Starting phenix.real_space_refine on Tue Aug 26 03:58:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wlo_37626/08_2025/8wlo_37626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wlo_37626/08_2025/8wlo_37626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wlo_37626/08_2025/8wlo_37626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wlo_37626/08_2025/8wlo_37626.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wlo_37626/08_2025/8wlo_37626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wlo_37626/08_2025/8wlo_37626.map" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2984 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 142 5.16 5 C 19396 2.51 5 N 5008 2.21 5 O 5917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30464 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8290 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 58, 'TRANS': 1002} Chain breaks: 6 Chain: "B" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8292 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 58, 'TRANS': 1002} Chain breaks: 6 Chain: "C" Number of atoms: 8322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8322 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 58, 'TRANS': 1006} Chain breaks: 6 Chain: "E" Number of atoms: 4873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4873 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 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: "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: "M" 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: "N" 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: "O" 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.84, per 1000 atoms: 0.19 Number of scatterers: 30464 At special positions: 0 Unit cell: (140.25, 147.05, 249.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 142 16.00 O 5917 8.00 N 5008 7.00 C 19396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " 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 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B 17 " " NAG B1306 " - " ASN B 165 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B 331 " " NAG B1312 " - " ASN B 61 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 17 " " NAG D 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 374 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 378 " 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7110 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 48 sheets defined 31.9% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.045A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.544A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.668A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.544A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.554A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.892A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.562A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.623A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.504A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.169A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.689A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.824A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.826A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.289A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.359A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.011A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.843A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.676A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.580A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.537A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 854 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.517A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.229A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.848A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.091A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.908A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.155A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 125 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.838A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.575A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.654A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.694A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.556A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.508A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.152A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.625A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.319A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.943A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 53 removed outlier: 3.857A pdb=" N GLN E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR E 28 " --> pdb=" O GLU E 24 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP E 39 " --> pdb=" O HIS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 81 removed outlier: 3.515A pdb=" N VAL E 60 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 103 removed outlier: 3.863A pdb=" N GLN E 103 " --> pdb=" O GLN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 109 removed outlier: 4.189A pdb=" N ALA E 108 " --> pdb=" O GLY E 105 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU E 109 " --> pdb=" O THR E 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 105 through 109' Processing helix chain 'E' and resid 110 through 127 removed outlier: 3.532A pdb=" N ILE E 127 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 131 removed outlier: 3.713A pdb=" N