Starting phenix.real_space_refine on Tue Jun 24 08:49:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ug9_42218/06_2025/8ug9_42218.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ug9_42218/06_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_42218/06_2025/8ug9_42218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ug9_42218/06_2025/8ug9_42218.map" model { file = "/net/cci-nas-00/data/ceres_data/8ug9_42218/06_2025/8ug9_42218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ug9_42218/06_2025/8ug9_42218.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.50, per 1000 atoms: 0.58 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: 6.40 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 4.19 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: 12.54 Time building geometry restraints manager: 7.70 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.080 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 63.500 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.870 ------------------------------------------------------------------------------- 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 : 5.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP B 432 HIS 0.009 0.001 HIS M 38 PHE 0.015 0.001 PHE A 561 TYR 0.019 0.001 TYR A 703 ARG 0.007 0.000 ARG O 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00714 ( 45) link_NAG-ASN : angle 4.64245 ( 135) link_BETA1-4 : bond 0.00473 ( 12) link_BETA1-4 : angle 1.86789 ( 36) hydrogen bonds : bond 0.15813 ( 1042) hydrogen bonds : angle 6.00956 ( 2832) SS BOND : bond 0.00417 ( 45) SS BOND : angle 1.42948 ( 90) covalent geometry : bond 0.00341 (29016) covalent geometry : angle 0.59609 (39462) *********************** 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 : 3.232 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: 0.3739 time to fit residues: 125.1134 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 : 3.320 ------------------------------------------------------------------------------- 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 296 optimal weight: 8.9990 chunk 266 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 275 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 167 optimal weight: 0.0050 chunk 204 optimal weight: 0.6980 chunk 318 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 38 HIS 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 470 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 = 0.3349 r_free = 0.3349 target = 0.084086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.059802 restraints weight = 72985.798| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.68 r_work: 0.2708 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29118 Z= 0.114 Angle : 0.581 13.989 39723 Z= 0.289 Chirality : 0.045 0.370 4620 Planarity : 0.004 0.051 5025 Dihedral : 9.691 101.395 4995 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.33 % Rotamer: Outliers : 1.86 % Allowed : 18.80 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3483 helix: 2.33 (0.21), residues: 663 sheet: 0.79 (0.18), residues: 843 loop : -1.36 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 432 HIS 0.007 0.001 HIS M 38 PHE 0.013 0.001 PHE N 67 TYR 0.016 0.001 TYR A1063 ARG 0.009 0.000 ARG N 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 45) link_NAG-ASN : angle 3.47868 ( 135) link_BETA1-4 : bond 0.00437 ( 12) link_BETA1-4 : angle 1.33911 ( 36) hydrogen bonds : bond 0.04843 ( 1042) hydrogen bonds : angle 5.00272 ( 2832) SS BOND : bond 0.00305 ( 45) SS BOND : angle 1.27773 ( 90) covalent geometry : bond 0.00250 (29016) covalent geometry : angle 0.54136 (39462) *********************** 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 230 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 173 time to evaluate : 3.094 Fit side-chains REVERT: N 35 GLU cc_start: 0.8541 (mp0) cc_final: 0.8267 (mp0) REVERT: N 43 LYS cc_start: 0.8554 (mmmm) cc_final: 0.8274 (tptp) REVERT: O 35 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8289 (mm-30) REVERT: O 64 LYS cc_start: 0.8822 (ptpt) cc_final: 0.8601 (mtmm) REVERT: A 235 GLN cc_start: 0.7190 (tp40) cc_final: 0.6507 (tp40) REVERT: A 374 LYS cc_start: 0.7995 (tppt) cc_final: 0.7697 (tptp) REVERT: A 452 PHE cc_start: 0.6781 (m-80) cc_final: 0.6526 (m-80) REVERT: B 49 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8109 (tm-30) REVERT: C 49 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8023 (tm-30) REVERT: C 752 TYR cc_start: 0.9252 (OUTLIER) cc_final: 0.7881 (t80) REVERT: C 826 ASP cc_start: 0.8357 (t0) cc_final: 0.7752 (t0) REVERT: C 1025 MET cc_start: 0.9313 (tpp) cc_final: 0.8818 (ttm) outliers start: 57 outliers final: 23 residues processed: 226 average time/residue: 0.3649 time to fit residues: 138.6790 Evaluate side-chains 187 