612 " " NAG A1308 " - " ASN A 653 " " NAG A1309 " - " ASN A 705 " " NAG A1310 " - " ASN A1070 " " NAG A1311 " - " ASN A1130 " " NAG B1301 " - " ASN B 119 " " NAG B1302 " - " ASN B 161 " " NAG B1303 " - " ASN B 230 " " NAG B1304 " - " ASN B 278 " " NAG B1305 " - " ASN B 327 " " NAG B1306 " - " ASN B 339 " " NAG B1307 " - " ASN B 612 " " NAG B1308 " - " ASN B 653 " " NAG B1309 " - " ASN B 705 " " NAG B1310 " - " ASN B1070 " " NAG B1311 " - " ASN B1130 " " NAG C1301 " - " ASN C 119 " " NAG C1302 " - " ASN C 161 " " NAG C1303 " - " ASN C 230 " " NAG C1304 " - " ASN C 278 " " NAG C1305 " - " ASN C 327 " " NAG C1306 " - " ASN C 339 " " NAG C1307 " - " ASN C 612 " " NAG C1308 " - " ASN C 653 " " NAG C1309 " - " ASN C 705 " " NAG C1310 " - " ASN C1070 " " NAG C1311 " - " ASN C1130 " " NAG D 1 " - " ASN A 58 " " NAG E 1 " - " ASN B 58 " " NAG F 1 " - " ASN C 58 " " NAG G 1 " - " ASN A 713 " " NAG H 1 " - " ASN A 797 " " NAG I 1 " - " ASN A1094 " " NAG J 1 " - " ASN B 713 " " NAG K 1 " - " ASN B 797 " " NAG L 1 " - " ASN B1094 " " NAG P 1 " - " ASN C 713 " " NAG Q 1 " - " ASN C 797 " " NAG R 1 " - " ASN C1094 " Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6606 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 66 sheets defined 22.4% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'N' and resid 86 through 90 removed outlier: 3.910A pdb=" N THR N 90 " --> pdb=" O ASP N 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 31 removed outlier: 3.511A pdb=" N MET O 31 " --> pdb=" O ILE O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 90 Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.617A pdb=" N PHE A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN A 339 " --> pdb=" O HIS A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 339' Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.732A pdb=" N LEU A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.540A pdb=" N TYR A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 743 through 750 Processing helix chain 'A' and resid 754 through 779 removed outlier: 3.647A pdb=" N GLN A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 832 through 838 removed outlier: 3.610A pdb=" N CYS A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 852 removed outlier: 3.815A pdb=" N ALA A 848 " --> pdb=" O ASP A 844 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 893 through 905 removed outlier: 3.771A pdb=" N ILE A 905 " --> pdb=" O ARG A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.513A pdb=" N TYR A 913 " --> pdb=" O GLN A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 937 removed outlier: 3.668A pdb=" N ILE A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 961 removed outlier: 3.670A pdb=" N GLN A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 947 " --> pdb=" O LYS A 943 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 985 through 1029 removed outlier: 4.372A pdb=" N ARG A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 992 " --> pdb=" O GLN A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 363 through 367 Processing helix chain 'B' and resid 379 through 383 removed outlier: 3.730A pdb=" N LEU B 383 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 412 through 418 Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 743 through 750 Processing helix chain 'B' and resid 754 through 779 removed outlier: 3.678A pdb=" N GLN B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 771 " --> pdb=" O ALA B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 822 Processing helix chain 'B' and resid 832 through 838 removed outlier: 3.620A pdb=" N CYS B 836 " --> pdb=" O GLN B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 852 removed outlier: 3.849A pdb=" N ALA B 848 " --> pdb=" O ASP B 844 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN B 852 " --> pdb=" O ALA B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 880 Processing helix chain 'B' and resid 882 through 886 Processing helix chain 'B' and resid 893 through 905 removed outlier: 3.805A pdb=" N ILE B 905 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.548A pdb=" N GLU B 914 " --> pdb=" O ASN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 937 removed outlier: 3.660A pdb=" N ILE B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN B 931 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP B 932 " --> pdb=" O GLY B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 961 removed outlier: 3.819A pdb=" N GLN B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 947 " --> pdb=" O LYS B 943 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 981 through 1029 removed outlier: 4.366A pdb=" N GLU B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 992 " --> pdb=" O GLN B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 334 through 339 removed outlier: 3.789A pdb=" N ASN C 339 " --> pdb=" O HIS C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 Processing helix chain 'C' and resid 379 through 383 removed outlier: 3.704A pdb=" N LEU C 383 " --> pdb=" O PRO C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 Processing helix chain 'C' and resid 412 through 418 removed outlier: 3.632A pdb=" N TYR C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 502 Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 743 through 751 removed outlier: 4.067A pdb=" N GLN C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 779 removed outlier: 3.655A pdb=" N GLN C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP C 771 " --> pdb=" O ALA C 767 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 779 " --> pdb=" O GLN C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 832 through 838 removed outlier: 3.655A pdb=" N CYS C 836 " --> pdb=" O GLN C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 851 removed outlier: 3.855A pdb=" N ALA C 848 " --> pdb=" O ASP C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 880 Processing helix chain 'C' and resid 882 through 886 Processing helix chain 'C' and resid 893 through 903 removed outlier: 3.641A pdb=" N ALA C 899 " --> pdb=" O PRO C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 906 No H-bonds generated for 'chain 'C' and resid 904 through 906' Processing helix chain 'C' and resid 909 through 914 removed outlier: 3.553A pdb=" N TYR C 913 " --> pdb=" O GLN