GLY E 131 " --> pdb=" O TYR E 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 128 through 131' Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.542A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 194 removed outlier: 3.743A pdb=" N GLU E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY E 173 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 4.200A pdb=" N GLU E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 220 through 249 removed outlier: 3.779A pdb=" N GLU E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.788A pdb=" N MET E 297 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 318 removed outlier: 3.591A pdb=" N PHE E 308 " --> pdb=" O THR E 304 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 317 " --> pdb=" O LYS E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 330 removed outlier: 4.013A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.585A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR E 381 " --> pdb=" O GLY E 377 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP E 382 " --> pdb=" O HIS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 3.901A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E 412 " --> pdb=" O MET E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 446 removed outlier: 3.873A pdb=" N ASN E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE E 438 " --> pdb=" O THR E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 469 through 473 removed outlier: 3.659A pdb=" N TRP E 473 " --> pdb=" O LYS E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.674A pdb=" N TRP E 478 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS E 481 " --> pdb=" O TRP E 477 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG E 482 " --> pdb=" O TRP E 478 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU E 483 " --> pdb=" O GLU E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 removed outlier: 4.170A pdb=" N ALA E 507 " --> pdb=" O LEU E 503 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 508 " --> pdb=" O PHE E 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 503 through 508' Processing helix chain 'E' and resid 512 through 534 removed outlier: 4.133A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 561 removed outlier: 3.623A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN E 552 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG E 553 " --> pdb=" O ASP E 549 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET E 557 " --> pdb=" O ARG E 553 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU E 560 " --> pdb=" O GLN E 556 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY E 561 " --> pdb=" O MET E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 3.717A pdb=" N ILE E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 596 Processing helix chain 'E' and resid 597 through 601 removed outlier: 3.722A pdb=" N ASN E 601 " --> pdb=" O GLN E 598 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.732A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.715A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.906A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.914A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.515A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.105A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.119A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.871A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.962A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.775A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.415A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.415A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.691A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AB7, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.064A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.979A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.056A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.805A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.058A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.095A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.770A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.073A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.073A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.530A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.784A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.843A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.515A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 117 removed outlier: 3.551A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 140 through 141 removed outlier: 4.292A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 189 through 190 removed outlier: 3.603A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 202 through 205 removed outlier: 7.056A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.102A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.738A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.693A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.663A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.547A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.731A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 715 through 728 removed outlier: 6.131A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.727A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.397A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.821A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 1161 hydrogen bonds defined for protein. 