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain O residue 11 LEU 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 1118 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 513 LEU 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 1118 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 567 ASP 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 1118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 149 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 193 optimal weight: 0.0370 chunk 94 optimal weight: 0.3980 chunk 277 optimal weight: 0.7980 chunk 345 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 337 optimal weight: 1.9990 chunk 256 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.082705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.057740 restraints weight = 73394.441| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 4.03 r_work: 0.2662 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29118 Z= 0.124 Angle : 0.562 13.654 39723 Z= 0.278 Chirality : 0.045 0.343 4620 Planarity : 0.003 0.051 5025 Dihedral : 8.482 95.820 4992 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 2.22 % Allowed : 18.83 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3483 helix: 2.39 (0.21), residues: 663 sheet: 0.88 (0.18), residues: 849 loop : -1.34 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 432 HIS 0.007 0.001 HIS M 38 PHE 0.014 0.001 PHE O 67 TYR 0.016 0.001 TYR A1063 ARG 0.009 0.000 ARG N 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 45) link_NAG-ASN : angle 3.27320 ( 135) link_BETA1-4 : bond 0.00412 ( 12) link_BETA1-4 : angle 1.46435 ( 36) hydrogen bonds : bond 0.04566 ( 1042) hydrogen bonds : angle 4.81855 ( 2832) SS BOND : bond 0.00219 ( 45) SS BOND : angle 1.15562 ( 90) covalent geometry : bond 0.00290 (29016) covalent geometry : angle 0.52514 (39462) *********************** 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 236 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 168 time to evaluate : 3.951 Fit side-chains REVERT: M 106 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7844 (mtm-85) REVERT: N 43 LYS cc_start: 0.8389 (mmmm) cc_final: 0.8108 (tptp) REVERT: O 2 VAL cc_start: 0.9350 (OUTLIER) cc_final: 0.9140 (m) REVERT: O 35 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7861 (mm-30) REVERT: A 19 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7407 (mp) REVERT: A 374 LYS cc_start: 0.7475 (tppt) cc_final: 0.7202 (tptp) REVERT: A 452 PHE cc_start: 0.6687 (m-80) cc_final: 0.6336 (m-80) REVERT: B 49 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 194 ASP cc_start: 0.8909 (m-30) cc_final: 0.8227 (t0) REVERT: C 49 GLN cc_start: 0.8699 (tm-30) cc_final: 0.7956 (tm-30) REVERT: C 752 TYR cc_start: 0.9270 (OUTLIER) cc_final: 0.7964 (t80) REVERT: C 826 ASP cc_start: 0.8374 (t0) cc_final: 0.7547 (t0) REVERT: C 1025 MET cc_start: 0.8881 (tpp) cc_final: 0.8583 (ttm) outliers start: 68 outliers final: 42 residues processed: 229 average time/residue: 0.3701 time to fit residues: 142.2161 Evaluate side-chains 203 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 3.331 ------------------------------------------------------------------------------- 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 51 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain O residue 2 VAL 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 124 VAL 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 645 CYS Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 1118 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 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 1100 VAL 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 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 567 ASP 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 862 THR 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 97 optimal weight: 3.9990 chunk 263 optimal weight: 9.9990 chunk 240 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 277 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 272 optimal weight: 0.9990 chunk 144 optimal weight: 0.3980 chunk 162 optimal weight: 0.0010 chunk 156 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.060092 restraints weight = 73696.943| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.69 r_work: 0.2720 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29118 Z= 0.094 Angle : 0.533 13.524 39723 Z= 0.263 Chirality : 0.044 0.328 4620 Planarity : 0.003 0.049 5025 Dihedral : 7.601 93.275 4992 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.22 % Favored : 96.76 % Rotamer: Outliers : 2.35 % Allowed : 19.03 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3483 helix: 2.50 (0.21), residues: 663 sheet: 0.96 (0.17), residues: 894 loop : -1.30 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 