C 909 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C 914 " --> pdb=" O ASN C 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 909 through 914' Processing helix chain 'C' and resid 915 through 937 removed outlier: 3.680A pdb=" N ILE C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN C 931 " --> pdb=" O ILE C 927 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP C 932 " --> pdb=" O GLY C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 961 removed outlier: 3.663A pdb=" N GLN C 945 " --> pdb=" O LEU C 941 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 Processing helix chain 'C' and resid 981 through 1029 removed outlier: 4.191A pdb=" N GLU C 986 " --> pdb=" O PRO C 982 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 4 through 7 removed outlier: 4.492A pdb=" N SER M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP M 72 " --> pdb=" O SER M 77 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE M 68 " --> pdb=" O GLN M 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.618A pdb=" N SER M 113 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG M 98 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU M 33 " --> pdb=" O ARG M 98 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET M 34 " --> pdb=" O THR M 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.618A pdb=" N SER M 113 " --> pdb=" O VAL M 12 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.191A pdb=" N GLY N 10 " --> pdb=" O THR N 111 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER N 113 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL N 12 " --> pdb=" O SER N 113 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU N 33 " --> pdb=" O ARG N 98 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N MET N 34 " --> pdb=" O THR N 50 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS N 38 " --> pdb=" O GLU N 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.191A pdb=" N GLY N 10 " --> pdb=" O THR N 111 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER N 113 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL N 12 " --> pdb=" O SER N 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 17 through 22 Processing sheet with id=AA7, first strand: chain 'O' and resid 4 through 5 removed outlier: 4.517A pdb=" N SER O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP O 72 " --> pdb=" O SER O 77 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE O 68 " --> pdb=" O GLN O 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 11 through 13 removed outlier: 3.846A pdb=" N ARG O 98 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU O 33 " --> pdb=" O ARG O 98 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N HIS O 38 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU O 47 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 11 through 13 Processing sheet with id=AB1, first strand: chain 'A' and resid 20 through 27 removed outlier: 3.533A pdb=" N THR A 26 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ASN A 58 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR A 265 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 263 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER A 201 " --> pdb=" O PRO A 221 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 39 through 40 removed outlier: 6.722A pdb=" N GLY C 562 " --> pdb=" O ASP C 570 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ASP C 570 " --> pdb=" O ILE C 583 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 45 through 52 removed outlier: 3.907A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.811A pdb=" N LEU A 237 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLY A 100 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 239 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE A 98 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AB6, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AB7, first strand: chain 'A' and resid 113 through 114 removed outlier: 3.613A pdb=" N PHE A 164 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 307 through 315 removed outlier: 7.153A pdb=" N VAL A 591 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN A 313 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY A 589 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY A 590 " --> pdb=" O GLN A 609 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 644 " --> pdb=" O THR A 641 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 321 through 324 Processing sheet with id=AC1, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AC2, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.697A pdb=" N CYS A 357 " --> pdb=" O CYS A 521 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 448 through 450 Processing sheet with id=AC4, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AC5, first strand: chain 'A' and resid 561 through 562 removed outlier: 7.038A pdb=" N PHE A 561 " --> pdb=" O PHE B 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 650 through 651 removed outlier: 5.855A pdb=" N GLU A 650 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 697 through 698 removed outlier: 6.993A pdb=" N ALA A 697 " --> pdb=" O ILE B 784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 707 through 724 removed outlier: 6.721A pdb=" N SER A 707 " --> pdb=" O THR A1072 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A1072 " --> pdb=" O SER A 707 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA A 709 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN A1070 " --> pdb=" O ALA A 709 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU A1068 " --> pdb=" O PRO A 711 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET A1046 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.779A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 783 through 784 Processing sheet with id=AD2, first strand: chain 'A' and resid 1116 through 1117 Processing sheet with id=AD3, first strand: chain 'A' and resid 1090 through 1093 Processing sheet with id=AD4, first strand: chain 'B' and resid 20 through 24 removed outlier: 5.786A pdb=" N SER B 201 " --> pdb=" O PRO B 221 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 45 through 52 removed outlier: 3.889A pdb=" N ASP B 283 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.799A pdb=" N LEU B 237 