3207 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: 6.41 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9739 1.34 - 1.46: 7560 1.46 - 1.58: 13686 1.58 - 1.70: 2 1.70 - 1.82: 189 Bond restraints: 31176 Sorted by residual: bond pdb=" CG PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.503 1.302 0.201 3.40e-02 8.65e+02 3.50e+01 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 1.492 1.673 -0.181 5.00e-02 4.00e+02 1.32e+01 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 31171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 42220 3.56 - 7.12: 183 7.12 - 10.68: 24 10.68 - 14.24: 3 14.24 - 17.80: 1 Bond angle restraints: 42431 Sorted by residual: angle pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 112.00 94.20 17.80 1.40e+00 5.10e-01 1.62e+02 angle pdb=" N PRO B 384 " pdb=" CD PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 103.20 89.79 13.41 1.50e+00 4.44e-01 7.99e+01 angle pdb=" CA PRO B 25 " pdb=" N PRO B 25 " pdb=" CD PRO B 25 " ideal model delta sigma weight residual 112.00 101.68 10.32 1.40e+00 5.10e-01 5.43e+01 angle pdb=" CA PRO B 384 " pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 104.50 94.41 10.09 1.90e+00 2.77e-01 2.82e+01 angle pdb=" CB MET E 462 " pdb=" CG MET E 462 " pdb=" SD MET E 462 " ideal model delta sigma weight residual 112.70 124.77 -12.07 3.00e+00 1.11e-01 1.62e+01 ... (remaining 42426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.74: 17768 24.74 - 49.49: 1241 49.49 - 74.23: 166 74.23 - 98.97: 44 98.97 - 123.72: 17 Dihedral angle restraints: 19236 sinusoidal: 8198 harmonic: 11038 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 173.79 -80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -165.64 79.64 1 1.00e+01 1.00e-02 7.87e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -30.61 -55.39 1 1.00e+01 1.00e-02 4.15e+01 ... (remaining 19233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 4864 0.130 - 0.259: 35 0.259 - 0.389: 3 0.389 - 0.518: 0 0.518 - 0.648: 3 Chirality restraints: 4905 Sorted by residual: chirality pdb=" C1 NAG B1312 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1312 " pdb=" O5 NAG B1312 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.28e+00 ... (remaining 4902 not shown) Planarity restraints: 5471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " 0.115 5.00e-02 4.00e+02 1.57e-01 3.94e+01 pdb=" N PRO B 384 " -0.270 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " 0.077 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO C 82 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " -0.058 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO B 25 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " -0.045 5.00e-02 4.00e+02 ... (remaining 5468 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 433 2.65 - 3.21: 27595 3.21 - 3.77: 45288 3.77 - 4.34: 61945 4.34 - 4.90: 102848 Nonbonded interactions: 238109 Sorted by model distance: nonbonded pdb=" CB HIS E 378 " pdb="ZN ZN E 701 " model vdw 2.086 2.104 nonbonded pdb=" N GLU A 309 " pdb=" OE1 GLU A 309 " model vdw 2.174 3.120 nonbonded pdb=" O THR C 124 " pdb=" OG1 THR C 124 " model vdw 2.179 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.188 3.040 nonbonded pdb=" OH TYR E 128 " pdb=" O LEU E 503 " model vdw 2.191 3.040 ... (remaining 238104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 257 or resid 262 through 1306)) selection = (chain 'B' and (resid 14 through 141 or resid 154 through 176 or resid 188 throu \ gh 1306)) selection = (chain 'C' and (resid 14 through 141 or resid 154 through 176 or resid 188 throu \ gh 257 or resid 262 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.830 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 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 : 0.004 0.201 31270 Z= 0.173 Angle : 0.691 17.797 42664 Z= 0.340 Chirality : 0.048 0.648 4905 Planarity : 0.005 0.157 5434 Dihedral : 16.704 123.718 11997 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.60 % Allowed : 25.04 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.14), residues: 3740 helix: 1.85 (0.18), residues: 957 sheet: 0.42 (0.20), residues: 670 loop : -0.83 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 357 TYR 0.039 0.001 TYR B 505 PHE 0.038 0.001 PHE C 168 TRP 0.034 0.001 TRP B 436 HIS 0.004 0.000 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00397 (31176) covalent geometry : angle 0.66373 (42431) SS BOND : bond 0.00223 ( 43) SS BOND : angle 1.01687 ( 86) hydrogen bonds : bond 0.20109 ( 1151) hydrogen bonds : angle 7.34098 ( 3207) metal coordination : bond 0.01645 ( 2) link_BETA1-4 : bond 0.00472 ( 12) link_BETA1-4 : angle 2.08923 ( 36) link_NAG-ASN : bond 0.00825 ( 37) link_NAG-ASN : angle 3.62780 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5208 (mmt) cc_final: 0.4934 (tpt) REVERT: B 853 GLN cc_start: 0.5084 (OUTLIER) cc_final: 0.3808 (mt0) REVERT: E 249 MET cc_start: -0.0369 (mmm) cc_final: -0.1187 (mmt) outliers start: 20 outliers final: 10 residues processed: 114 average time/residue: 0.4698 time to fit residues: 66.3165 Evaluate side-chains 78 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain E residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 188 ASN A 334 ASN A 414 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 613 GLN A 690 GLN A 804 GLN A 953 ASN A 965 GLN B 14 GLN B 121 ASN B 218 GLN B 239 GLN B 354 ASN B 422 ASN B 439 ASN B 493 GLN B 501 ASN B 544 ASN B 613 GLN B 628 GLN B 658 ASN B 901 GLN B 955 ASN B 978 ASN C 23 GLN C 122 ASN C 196 ASN C 321 GLN C 448 ASN C 501 ASN C 658 ASN C 675 GLN C 901 GLN E 77 GLN E 102 GLN E 137 ASN E 277 ASN E 374 HIS E 475 GLN E 524 GLN E 531 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.103539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.065161 restraints weight = 110202.071| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.05 r_work: 0.2785 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.670 31270 Z= 0.214 Angle : 0.658 15.515 42664 Z= 0.322 Chirality : 0.047 0.388 4905 Planarity : 0.004 0.070 5434 Dihedral : 9.584 105.938 5107 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.13 % Allowed : 20.79 % Favored : 76.