432 HIS 0.006 0.001 HIS M 38 PHE 0.014 0.001 PHE O 67 TYR 0.016 0.001 TYR A1063 ARG 0.011 0.000 ARG N 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 45) link_NAG-ASN : angle 3.12654 ( 135) link_BETA1-4 : bond 0.00376 ( 12) link_BETA1-4 : angle 1.57772 ( 36) hydrogen bonds : bond 0.03895 ( 1042) hydrogen bonds : angle 4.63620 ( 2832) SS BOND : bond 0.00297 ( 45) SS BOND : angle 0.95195 ( 90) covalent geometry : bond 0.00208 (29016) covalent geometry : angle 0.49841 (39462) *********************** 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 239 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 167 time to evaluate : 3.555 Fit side-chains REVERT: M 106 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7766 (mtm-85) REVERT: N 43 LYS cc_start: 0.8394 (mmmm) cc_final: 0.8120 (tptp) REVERT: O 32 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8788 (tm-30) REVERT: O 35 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8131 (mm-30) REVERT: O 46 GLU cc_start: 0.8493 (tt0) cc_final: 0.8248 (pt0) REVERT: O 64 LYS cc_start: 0.8789 (ptpt) cc_final: 0.8575 (mtmm) REVERT: O 88 GLU cc_start: 0.8211 (pm20) cc_final: 0.7900 (pm20) REVERT: A 374 LYS cc_start: 0.7996 (tppt) cc_final: 0.7710 (tptp) REVERT: A 452 PHE cc_start: 0.6753 (m-80) cc_final: 0.6440 (m-80) REVERT: B 49 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8190 (tm-30) REVERT: B 194 ASP cc_start: 0.8909 (m-30) cc_final: 0.8345 (t0) REVERT: B 728 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.9027 (p) REVERT: C 49 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8113 (tm-30) REVERT: C 752 TYR cc_start: 0.9246 (OUTLIER) cc_final: 0.7924 (t80) REVERT: C 826 ASP cc_start: 0.8356 (t0) cc_final: 0.7626 (t0) REVERT: C 865 MET cc_start: 0.8779 (mtt) cc_final: 0.8484 (mtt) outliers start: 72 outliers final: 45 residues processed: 234 average time/residue: 0.3750 time to fit residues: 146.2310 Evaluate side-chains 207 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 3.196 ------------------------------------------------------------------------------- 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 50 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain O residue 52 ASN 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 240 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 388 PHE 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 862 THR Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1118 VAL 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 728 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 819 PHE Chi-restraints excluded: chain B residue 862 THR 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 C residue 18 LEU 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 521 CYS Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 567 ASP Chi-restraints excluded: chain C residue 645 CYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 205 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 296 optimal weight: 0.5980 chunk 245 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 300 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 868 GLN B 203 HIS ** B 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 = 0.3304 r_free = 0.3304 target = 0.081005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.056718 restraints weight = 73878.477| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.67 r_work: 0.2647 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 29118 Z= 0.193 Angle : 0.597 12.778 39723 Z= 0.298 Chirality : 0.046 0.330 4620 Planarity : 0.004 0.051 5025 Dihedral : 7.434 90.944 4992 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 2.57 % Allowed : 19.13 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3483 helix: 2.26 (0.21), residues: 681 sheet: 0.87 (0.18), residues: 891 loop : -1.34 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 61 HIS 0.006 0.001 HIS C1060 PHE 0.017 0.001 PHE O 67 TYR 0.017 0.001 TYR C1063 ARG 0.013 0.000 ARG A 210 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 45) link_NAG-ASN : angle 3.09315 ( 135) link_BETA1-4 : bond 0.00299 ( 12) link_BETA1-4 : angle 1.70332 ( 36) hydrogen bonds : bond 0.05001 ( 1042) hydrogen bonds : angle 4.80616 ( 2832) SS BOND : bond 0.00318 ( 45) SS BOND : angle 1.28844 ( 90) covalent geometry : bond 0.00466 (29016) covalent geometry : angle 0.56544 (39462) *********************** 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 243 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 164 time to evaluate : 3.296 Fit side-chains REVERT: M 35 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8484 (mt-10) REVERT: M 106 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7718 (mtm-85) REVERT: N 43 LYS cc_start: 0.8468 (mmmm) cc_final: 0.8189 (tptp) REVERT: O 35 