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLY B 100 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA B 239 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 98 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AD8, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AD9, first strand: chain 'B' and resid 113 through 114 removed outlier: 3.883A pdb=" N PHE B 164 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 307 through 315 removed outlier: 7.117A pdb=" N VAL B 591 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASN B 313 " --> pdb=" O GLY B 589 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY B 589 " --> pdb=" O ASN B 313 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY B 590 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 321 through 324 Processing sheet with id=AE3, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AE4, first strand: chain 'B' and resid 357 through 358 removed outlier: 6.658A pdb=" N CYS B 357 " --> pdb=" O CYS B 521 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 448 through 450 Processing sheet with id=AE6, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AE7, first strand: chain 'B' and resid 561 through 562 removed outlier: 6.993A pdb=" N PHE B 561 " --> pdb=" O PHE C 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 650 through 651 removed outlier: 5.993A pdb=" N GLU B 650 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N THR B 692 " --> pdb=" O GLU B 650 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 697 through 698 removed outlier: 7.117A pdb=" N ALA B 697 " --> pdb=" O ILE C 784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'B' and resid 707 through 708 Processing sheet with id=AF2, first strand: chain 'B' and resid 711 through 724 removed outlier: 6.274A pdb=" N GLU B1068 " --> pdb=" O PRO B 711 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET B1046 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR B1063 " --> pdb=" O HIS B1044 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS B1044 " --> pdb=" O TYR B1063 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.780A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1116 through 1117 Processing sheet with id=AF5, first strand: chain 'B' and resid 1090 through 1093 Processing sheet with id=AF6, first strand: chain 'C' and resid 20 through 27 removed outlier: 3.689A pdb=" N THR C 26 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASN C 58 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TYR C 265 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 263 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 223 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N SER C 201 " --> pdb=" O PRO C 221 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 45 through 52 removed outlier: 3.908A pdb=" N ASP C 283 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 81 through 82 removed outlier: 4.062A pdb=" N LEU C 237 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLY C 100 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA C 239 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE C 98 " --> pdb=" O ALA C 239 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AG1, first strand: chain 'C' and resid 113 through 114 Processing sheet with id=AG2, first strand: chain 'C' and resid 113 through 114 removed outlier: 3.855A pdb=" N PHE C 164 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 307 through 315 removed outlier: 7.155A pdb=" N VAL C 591 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN C 313 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY C 589 " --> pdb=" O ASN C 313 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY C 590 " --> pdb=" O GLN C 609 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY C 644 " --> pdb=" O THR C 641 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 350 through 354 removed outlier: 3.750A pdb=" N ASN C 350 " --> pdb=" O SER C 395 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER C 395 " --> pdb=" O ASN C 350 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.722A pdb=" N CYS C 357 " --> pdb=" O CYS C 521 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 448 through 450 Processing sheet with id=AG7, first strand: chain 'C' and resid 469 through 470 Processing sheet with id=AG8, first strand: chain 'C' and resid 650 through 651 removed outlier: 5.903A pdb=" N GLU C 650 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N THR C 692 " --> pdb=" O GLU C 650 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.668A pdb=" N SER C 707 " --> pdb=" O THR C1072 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR C1072 " --> pdb=" O SER C 707 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA C 709 " --> pdb=" O ASN C1070 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN C1070 " --> pdb=" O ALA C 709 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU C1068 " --> pdb=" O PRO C 711 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET C1046 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR C1063 " --> pdb=" O HIS C1044 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N HIS C1044 " --> pdb=" O TYR C1063 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.791A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 1116 through 1117 Processing sheet with id=AH3, first strand: chain 'C' and resid 1090 through 1093 1069 hydrogen bonds defined for protein. 