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.14), residues: 3740 helix: 1.68 (0.17), residues: 999 sheet: 0.43 (0.19), residues: 715 loop : -0.86 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 357 TYR 0.018 0.001 TYR B 369 PHE 0.018 0.001 PHE C 168 TRP 0.018 0.001 TRP A 633 HIS 0.004 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00401 (31176) covalent geometry : angle 0.63426 (42431) SS BOND : bond 0.00236 ( 43) SS BOND : angle 0.87361 ( 86) hydrogen bonds : bond 0.05708 ( 1151) hydrogen bonds : angle 5.48272 ( 3207) metal coordination : bond 0.47370 ( 2) link_BETA1-4 : bond 0.00531 ( 12) link_BETA1-4 : angle 1.98687 ( 36) link_NAG-ASN : bond 0.00685 ( 37) link_NAG-ASN : angle 3.24551 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 73 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 LEU cc_start: 0.8889 (mt) cc_final: 0.8568 (tp) REVERT: A 586 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8652 (m-30) REVERT: A 675 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8675 (pp30) REVERT: B 153 MET cc_start: 0.5543 (OUTLIER) cc_final: 0.5258 (tpt) REVERT: B 335 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8962 (tm) REVERT: B 853 GLN cc_start: 0.5483 (OUTLIER) cc_final: 0.4795 (mt0) REVERT: C 324 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: C 1038 LYS cc_start: 0.9546 (OUTLIER) cc_final: 0.9279 (mmtm) REVERT: E 360 MET cc_start: 0.5321 (pmm) cc_final: 0.3302 (tpp) REVERT: E 579 MET cc_start: 0.6076 (mmp) cc_final: 0.4588 (tpt) outliers start: 104 outliers final: 27 residues processed: 164 average time/residue: 0.4292 time to fit residues: 88.6331 Evaluate side-chains 101 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 67 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain E residue 261 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 374 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 278 optimal weight: 0.8980 chunk 223 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 173 GLN B1135 ASN C 137 ASN C 245 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.101762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.062726 restraints weight = 103584.864| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 4.48 r_work: 0.2772 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 31270 Z= 0.195 Angle : 0.637 14.195 42664 Z= 0.312 Chirality : 0.047 0.388 4905 Planarity : 0.004 0.058 5434 Dihedral : 8.327 103.870 5104 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.77 % Allowed : 20.16 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.14), residues: 3740 helix: 1.66 (0.17), residues: 1009 sheet: 0.42 (0.19), residues: 720 loop : -0.87 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 357 TYR 0.015 0.001 TYR A1067 PHE 0.037 0.001 PHE C 168 TRP 0.020 0.001 TRP A 633 HIS 0.010 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00463 (31176) covalent geometry : angle 0.61138 (42431) SS BOND : bond 0.00269 ( 43) SS BOND : angle 1.58523 ( 86) hydrogen bonds : bond 0.05751 ( 1151) hydrogen bonds : angle 5.22710 ( 3207) metal coordination : bond 0.02598 ( 2) link_BETA1-4 : bond 0.00470 ( 12) link_BETA1-4 : angle 2.01285 ( 36) link_NAG-ASN : bond 0.00550 ( 37) link_NAG-ASN : angle 3.14958 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 69 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 LEU cc_start: 0.8798 (mt) cc_final: 0.8471 (tt) REVERT: A 586 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8579 (m-30) REVERT: A 645 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8886 (p) REVERT: A 675 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8711 (pp30) REVERT: B 34 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7852 (mtp85) REVERT: B 153 MET cc_start: 0.5534 (OUTLIER) cc_final: 0.5244 (tpt) REVERT: B 335 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8988 (tm) REVERT: B 591 SER cc_start: 0.9259 (OUTLIER) cc_final: 0.9008 (p) REVERT: B 825 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8800 (mmmt) REVERT: C 153 MET cc_start: 0.4773 (pmt) cc_final: 0.4252 (pmt) REVERT: C 324 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8381 (pm20) REVERT: C 1038 LYS cc_start: 0.9554 (OUTLIER) cc_final: 0.9288 (mmtm) REVERT: E 579 MET cc_start: 0.6127 (mmp) cc_final: 0.5817 (mmp) outliers start: 92 outliers final: 38 residues processed: 153 average time/residue: 0.4753 time to fit residues: 89.9096 Evaluate side-chains 113 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 65 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 92 optimal weight: 2.9990 chunk 310 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 81 optimal weight: 0.3980 chunk 353 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 371 optimal weight: 20.0000 chunk 40 optimal weight: 40.0000 chunk 50 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 173 GLN B 853 GLN C 245 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.101735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.061910 restraints weight = 103028.622| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 4.66 r_work: 0.2769 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 31270 