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8204 (mm-30) REVERT: O 46 GLU cc_start: 0.8464 (tt0) cc_final: 0.8167 (pt0) REVERT: O 64 LYS cc_start: 0.8773 (ptpt) cc_final: 0.8515 (mtmm) REVERT: A 19 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7602 (mp) REVERT: A 374 LYS cc_start: 0.8015 (tppt) cc_final: 0.7745 (tptp) REVERT: A 452 PHE cc_start: 0.6896 (m-80) cc_final: 0.6591 (m-80) REVERT: A 984 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.9165 (mt-10) REVERT: B 49 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8218 (tm-30) REVERT: B 194 ASP cc_start: 0.8907 (m-30) cc_final: 0.8547 (t0) REVERT: B 728 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.8979 (p) REVERT: C 49 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8020 (tm-30) REVERT: C 194 ASP cc_start: 0.8745 (m-30) cc_final: 0.8544 (t0) REVERT: C 728 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9115 (p) REVERT: C 752 TYR cc_start: 0.9353 (OUTLIER) cc_final: 0.8070 (t80) REVERT: C 826 ASP cc_start: 0.8489 (t0) cc_final: 0.7943 (t0) REVERT: C 855 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8370 (p) outliers start: 79 outliers final: 57 residues processed: 236 average time/residue: 0.3685 time to fit residues: 145.5042 Evaluate side-chains 219 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 155 time to evaluate : 3.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 22 CYS 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 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 O residue 52 ASN 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 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 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 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 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 728 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 911 VAL Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain C residue 18 LEU 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 580 ILE Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 728 THR 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 855 THR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 902 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 101 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 301 optimal weight: 5.9990 chunk 335 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 180 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3311 r_free = 0.3311 target = 0.081510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.057212 restraints weight = 74246.984| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.68 r_work: 0.2656 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29118 Z= 0.144 Angle : 0.558 12.273 39723 Z= 0.278 Chirality : 0.045 0.323 4620 Planarity : 0.003 0.050 5025 Dihedral : 7.192 89.095 4992 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 3.23 % Allowed : 18.54 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3483 helix: 2.39 (0.21), residues: 663 sheet: 0.87 (0.18), residues: 897 loop : -1.34 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 432 HIS 0.006 0.001 HIS M 38 PHE 0.020 0.001 PHE A 164 TYR 0.017 0.001 TYR A1063 ARG 0.006 0.000 ARG N 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 45) link_NAG-ASN : angle 3.00192 ( 135) link_BETA1-4 : bond 0.00344 ( 12) link_BETA1-4 : angle 1.58879 ( 36) hydrogen bonds : bond 0.04580 ( 1042) hydrogen bonds : angle 4.71870 ( 2832) SS BOND : bond 0.00257 ( 45) SS BOND : angle 1.14472 ( 90) covalent geometry : bond 0.00343 (29016) covalent geometry : angle 0.52661 (39462) *********************** 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 253 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 154 time to evaluate : 3.343 Fit side-chains REVERT: M 35 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8495 (mt-10) REVERT: M 106 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7660 (mtm-85) REVERT: N 35 GLU cc_start: 0.8432 (mp0) cc_final: 0.8198 (mp0) REVERT: N 43 LYS cc_start: 0.8427 (mmmm) cc_final: 0.8123 (tptp) REVERT: O 35 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8065 (mm-30) REVERT: O 46 GLU cc_start: 0.8494 (tt0) cc_final: 0.8154 (pt0) REVERT: O 64 LYS cc_start: 0.8818 (ptpt) cc_final: 0.8583 (mtmm) REVERT: A 19 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7609 (mp) REVERT: A 374 LYS cc_start: 0.7996 (tppt) cc_final: 0.7722 (tptp) REVERT: A 452 PHE cc_start: 0.6912 (m-80) cc_final: 0.6591 (m-80) REVERT: A 984 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.9095 (mt-10) REVERT: B 49 GLN cc_start: 0.8961 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 194 ASP cc_start: 0.8903 (m-30) cc_final: 0.8553 (t0) REVERT: C 49 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8095 (tm-30) REVERT: C 728 THR cc_start: 0.9373 (OUTLIER) cc_final: 0.9164 (p) REVERT: C 752 TYR cc_start: 0.9321 (OUTLIER) cc_final: 0.7974 (t80) REVERT: C 826 ASP cc_start: 0.8462 (t0) cc_final: 0.7945 (t0) REVERT: C 855 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8354 (p) REVERT: C 1025 MET cc_start: 0.9189 (tpp) cc_final: 0.8798 (ttm) outliers start: 99 outliers final: 75 residues processed: 248 average time/residue: 0.3607 time to fit residues: 150.6596 Evaluate side-chains 234 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 153 time to evaluate : 3.402 ------------------------------------------------------------------------------- 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 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 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 92 VAL 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 85 ASP Chi-restraints excluded: chain A residue 111 THR 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 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 862 THR Chi-restraints excluded: chain A residue 883 THR 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 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 214 GLN Chi-restraints excluded: chain B residue 240 LEU 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 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 628 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 819 PHE Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 874 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 927 ILE Chi-restraints excluded: chain B residue 1100 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 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 645 CYS Chi-restraints excluded: chain C residue 728 THR 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 855 THR Chi-restraints excluded: chain C residue 862 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 30 optimal weight: 7.9990 chunk 290 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 350 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3302 r_free = 0.3302 target = 0.081183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.056948 restraints weight = 74010.417| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.66 r_work: 0.2644 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29118 Z= 0.159 Angle : 0.576 11.564 39723 Z= 0.287 Chirality : 0.045 0.321 4620 Planarity : 0.004 0.051 5025 Dihedral : 7.104 87.756 4992 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 3.23 % Allowed : 18.90 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3483 helix: 2.42 (0.22), residues: 648 sheet: 0.78 (0.18), residues: 879 loop : -1.33 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 100 HIS 0.005 0.001 HIS M 38 PHE 0.018 0.001 PHE O 67 TYR 0.017 0.001 TYR C1063 ARG 0.013 0.000 ARG O 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 45) link_NAG-ASN : angle 2.96313 ( 135) link_BETA1-4 : bond 0.00331 ( 12) link_BETA1-4 : angle 1.58201 ( 36) hydrogen bonds : bond 0.04751 ( 1042) hydrogen bonds : angle 4.75729 ( 2832) SS BOND : bond 0.00293 ( 45) SS BOND : angle 1.42517 ( 90) covalent geometry : bond 0.00382 (29016) covalent geometry : angle 0.54496 (39462) *********************** 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 251 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 152 time to evaluate : 6.148 Fit side-chains REVERT: M 35 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8487 (mt-10) REVERT: M 106 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7603 (mtm-85) REVERT: N 35 GLU cc_start: 0.8448 (mp0) cc_final: 0.8192 (mp0) REVERT: O 35 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8059 (mm-30) REVERT: O 46 GLU cc_start: 0.8487 (tt0) cc_final: 0.8150 (pt0) REVERT: O 64 LYS cc_start: 0.8805 (ptpt) cc_final: 0.8552 (mtmm) REVERT: A 19 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7667 (mp) REVERT: A 374 LYS cc_start: 0.8006 (tppt) cc_final: 0.7734 (tptp) REVERT: A 984 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.9077 (mt-10) REVERT: B 49 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 194 ASP cc_start: 0.8909 (m-30) cc_final: 0.8553 (t0) REVERT: B 728 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8978 (p) REVERT: C 336 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8356 (pm20) REVERT: C 728 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9176 (p) REVERT: C 752 TYR cc_start: 0.9337 (OUTLIER) cc_final: 0.8058 (t80) REVERT: C 826 ASP cc_start: 0.8521 (t0) cc_final: 0.8023 (t0) REVERT: C 855 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8354 (p) REVERT: C 1025 MET cc_start: 0.9183 (tpp) cc_final: 0.8820 (ttm) outliers start: 99 outliers final: 80 residues processed: 243 average time/residue: 0.4521 time to fit residues: 193.2619 Evaluate side-chains 234 