2832 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: 7.60 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7057 1.33 - 1.46: 7089 1.46 - 1.58: 14702 1.58 - 1.71: 0 1.71 - 1.83: 168 Bond restraints: 29016 Sorted by residual: bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C PRO B 982 " pdb=" O PRO B 982 " ideal model delta sigma weight residual 1.240 1.206 0.034 1.12e-02 7.97e+03 9.24e+00 bond pdb=" C PRO C 982 " pdb=" O PRO C 982 " ideal model delta sigma weight residual 1.240 1.207 0.033 1.12e-02 7.97e+03 8.83e+00 ... (remaining 29011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 38643 1.90 - 3.80: 732 3.80 - 5.70: 74 5.70 - 7.60: 10 7.60 - 9.50: 3 Bond angle restraints: 39462 Sorted by residual: angle pdb=" N THR A 614 " pdb=" CA THR A 614 " pdb=" C THR A 614 " ideal model delta sigma weight residual 114.39 105.59 8.80 1.45e+00 4.76e-01 3.68e+01 angle pdb=" N PRO B 982 " pdb=" CA PRO B 982 " pdb=" C PRO B 982 " ideal model delta sigma weight residual 110.70 115.09 -4.39 1.22e+00 6.72e-01 1.29e+01 angle pdb=" N THR C 614 " pdb=" CA THR C 614 " pdb=" C THR C 614 " ideal model delta sigma weight residual 114.12 109.12 5.00 1.39e+00 5.18e-01 1.29e+01 angle pdb=" N PRO C 982 " pdb=" CA PRO C 982 " pdb=" C PRO C 982 " ideal model delta sigma weight residual 110.70 114.97 -4.27 1.22e+00 6.72e-01 1.22e+01 angle pdb=" CA PRO B 982 " pdb=" C PRO B 982 " pdb=" N PRO B 983 " ideal model delta sigma weight residual 117.93 121.98 -4.05 1.20e+00 6.94e-01 1.14e+01 ... (remaining 39457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.91: 16486 22.91 - 45.82: 1308 45.82 - 68.73: 181 68.73 - 91.64: 51 91.64 - 114.55: 19 Dihedral angle restraints: 18045 sinusoidal: 7773 harmonic: 10272 Sorted by residual: dihedral pdb=" CB CYS B 613 " pdb=" SG CYS B 613 " pdb=" SG CYS B 645 " pdb=" CB CYS B 645 " ideal model delta sinusoidal sigma weight residual 93.00 35.55 57.45 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS C1078 " pdb=" SG CYS C1078 " pdb=" SG CYS C1122 " pdb=" CB CYS C1122 " ideal model delta sinusoidal sigma weight residual -86.00 -142.29 56.29 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CB CYS A1078 " pdb=" SG CYS A1078 " pdb=" SG CYS A1122 " pdb=" CB CYS A1122 " ideal model delta sinusoidal sigma weight residual -86.00 -139.81 53.81 1 1.00e+01 1.00e-02 3.93e+01 ... (remaining 18042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 4596 0.141 - 0.282: 18 0.282 - 0.423: 5 0.423 - 0.564: 0 0.564 - 0.704: 1 Chirality restraints: 4620 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 58 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A 705 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 58 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 4617 not shown) Planarity restraints: 5070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 230 " -0.001 2.00e-02 2.50e+03 5.58e-02 3.90e+01 pdb=" CG ASN A 230 " -0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN A 230 " 0.067 2.00e-02 2.50e+03 pdb=" ND2 ASN A 230 " -0.057 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 58 " 0.030 2.00e-02 2.50e+03 3.13e-02 1.22e+01 pdb=" CG ASN A 58 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 58 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 58 " -0.048 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 230 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" CG ASN A 230 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN A 230 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 230 " 0.018 2.00e-02 2.50e+03 ... (remaining 5067 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1388 2.73 - 3.27: 26158 3.27 - 3.81: 42297 3.81 - 4.36: 50325 4.36 - 4.90: 92253 Nonbonded interactions: 212421 Sorted by model distance: nonbonded pdb=" O LEU N 47 " pdb=" OG SER N 60 " model vdw 2.182 3.040 nonbonded pdb=" OE1 GLU O 35 " pdb=" OG1 THR O 50 " model vdw 2.208 3.040 nonbonded pdb=" O SER N 21 " pdb=" OG SER N 21 " model vdw 2.226 3.040 nonbonded pdb=" O THR C 389 " pdb=" OG1 THR C 519 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR B 34 " pdb=" O LEU B 51 " model vdw 2.245 3.040 ... (remaining 212416 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.930 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.003 0.075 29118 Z= 0.177 Angle : 0.659 22.955 39723 Z= 0.324 Chirality : 0.049 0.704 4620 Planarity : 0.004 0.079 5025 Dihedral : 16.414 114.549 11304 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.12 % Rotamer: Outliers : 0.23 % Allowed : 19.49 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.14), residues: 3483 helix: 2.33 (0.22), residues: 636 sheet: 0.57 (0.18), residues: 864 loop : -1.41 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 106 TYR 0.019 0.001 TYR A 703 PHE 0.015 0.001 PHE A 561 TRP 0.010 0.001 TRP B 432 HIS 0.009 0.001 HIS M 38 Details of bonding type rmsd covalent geometry : bond 0.00341 (29016) covalent geometry : angle 0.59609 (39462) SS BOND : bond 0.00417 ( 45) SS BOND : angle 1.42948 ( 90) hydrogen bonds : bond 0.15813 ( 1042) hydrogen bonds : angle 6.00956 ( 2832) link_BETA1-4 : bond 0.00473 ( 12) link_BETA1-4 : angle 1.86789 ( 36) link_NAG-ASN : bond 0.00714 ( 45) link_NAG-ASN : angle 4.64245 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 196 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: B 49 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7213 (tm-30) REVERT: C 49 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7612 (tm-30) outliers start: 7 outliers final: 2 residues processed: 202 average time/residue: 0.1912 time to fit residues: 64.0189 Evaluate side-chains 164 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 362 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1102 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1102 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.057301 restraints weight = 74179.113| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.69 r_work: 0.2657 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29118 Z= 0.185 Angle : 0.624 14.292 39723 Z= 0.312 Chirality : 0.047 0.378 4620 Planarity : 0.004 0.054 5025 Dihedral : 9.679 100.611 4995 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 2.44 % Allowed : 18.74 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.14), residues: 3483 helix: 2.05 (0.21), residues: 693 sheet: 0.67 (0.18), residues: 843 loop : -1.43 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 106 TYR 0.017 0.001 TYR C1063 PHE 0.014 0.001 PHE O 67 TRP 0.010 0.001 TRP B 432 HIS 0.006 0.001 HIS M 38 Details of bonding type rmsd covalent geometry : bond 0.00440 (29016) covalent geometry : angle 0.58637 (39462) SS BOND : bond 0.00350 ( 45) SS BOND : angle 1.28641 ( 90) hydrogen bonds : bond 0.05436 ( 1042) hydrogen bonds : angle 5.09581 ( 2832) link_BETA1-4 : bond 0.00341 ( 12) link_BETA1-4 : angle 1.41211 ( 36) link_NAG-ASN : bond 0.00469 ( 45) link_NAG-ASN : angle 3.50337 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 166 time to evaluate : 1.201 Fit side-chains REVERT: M 106 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7716 (mtm-85) REVERT: N 43 LYS cc_start: 0.8586 (mmmm) cc_final: 0.8281 (tptp) REVERT: O 35 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8381 (mm-30) REVERT: O 64 LYS cc_start: 0.8813 (ptpt) cc_final: 0.8569 (mtmm) REVERT: A 19 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7454 (mp) REVERT: A 374 LYS cc_start: 0.8082 (tppt) cc_final: 0.7790 (tptp) REVERT: A 452 PHE cc_start: 0.6936 (m-80) cc_final: 0.6630 (m-10) REVERT: B 49 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8085 (tm-30) REVERT: C 49 GLN cc_start: 0.8876 (tm-30) cc_final: 0.7988 (tm-30) REVERT: C 826 ASP cc_start: 0.8447 (t0) cc_final: 0.7712 (t0) REVERT: C 1025 MET cc_start: 0.9285 (tpp) cc_final: 0.8834 (ttm) outliers start: 75 outliers final: 40 residues processed: 235 average time/residue: 0.1808 time to fit residues: 71.2555 Evaluate side-chains 201 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 106 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 730 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 313 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 0.0020 chunk 27 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 287 optimal weight: 30.0000 chunk 150 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 overall best weight: 1.0132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.082254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.057159 restraints weight = 74137.513| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 4.07 r_work: 0.2649 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29118 Z= 0.121 Angle : 0.564 13.953 39723 Z= 0.280 Chirality : 0.045 0.339 4620 Planarity : 0.004 0.052 5025 Dihedral : 8.536 95.912 4992 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 2.18 % Allowed : 19.39 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.14), residues: 3483 helix: 2.24 (0.21), residues: 681 sheet: 0.83 (0.18), residues: 849 loop : -1.36 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 106 TYR 0.020 0.001 TYR C 469 PHE 0.014 0.001 PHE O 67 TRP 0.010 0.001 TRP B 432 HIS 0.008 0.001 HIS M 38 Details of bonding type rmsd covalent geometry : bond 0.00278 (29016) covalent geometry : angle 0.52765 (39462) SS BOND : bond 0.00237 ( 45) SS BOND : angle 1.12450 ( 90) hydrogen bonds : bond 0.04654 ( 1042) hydrogen bonds : angle 4.85522 ( 2832) link_BETA1-4 : bond 0.00370 ( 12) link_BETA1-4 : angle 1.44921 ( 36) link_NAG-ASN : bond 0.00449 ( 45) link_NAG-ASN : angle 3.28317 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 171 time to evaluate : 1.172 Fit side-chains REVERT: M 106 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7837 (mtm-85) REVERT: N 43 LYS cc_start: 0.8382 (mmmm) cc_final: 0.8088 (tptp) REVERT: O 2 VAL cc_start: 0.9362 (OUTLIER) cc_final: 0.9157 (m) REVERT: A 235 GLN cc_start: 0.6953 (tp40) cc_final: 0.6642 (tp40) REVERT: A 374 LYS cc_start: 0.7477 (tppt) cc_final: 0.7204 (tptp) REVERT: A 452 PHE cc_start: 0.6710 (m-80) cc_final: 0.6362 (m-80) REVERT: B 49 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8136 (tm-30) REVERT: C 49 GLN cc_start: 0.8680 (tm-30) cc_final: 0.7926 (tm-30) REVERT: C 752 TYR cc_start: 0.9282 (OUTLIER) cc_final: 0.7897 (t80) REVERT: C 826 ASP cc_start: 0.8373 (t0) cc_final: 0.7531 (t0) REVERT: C 1025 MET cc_start: 0.8854 (tpp) cc_final: 0.8549 (ttm) outliers start: 67 outliers final: 41 residues processed: 231 average time/residue: 0.1843 time to fit residues: 71.0032 Evaluate side-chains 208 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 106 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 819 PHE Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 752 TYR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 249 optimal weight: 5.9990 chunk 304 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 chunk 240 optimal weight: 0.2980 chunk 99 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 320 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 96 HIS O 1 GLN A 112 GLN A 868 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 868 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.078998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.054719 restraints weight = 74978.852| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.68 r_work: 0.2591 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 29118 Z= 0.264 Angle : 0.678 13.701 39723 Z= 0.341 Chirality : 0.048 0.358 4620 Planarity : 0.004 0.054 5025 Dihedral : 8.198 93.371 4992 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 4.46 % Allowed : 18.34 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.14), residues: 3483 helix: 2.01 (0.21), residues: 675 sheet: 0.53 (0.18), residues: 897 loop : -1.55 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 106 TYR 0.020 0.002 TYR A 261 PHE 0.017 0.002 PHE O 67 TRP 0.013 0.001 TRP N 100 HIS 0.008 0.001 HIS C1060 Details of bonding type rmsd covalent geometry : bond 0.00633 (29016) covalent geometry : angle 0.64501 (39462) SS BOND : bond 0.00368 ( 45) SS BOND : angle 1.58929 ( 90) hydrogen bonds : bond 0.06111 ( 1042) hydrogen bonds : angle 5.12608 ( 2832) link_BETA1-4 : bond 0.00148 ( 12) link_BETA1-4 : angle 1.90108 ( 36) link_NAG-ASN : bond 0.00471 ( 45) link_NAG-ASN : angle 3.31832 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 152 time to evaluate : 1.200 Fit side-chains REVERT: M 106 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7633 (mtm-85) REVERT: O 35 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8324 (mm-30) REVERT: A 19 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7613 (mp) REVERT: A 728 THR cc_start: 0.9316 (OUTLIER) cc_final: 0.9026 (p) REVERT: B 194 ASP cc_start: 0.8918 (m-30) cc_final: 0.8505 (t0) REVERT: B 374 LYS cc_start: 0.8242 (tptp) cc_final: 0.7995 (tptp) REVERT: B 728 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8956 (p) REVERT: C 728 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9049 (p) REVERT: C 752 TYR cc_start: 0.9386 (OUTLIER) cc_final: 0.8124 (t80) REVERT: C 826 ASP cc_start: 0.8593 (t0) cc_final: 0.8100 (t0) REVERT: C 1025 MET cc_start: 0.9254 (tpp) cc_final: 0.8788 (ttm) outliers start: 137 outliers final: 87 residues processed: 279 average time/residue: 0.1779 time to fit residues: 83.3087 Evaluate side-chains 235 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 142 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 106 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 96 HIS Chi-restraints excluded: chain O residue 52 