Z= 0.161 Angle : 0.599 11.216 42664 Z= 0.292 Chirality : 0.046 0.404 4905 Planarity : 0.004 0.056 5434 Dihedral : 7.514 101.938 5099 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.89 % Allowed : 19.58 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.14), residues: 3740 helix: 1.70 (0.17), residues: 1015 sheet: 0.44 (0.19), residues: 712 loop : -0.81 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 357 TYR 0.015 0.001 TYR A 636 PHE 0.018 0.001 PHE B 342 TRP 0.028 0.001 TRP A 633 HIS 0.007 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00379 (31176) covalent geometry : angle 0.57635 (42431) SS BOND : bond 0.00251 ( 43) SS BOND : angle 1.21666 ( 86) hydrogen bonds : bond 0.05269 ( 1151) hydrogen bonds : angle 4.97518 ( 3207) metal coordination : bond 0.01928 ( 2) link_BETA1-4 : bond 0.00432 ( 12) link_BETA1-4 : angle 1.94131 ( 36) link_NAG-ASN : bond 0.00493 ( 37) link_NAG-ASN : angle 2.95169 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 64 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 LEU cc_start: 0.8782 (mt) cc_final: 0.8447 (tt) REVERT: A 583 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8544 (pm20) REVERT: A 586 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8591 (m-30) REVERT: A 645 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8920 (p) REVERT: A 675 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8731 (pp30) REVERT: B 34 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7988 (mtp85) REVERT: B 153 MET cc_start: 0.5574 (OUTLIER) cc_final: 0.5242 (tpt) REVERT: B 335 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8999 (tm) REVERT: B 591 SER cc_start: 0.9256 (OUTLIER) cc_final: 0.9007 (p) REVERT: B 616 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7531 (t160) REVERT: C 153 MET cc_start: 0.4704 (pmt) cc_final: 0.4164 (pmt) REVERT: C 324 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8375 (pm20) REVERT: C 457 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8276 (tpt-90) REVERT: C 619 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: C 1038 LYS cc_start: 0.9547 (OUTLIER) cc_final: 0.9282 (mmtm) REVERT: C 1092 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8946 (pm20) REVERT: E 360 MET cc_start: 0.5217 (pmm) cc_final: 0.3042 (tpt) REVERT: E 579 MET cc_start: 0.5736 (mmp) cc_final: 0.5392 (mmp) outliers start: 96 outliers final: 37 residues processed: 149 average time/residue: 0.5129 time to fit residues: 93.8281 Evaluate side-chains 116 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 65 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain E residue 261 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 67 optimal weight: 0.9980 chunk 265 optimal weight: 10.0000 chunk 208 optimal weight: 0.5980 chunk 345 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 356 optimal weight: 50.0000 chunk 266 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 260 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.101693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.059848 restraints weight = 103534.983| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.54 r_work: 0.2792 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 31270 Z= 0.154 Angle : 0.588 11.628 42664 Z= 0.285 Chirality : 0.045 0.361 4905 Planarity : 0.004 0.054 5434 Dihedral : 7.201 100.902 5098 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.04 % Allowed : 19.40 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.14), residues: 3740 helix: 1.78 (0.17), residues: 1016 sheet: 0.47 (0.19), residues: 714 loop : -0.80 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 357 TYR 0.015 0.001 TYR C 200 PHE 0.016 0.001 PHE C 800 TRP 0.022 0.001 TRP A 633 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00361 (31176) covalent geometry : angle 0.56605 (42431) SS BOND : bond 0.00285 ( 43) SS BOND : angle 1.17069 ( 86) hydrogen bonds : bond 0.05120 ( 1151) hydrogen bonds : angle 4.83285 ( 3207) metal coordination : bond 0.01249 ( 2) link_BETA1-4 : bond 0.00456 ( 12) link_BETA1-4 : angle 1.92371 ( 36) link_NAG-ASN : bond 0.00460 ( 37) link_NAG-ASN : angle 2.85774 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 66 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 LEU cc_start: 0.8760 (mt) cc_final: 0.8423 (tt) REVERT: A 583 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8531 (pm20) REVERT: A 586 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8605 (m-30) REVERT: A 645 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8957 (p) REVERT: A 675 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8740 (pp30) REVERT: B 34 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8065 (mtp85) REVERT: B 153 MET cc_start: 0.5562 (OUTLIER) cc_final: 0.5228 (tpt) REVERT: B 335 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9042 (tm) REVERT: B 591 SER cc_start: 0.9246 (OUTLIER) cc_final: 0.9000 (p) REVERT: B 616 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7604 (t160) REVERT: B 825 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8795 (mmmt) REVERT: C 153 MET cc_start: 0.4767 (OUTLIER) cc_final: 0.4191 (pmt) REVERT: C 231 ILE cc_start: 0.6031 (OUTLIER) cc_final: 0.5795 (mp) REVERT: C 324 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8402 (pm20) REVERT: C 787 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8640 (mt0) REVERT: C 1038 LYS cc_start: 0.9534 (OUTLIER) cc_final: 0.9284 (mmtm) REVERT: C 1092 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8887 (pm20) REVERT: E 579 MET cc_start: 0.4588 (mmp) cc_final: 0.4258 (mmp) outliers start: 101 outliers final: 45 residues processed: 155 average time/residue: 