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 146 time to evaluate : 4.515 ------------------------------------------------------------------------------- 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 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 92 VAL 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 85 ASP 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 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 832 GLN Chi-restraints excluded: chain A residue 883 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 18 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 163 THR 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 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 862 THR 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 927 ILE Chi-restraints excluded: chain B residue 1100 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 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 728 THR 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 855 THR Chi-restraints excluded: chain C residue 862 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 125 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 288 optimal weight: 7.9990 chunk 342 optimal weight: 2.9990 chunk 322 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 324 optimal weight: 0.9980 chunk 294 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN ** O 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3262 r_free = 0.3262 target = 0.078816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.054545 restraints weight = 74906.577| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.68 r_work: 0.2592 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 29118 Z= 0.274 Angle : 0.665 11.631 39723 Z= 0.335 Chirality : 0.048 0.346 4620 Planarity : 0.004 0.052 5025 Dihedral : 7.330 86.601 4992 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 3.42 % Allowed : 19.00 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3483 helix: 2.10 (0.21), residues: 666 sheet: 0.49 (0.18), residues: 909 loop : -1.46 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 432 HIS 0.006 0.001 HIS C1060 PHE 0.024 0.002 PHE O 67 TYR 0.028 0.002 TYR B 900 ARG 0.010 0.001 ARG O 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 45) link_NAG-ASN : angle 3.01750 ( 135) link_BETA1-4 : bond 0.00282 ( 12) link_BETA1-4 : angle 1.65046 ( 36) hydrogen bonds : bond 0.05783 ( 1042) hydrogen bonds : angle 5.00355 ( 2832) SS BOND : bond 0.00373 ( 45) SS BOND : angle 1.62677 ( 90) covalent geometry : bond 0.00662 (29016) covalent geometry : angle 0.63727 (39462) *********************** 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 249 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 144 time to evaluate : 3.510 Fit side-chains REVERT: M 35 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8522 (mt-10) REVERT: M 106 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7478 (mtm-85) REVERT: N 35 GLU cc_start: 0.8595 (mp0) cc_final: 0.8336 (mp0) REVERT: O 46 GLU cc_start: 0.8482 (tt0) cc_final: 0.8013 (pt0) REVERT: A 19 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7764 (mp) REVERT: A 374 LYS cc_start: 0.8022 (tppt) cc_final: 0.7749 (tptp) REVERT: A 728 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.9007 (p) REVERT: B 173 MET cc_start: 0.4465 (mmt) cc_final: 0.4206 (mmt) REVERT: B 194 ASP cc_start: 0.8929 (m-30) cc_final: 0.8527 (t0) REVERT: B 728 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8939 (p) REVERT: C 336 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8352 (pm20) REVERT: C 560 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: C 728 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.9114 (p) REVERT: C 826 ASP cc_start: 0.8649 (t0) cc_final: 0.8227 (t0) REVERT: C 1025 MET cc_start: 0.9228 (tpp) cc_final: 0.8816 (ttm) outliers start: 105 outliers final: 84 residues processed: 241 average time/residue: 0.3607 time to fit residues: 150.6616 Evaluate side-chains 232 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 141 time to evaluate : 3.086 ------------------------------------------------------------------------------- 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 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 64 LYS 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 85 ASP 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 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 728 THR Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 883 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 107 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 163 THR 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 311 THR 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 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 911 