ASN Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 819 PHE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 752 TYR Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 211 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 319 optimal weight: 1.9990 chunk 335 optimal weight: 1.9990 chunk 223 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 232 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 96 HIS ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN B 686 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.081023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.056827 restraints weight = 74067.381| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.64 r_work: 0.2652 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29118 Z= 0.111 Angle : 0.564 12.763 39723 Z= 0.281 Chirality : 0.045 0.332 4620 Planarity : 0.003 0.052 5025 Dihedral : 7.698 91.844 4992 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 2.74 % Allowed : 19.94 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.15), residues: 3483 helix: 2.21 (0.21), residues: 681 sheet: 0.71 (0.18), residues: 891 loop : -1.43 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 106 TYR 0.018 0.001 TYR B 900 PHE 0.017 0.001 PHE C 452 TRP 0.015 0.001 TRP N 100 HIS 0.016 0.001 HIS N 96 Details of bonding type rmsd covalent geometry : bond 0.00252 (29016) covalent geometry : angle 0.52962 (39462) SS BOND : bond 0.00262 ( 45) SS BOND : angle 1.18269 ( 90) hydrogen bonds : bond 0.04717 ( 1042) hydrogen bonds : angle 4.83029 ( 2832) link_BETA1-4 : bond 0.00405 ( 12) link_BETA1-4 : angle 1.59335 ( 36) link_NAG-ASN : bond 0.00407 ( 45) link_NAG-ASN : angle 3.14659 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 148 time to evaluate : 1.217 Fit side-chains REVERT: M 106 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7714 (mtm-85) REVERT: N 35 GLU cc_start: 0.8141 (mp0) cc_final: 0.7767 (mp0) REVERT: A 452 PHE cc_start: 0.6870 (m-80) cc_final: 0.6556 (m-80) REVERT: B 194 ASP cc_start: 0.8904 (m-30) cc_final: 0.8326 (t0) REVERT: C 560 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: C 752 TYR cc_start: 0.9294 (OUTLIER) cc_final: 0.8029 (t80) REVERT: C 826 ASP cc_start: 0.8558 (t0) cc_final: 0.7954 (t0) REVERT: C 1025 MET cc_start: 0.9194 (tpp) cc_final: 0.8811 (ttm) outliers start: 84 outliers final: 63 residues processed: 227 average time/residue: 0.1769 time to fit residues: 67.8305 Evaluate side-chains 208 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 142 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 106 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain O residue 52 ASN Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 819 PHE Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 752 TYR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 97 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 335 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN O 38 HIS ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.078982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.054718 restraints weight = 74743.840| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.68 r_work: 0.2597 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 29118 Z= 0.237 Angle : 0.636 12.185 39723 Z= 0.319 Chirality : 0.047 0.349 4620 Planarity : 0.004 0.054 5025 Dihedral : 7.656 90.336 4992 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.25 % Favored : 94.72 % Rotamer: Outliers : 3.71 % Allowed : 19.42 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.14), residues: 3483 helix: 2.10 (0.21), residues: 675 sheet: 0.53 (0.17), residues: 927 loop : -1.56 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG O 106 TYR 0.019 0.001 TYR B 900 PHE 0.017 0.002 PHE O 67 TRP 0.011 0.001 TRP A 432 HIS 0.006 0.001 HIS M 38 Details of bonding type rmsd covalent geometry : bond 0.00571 (29016) covalent geometry : angle 0.60560 (39462) SS BOND : bond 0.00338 ( 45) SS BOND : angle 1.45692 ( 90) hydrogen bonds : bond 0.05586 ( 1042) hydrogen bonds : angle 4.98883 ( 2832) link_BETA1-4 : bond 0.00340 ( 12) link_BETA1-4 : angle 1.69441 ( 36) link_NAG-ASN : bond 0.00395 ( 45) link_NAG-ASN : angle 3.11088 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 146 time to evaluate : 1.093 Fit side-chains REVERT: M 106 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7561 (mtm-85) REVERT: O 46 GLU cc_start: 0.8480 (tt0) cc_final: 0.8153 (pt0) REVERT: A 19 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7697 (mp) REVERT: A 548 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8462 (mt) REVERT: B 173 MET cc_start: 0.4582 (mmt) cc_final: 0.4307 (mmt) REVERT: B 194 ASP cc_start: 0.8921 (m-30) cc_final: 0.8307 (t0) REVERT: B 374 LYS cc_start: 0.8287 (tptp) cc_final: 0.8042 (tptp) REVERT: B 728 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.9000 (p) REVERT: C 336 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8324 (pm20) REVERT: C 560 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: C 752 TYR cc_start: 0.9362 (OUTLIER) cc_final: 0.8036 (t80) REVERT: C 826 ASP cc_start: 0.8707 (t0) cc_final: 0.8263 (t0) REVERT: C 1025 MET cc_start: 0.9233 (tpp) cc_final: 0.8790 (ttm) outliers start: 114 outliers final: 86 residues processed: 250 average time/residue: 0.1587 time to fit residues: 67.4920 Evaluate side-chains 234 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 141 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 106 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 52 ASN Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 819 PHE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 730 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 752 TYR Chi-restraints excluded: chain C residue 776 GLU Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 7 optimal weight: 0.2980 chunk 98 optimal weight: 0.4980 chunk 15 optimal weight: 7.9990 chunk 302 optimal weight: 1.9990 chunk 350 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 329 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.080716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.056611 restraints weight = 74087.504| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.67 r_work: 0.2646 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29118 Z= 0.116 Angle : 0.559 11.511 39723 Z= 0.279 Chirality : 0.044 