VAL Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 1100 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 311 THR 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 560 GLN 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 776 GLU Chi-restraints excluded: chain C residue 832 GLN 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 927 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 14 optimal weight: 2.9990 chunk 211 optimal weight: 0.4980 chunk 169 optimal weight: 5.9990 chunk 138 optimal weight: 0.0030 chunk 26 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 308 optimal weight: 0.8980 chunk 228 optimal weight: 0.8980 chunk 283 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 1 GLN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 GLN ** 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 = 0.3313 r_free = 0.3313 target = 0.081436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.056972 restraints weight = 73463.566| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.79 r_work: 0.2654 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29118 Z= 0.104 Angle : 0.555 11.130 39723 Z= 0.278 Chirality : 0.044 0.318 4620 Planarity : 0.003 0.050 5025 Dihedral : 6.953 85.616 4992 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 2.41 % Allowed : 20.33 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3483 helix: 2.42 (0.22), residues: 648 sheet: 0.70 (0.18), residues: 876 loop : -1.35 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 100 HIS 0.007 0.001 HIS N 38 PHE 0.019 0.001 PHE O 67 TYR 0.018 0.001 TYR A1063 ARG 0.007 0.000 ARG N 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 45) link_NAG-ASN : angle 2.86828 ( 135) link_BETA1-4 : bond 0.00428 ( 12) link_BETA1-4 : angle 1.48538 ( 36) hydrogen bonds : bond 0.04349 ( 1042) hydrogen bonds : angle 4.73003 ( 2832) SS BOND : bond 0.00372 ( 45) SS BOND : angle 1.19578 ( 90) covalent geometry : bond 0.00234 (29016) covalent geometry : angle 0.52646 (39462) *********************** 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 224 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 150 time to evaluate : 3.509 Fit side-chains REVERT: M 35 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8490 (mt-10) REVERT: M 106 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7648 (mtm-85) REVERT: N 13 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8441 (mp10) REVERT: N 35 GLU cc_start: 0.8341 (mp0) cc_final: 0.8058 (mp0) REVERT: N 43 LYS cc_start: 0.7919 (mtmm) cc_final: 0.7493 (pttm) REVERT: N 58 ASN cc_start: 0.8283 (m-40) cc_final: 0.7848 (t0) REVERT: O 44 GLN cc_start: 0.7772 (pm20) cc_final: 0.7542 (pp30) REVERT: O 46 GLU cc_start: 0.8431 (tt0) cc_final: 0.8138 (pt0) REVERT: A 374 LYS cc_start: 0.7735 (tppt) cc_final: 0.7456 (tptp) REVERT: B 173 MET cc_start: 0.4681 (mmt) cc_final: 0.4462 (mmt) REVERT: B 194 ASP cc_start: 0.8924 (m-30) cc_final: 0.8298 (t0) REVERT: B 728 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8924 (p) REVERT: C 560 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.6740 (tm-30) REVERT: C 752 TYR cc_start: 0.9298 (OUTLIER) cc_final: 0.7937 (t80) REVERT: C 826 ASP cc_start: 0.8630 (t0) cc_final: 0.8193 (t0) REVERT: C 855 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.8091 (p) REVERT: C 1025 MET cc_start: 0.8964 (tpp) cc_final: 0.8665 (ttm) outliers start: 74 outliers final: 61 residues processed: 220 average time/residue: 0.3722 time to fit residues: 137.5876 Evaluate side-chains 209 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 143 time to evaluate : 3.071 ------------------------------------------------------------------------------- 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 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 96 HIS Chi-restraints excluded: chain O residue 52 ASN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 111 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 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 832 GLN 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 33 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 163 THR 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 463 ASP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 521 CYS 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 1100 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 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 577 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 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 131 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 310 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 281 optimal weight: 0.0970 chunk 272 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 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 = 0.3308 r_free = 0.3308 target = 0.081172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.056741 restraints weight = 73543.481| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.79 r_work: 0.2649 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29118 Z= 0.122 Angle : 0.558 10.755 39723 Z= 0.278 Chirality : 0.044 0.316 4620 Planarity : 0.004 0.050 5025 Dihedral : 6.780 84.516 4992 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 2.41 % Allowed : 20.43 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3483 helix: 2.47 (0.22), residues: 648 sheet: 0.84 (0.18), residues: 846 loop : -1.33 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.006 0.001 HIS M 38 PHE 0.021 0.001 PHE O 67 TYR 0.020 0.001 TYR B 900 ARG 0.012 0.000 ARG O 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 45) link_NAG-ASN : angle 2.79945 ( 135) link_BETA1-4 : bond 0.00349 ( 12) link_BETA1-4 : angle 1.49148 ( 36) hydrogen bonds : bond 0.04308 ( 1042) hydrogen bonds : angle 4.66458 ( 2832) SS BOND : bond 0.00289 ( 45) SS BOND : angle 1.22722 ( 90) covalent geometry : bond 0.00289 (29016) covalent geometry : angle 0.53003 (39462) ********************** 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 222 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 148 time to evaluate : 3.088 Fit side-chains REVERT: M 35 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8517 (mt-10) REVERT: M 106 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7664 (mtm-85) REVERT: N 13 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8436 (mp10) REVERT: N 35 GLU cc_start: 0.8330 (mp0) cc_final: 0.8063 (mp0) REVERT: N 58 ASN cc_start: 0.8285 (m-40) cc_final: 0.7861 (t0) REVERT: O 46 GLU cc_start: 0.8462 (tt0) cc_final: 0.8093 (pt0) REVERT: A 374 LYS cc_start: 0.7766 (tppt) cc_final: 0.7491 (tptp) REVERT: B 194 ASP cc_start: 0.8919 (m-30) cc_final: 0.8304 (t0) REVERT: B 728 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8946 (p) REVERT: C 560 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.6721 (tm-30) REVERT: C 752 TYR cc_start: 0.9331 (OUTLIER) cc_final: 0.8011 (t80) REVERT: C 826 ASP cc_start: 0.8604 (t0) cc_final: 0.8170 (t0) REVERT: C 855 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.8143 (p) REVERT: C 1025 MET cc_start: 0.9023 (tpp) cc_final: 0.8726 (ttm) outliers start: 74 outliers final: 68 residues processed: 217 average time/residue: 0.4507 time to fit residues: 165.2710 Evaluate side-chains 220 residues out of total 3069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 147 time to evaluate : 3.311 ------------------------------------------------------------------------------- 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 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 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 96 HIS Chi-restraints excluded: chain O residue 52 ASN Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 111 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 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 18 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 163 THR 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 513 LEU Chi-restraints excluded: chain B residue 521 CYS 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 1100 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 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 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 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 927 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 56 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.079722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.055173 restraints weight = 74248.687| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.80 r_work: 0.2610 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 29118 Z= 0.193 Angle : 0.608 10.996 39723 Z= 0.305 Chirality : 0.045 0.332 4620 Planarity : 0.004 0.051 5025 Dihedral : 6.884 83.028 4992 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 2.48 % Allowed : 20.40 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3483 helix: 2.38 (0.22), residues: 648 sheet: 0.55 (0.18), residues: 915 loop : -1.35 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 432 HIS 0.005 0.001 HIS M 38 PHE 0.021 0.001 PHE O 67 TYR 0.026 0.001 TYR B 900 ARG 0.009 0.000 ARG N 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 45) link_NAG-ASN : angle 2.83395 ( 135) link_BETA1-4 : bond 0.00291 ( 12) link_BETA1-4 : angle 1.52968 ( 36) hydrogen bonds : bond 0.05046 ( 1042) hydrogen bonds : angle 4.81227 ( 2832) SS BOND : bond 0.00343 ( 45) SS BOND : angle 1.44913 ( 90) covalent geometry : bond 0.00462 (29016) covalent geometry : angle 0.58082 (39462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11362.23 seconds wall clock time: 200 minutes 0.03 seconds (12000.03 seconds total)