0.329 4620 Planarity : 0.004 0.052 5025 Dihedral : 7.273 89.020 4992 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 3.29 % Allowed : 19.88 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.15), residues: 3483 helix: 2.33 (0.21), residues: 663 sheet: 0.50 (0.18), residues: 906 loop : -1.40 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 106 TYR 0.020 0.001 TYR B 900 PHE 0.018 0.001 PHE B 588 TRP 0.011 0.001 TRP N 100 HIS 0.007 0.001 HIS M 38 Details of bonding type rmsd covalent geometry : bond 0.00268 (29016) covalent geometry : angle 0.52843 (39462) SS BOND : bond 0.00304 ( 45) SS BOND : angle 1.13992 ( 90) hydrogen bonds : bond 0.04550 ( 1042) hydrogen bonds : angle 4.77888 ( 2832) link_BETA1-4 : bond 0.00380 ( 12) link_BETA1-4 : angle 1.57900 ( 36) link_NAG-ASN : bond 0.00382 ( 45) link_NAG-ASN : angle 2.98974 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 149 time to evaluate : 1.019 Fit side-chains REVERT: M 106 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7664 (mtm-85) REVERT: N 35 GLU cc_start: 0.8457 (mp0) cc_final: 0.8234 (mp0) REVERT: O 46 GLU cc_start: 0.8459 (tt0) cc_final: 0.8094 (pt0) REVERT: B 173 MET cc_start: 0.4618 (mmt) cc_final: 0.4351 (mmt) REVERT: B 194 ASP cc_start: 0.8907 (m-30) cc_final: 0.8328 (t0) REVERT: C 336 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8352 (pm20) REVERT: C 560 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: C 752 TYR cc_start: 0.9310 (OUTLIER) cc_final: 0.7977 (t80) REVERT: C 826 ASP cc_start: 0.8650 (t0) cc_final: 0.8227 (t0) REVERT: C 855 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8352 (p) REVERT: C 1025 MET cc_start: 0.9158 (tpp) cc_final: 0.8821 (ttm) outliers start: 101 outliers final: 83 residues processed: 242 average time/residue: 0.1674 time to fit residues: 68.8797 Evaluate side-chains 232 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 144 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 106 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain O residue 52 ASN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 819 PHE Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 752 TYR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 220 optimal weight: 2.9990 chunk 267 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 337 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.055910 restraints weight = 74315.658| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.67 r_work: 0.2641 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29118 Z= 0.140 Angle : 0.574 11.215 39723 Z= 0.286 Chirality : 0.045 0.327 4620 Planarity : 0.004 0.053 5025 Dihedral : 7.135 87.997 4992 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 3.26 % Allowed : 20.20 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.15), residues: 3483 helix: 2.28 (0.21), residues: 666 sheet: 0.49 (0.18), residues: 903 loop : -1.36 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG O 106 TYR 0.017 0.001 TYR C1063 PHE 0.019 0.001 PHE O 67 TRP 0.010 0.001 TRP A 432 HIS 0.006 0.001 HIS M 38 Details of bonding type rmsd covalent geometry : bond 0.00333 (29016) covalent geometry : angle 0.54325 (39462) SS BOND : bond 0.00275 ( 45) SS BOND : angle 1.42699 ( 90) hydrogen bonds : bond 0.04612 ( 1042) hydrogen bonds : angle 4.76368 ( 2832) link_BETA1-4 : bond 0.00347 ( 12) link_BETA1-4 : angle 1.56955 ( 36) link_NAG-ASN : bond 0.00345 ( 45) link_NAG-ASN : angle 2.93131 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 148 time to evaluate : 1.075 Fit side-chains REVERT: M 106 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7663 (mtm-85) REVERT: N 35 GLU cc_start: 0.8472 (mp0) cc_final: 0.8217 (mp0) REVERT: N 58 ASN cc_start: 0.8391 (m-40) cc_final: 0.7878 (t0) REVERT: O 46 GLU cc_start: 0.8470 (tt0) cc_final: 0.8092 (pt0) REVERT: A 548 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8429 (mt) REVERT: B 173 MET cc_start: 0.4657 (mmt) cc_final: 0.4391 (mmt) REVERT: B 194 ASP cc_start: 0.8916 (m-30) cc_final: 0.8339 (t0) REVERT: B 728 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.9024 (p) REVERT: C 336 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8365 (pm20) REVERT: C 560 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: C 728 THR cc_start: 0.9402 (OUTLIER) cc_final: 0.9202 (p) REVERT: C 752 TYR cc_start: 0.9327 (OUTLIER) cc_final: 0.8030 (t80) REVERT: C 826 ASP cc_start: 0.8631 (t0) cc_final: 0.8220 (t0) REVERT: C 855 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8345 (p) REVERT: C 1025 MET cc_start: 0.9154 (tpp) cc_final: 0.8800 (ttm) outliers start: 100 outliers final: 84 residues processed: 242 average time/residue: 0.1568 time to fit residues: 63.8034 Evaluate side-chains 238 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 146 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 106 ARG Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain O residue 52 ASN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 819 PHE Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 752 TYR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 313 optimal weight: 2.9990 chunk 293 optimal weight: 0.9980 chunk 292 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 331 optimal weight: 0.9980 chunk 343 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 221 optimal weight: 0.6980 chunk 210 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.081318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.057106 restraints weight = 73909.079| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.69 r_work: 0.2662 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29118 Z= 0.110 Angle : 0.548 10.715 39723 Z= 0.273 Chirality : 0.044 0.317 4620 Planarity : 0.003 0.052 5025 Dihedral : 6.826 86.052 4992 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 3.06 % Allowed : 20.27 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.14), residues: 3483 helix: 2.36 (0.21), residues: 666 sheet: 0.68 (0.18), residues: 873 loop : -1.33 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG O 106 TYR 0.017 0.001 TYR A1063 PHE 0.018 0.001 PHE N 67 TRP 0.032 0.001 TRP O 100 HIS 0.006 0.001 HIS M 38 Details of bonding type rmsd covalent geometry : bond 0.00257 (29016) covalent geometry : angle 0.51924 (39462) SS BOND : bond 0.00295 ( 45) SS BOND : angle 1.11489 ( 90) hydrogen bonds : bond 0.04125 ( 1042) hydrogen bonds : angle 4.66100 ( 2832) link_BETA1-4 : bond 0.00397 ( 12) link_BETA1-4 : angle 1.50272 ( 36) link_NAG-ASN : bond 0.00369 ( 45) link_NAG-ASN : angle 2.82407 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 149 time to evaluate : 1.139 Fit side-chains REVERT: M 106 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7817 (mtm-85) REVERT: N 58 ASN cc_start: 0.8429 (m-40) cc_final: 0.7997 (t0) REVERT: O 46 GLU cc_start: 0.8473 (tt0) cc_final: 0.8094 (pt0) REVERT: B 194 ASP cc_start: 0.8909 (m-30) cc_final: 0.8350 (t0) REVERT: B 728 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.9005 (p) REVERT: C 214 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7611 (mm-40) REVERT: C 336 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: C 452 PHE cc_start: 0.7072 (m-80) cc_final: 0.6795 (m-80) REVERT: C 560 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.6975 (tm-30) REVERT: C 752 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.7976 (t80) REVERT: C 826 ASP cc_start: 0.8629 (t0) cc_final: 0.8241 (t0) REVERT: C 855 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8357 (p) outliers start: 94 outliers final: 77 residues processed: 238 average time/residue: 0.1754 time to fit residues: 70.3001 Evaluate side-chains 229 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 145 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 106 ARG Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain O residue 52 ASN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 819 PHE Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 752 TYR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 908 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 84 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 341 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 241 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.055295 restraints weight = 73814.335| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.77 r_work: 0.2612 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29118 Z= 0.183 Angle : 0.595 10.658 39723 Z= 0.298 Chirality : 0.045 0.327 4620 Planarity : 0.004 0.059 5025 Dihedral : 6.886 84.703 4992 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.21 % Rotamer: Outliers : 3.10 % Allowed : 20.40 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.14), residues: 3483 helix: 2.29 (0.21), residues: 666 sheet: 0.73 (0.18), residues: 849 loop : -1.41 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG O 106 TYR 0.019 0.001 TYR B 900 PHE 0.022 0.001 PHE O 67 TRP 0.010 0.001 TRP O 100 HIS 0.006 0.001 HIS M 38 Details of bonding type rmsd covalent geometry : bond 0.00439 (29016) covalent geometry : angle 0.56781 (39462) SS BOND : bond 0.00333 ( 45) SS BOND : angle 1.41384 ( 90) hydrogen bonds : bond 0.04838 ( 1042) hydrogen bonds : angle 4.77618 ( 2832) link_BETA1-4 : bond 0.00289 ( 12) link_BETA1-4 : angle 1.53672 ( 36) link_NAG-ASN : bond 0.00333 ( 45) link_NAG-ASN : angle 2.83594 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 143 time to evaluate : 1.119 Fit side-chains REVERT: M 106 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7689 (mtm-85) REVERT: N 13 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8431 (mp10) REVERT: N 35 GLU cc_start: 0.8390 (mp0) cc_final: 0.8009 (mp0) REVERT: N 58 ASN cc_start: 0.8275 (m-40) cc_final: 0.7836 (t0) REVERT: O 46 GLU cc_start: 0.8381 (tt0) cc_final: 0.7963 (pt0) REVERT: A 548 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8196 (mt) REVERT: B 194 ASP cc_start: 0.8930 (m-30) cc_final: 0.8314 (t0) REVERT: B 728 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8912 (p) REVERT: C 336 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: C 560 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: C 752 TYR cc_start: 0.9363 (OUTLIER) cc_final: 0.8057 (t80) REVERT: C 826 ASP cc_start: 0.8650 (t0) cc_final: 0.8244 (t0) REVERT: C 855 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8167 (p) outliers start: 95 outliers final: 83 residues processed: 233 average time/residue: 0.1653 time to fit residues: 65.0884 Evaluate side-chains 231 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 141 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 96 HIS Chi-restraints excluded: chain M residue 106 ARG Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain O residue 52 ASN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 819 PHE Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 521 CYS Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 577 THR Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 730 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 752 TYR Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 908 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 133 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 317 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 257 optimal weight: 9.9990 chunk 213 optimal weight: 0.8980 chunk 342 optimal weight: 0.9980 chunk 114 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.080979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.056615 restraints weight = 73703.898| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.79 r_work: 0.2647 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29118 Z= 0.111 Angle : 0.549 10.430 39723 Z= 0.274 Chirality : 0.044 0.316 4620 Planarity : 0.003 0.058 5025 Dihedral : 6.662 83.375 4992 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 3.00 % Allowed : 20.50 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.14), residues: 3483 helix: 2.34 (0.21), residues: 666 sheet: 0.83 (0.18), residues: 843 loop : -1.35 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG O 106 TYR 0.017 0.001 TYR B 900 PHE 0.020 0.001 PHE O 67 TRP 0.018 0.001 TRP O 100 HIS 0.006 0.001 HIS M 38 Details of bonding type rmsd covalent geometry : bond 0.00262 (29016) covalent geometry : angle 0.52217 (39462) SS BOND : bond 0.00266 ( 45) SS BOND : angle 1.12883 ( 90) hydrogen bonds : bond 0.04187 ( 1042) hydrogen bonds : angle 4.65239 ( 2832) link_BETA1-4 : bond 0.00406 ( 12) link_BETA1-4 : angle 1.47574 ( 36) link_NAG-ASN : bond 0.00351 ( 45) link_NAG-ASN : angle 2.76338 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5159.29 seconds wall clock time: 90 minutes 1.97 seconds (5401.97 seconds total)