0.5020 time to fit residues: 95.9233 Evaluate side-chains 126 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 65 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain E residue 261 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 258 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 241 optimal weight: 10.0000 chunk 206 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 348 optimal weight: 10.0000 chunk 339 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 302 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.101227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.059485 restraints weight = 103082.794| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 4.44 r_work: 0.2777 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 31270 Z= 0.191 Angle : 0.608 12.528 42664 Z= 0.297 Chirality : 0.046 0.390 4905 Planarity : 0.004 0.056 5434 Dihedral : 7.130 99.896 5098 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.68 % Allowed : 19.58 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.14), residues: 3740 helix: 1.82 (0.17), residues: 1022 sheet: 0.42 (0.19), residues: 724 loop : -0.79 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 634 TYR 0.015 0.001 TYR C1067 PHE 0.017 0.001 PHE C 800 TRP 0.023 0.001 TRP A 633 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00455 (31176) covalent geometry : angle 0.58479 (42431) SS BOND : bond 0.00304 ( 43) SS BOND : angle 1.38666 ( 86) hydrogen bonds : bond 0.05361 ( 1151) hydrogen bonds : angle 4.84137 ( 3207) metal coordination : bond 0.01229 ( 2) link_BETA1-4 : bond 0.00476 ( 12) link_BETA1-4 : angle 1.93388 ( 36) link_NAG-ASN : bond 0.00484 ( 37) link_NAG-ASN : angle 2.92098 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 68 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 LEU cc_start: 0.8720 (mt) cc_final: 0.8406 (tt) REVERT: A 583 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8544 (pm20) REVERT: A 586 ASP cc_start: 0.9028 (OUTLIER) cc_final: 0.8592 (m-30) REVERT: A 634 ARG cc_start: 0.7733 (pmt-80) cc_final: 0.7476 (tmm160) REVERT: A 645 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8994 (p) REVERT: A 675 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8743 (pp30) REVERT: B 34 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8131 (mtp85) REVERT: B 153 MET cc_start: 0.5516 (OUTLIER) cc_final: 0.5227 (tpt) REVERT: B 335 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9023 (tm) REVERT: B 591 SER cc_start: 0.9259 (OUTLIER) cc_final: 0.9007 (p) REVERT: B 616 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7661 (t160) REVERT: B 825 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8868 (mmmt) REVERT: C 153 MET cc_start: 0.4753 (OUTLIER) cc_final: 0.4171 (pmt) REVERT: C 231 ILE cc_start: 0.5986 (OUTLIER) cc_final: 0.5753 (mp) REVERT: C 324 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: C 1038 LYS cc_start: 0.9544 (OUTLIER) cc_final: 0.9298 (mmtm) REVERT: E 360 MET cc_start: 0.5023 (pmm) cc_final: 0.2755 (tpt) REVERT: E 579 MET cc_start: 0.4511 (mmp) cc_final: 0.4243 (mmp) outliers start: 89 outliers final: 53 residues processed: 146 average time/residue: 0.4979 time to fit residues: 90.0599 Evaluate side-chains 134 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 67 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 283 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 79 optimal weight: 0.8980 chunk 42 optimal weight: 0.0570 chunk 345 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.101519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.061986 restraints weight = 103694.365| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.51 r_work: 0.2782 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31270 Z= 0.126 Angle : 0.572 12.097 42664 Z= 0.278 Chirality : 0.045 0.378 4905 Planarity : 0.004 0.056 5434 Dihedral : 6.819 98.139 5098 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.50 % Allowed : 19.73 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.14), residues: 3740 helix: 1.90 (0.17), residues: 1021 sheet: 0.51 (0.19), residues: 714 loop : -0.74 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 634 TYR 0.015 0.001 TYR C1067 PHE 0.017 0.001 PHE A 79 TRP 0.018 0.001 TRP A 633 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00291 (31176) covalent geometry : angle 0.54994 (42431) SS BOND : bond 0.00230 ( 43) SS BOND : angle 1.06983 ( 86) hydrogen bonds : bond 0.04724 ( 1151) hydrogen bonds : angle 4.67304 ( 3207) metal coordination : bond 0.01165 ( 2) link_BETA1-4 : bond 0.00489 ( 12) link_BETA1-4 : angle 1.88124 ( 36) link_NAG-ASN : bond 0.00464 ( 37) link_NAG-ASN : angle 2.84772 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 74 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8522 (pm20) REVERT: A 586 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8542 (m-30) REVERT: A 634 ARG cc_start: 0.7843 (pmt-80) cc_final: 0.7477 (ttp80) REVERT: A 645 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8955 (p) REVERT: A 675 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8751 (pp30) REVERT: B 34 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8105 (mtp85) REVERT: B 153 MET cc_start: 0.5512 (OUTLIER) cc_final: 0.5139 (tpt) REVERT: B 214 ARG cc_start: 0.8499 (ptp-170) cc_final: 0.8252 (pmm-80) REVERT: B 335 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9000 (tm) REVERT: B 591 SER cc_start: 0.9237 (OUTLIER) cc_final: 0.8979 (p) REVERT: B 616 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7611 (t160) REVERT: B 825 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8752 (mmmt) REVERT: C 153 MET cc_start: 0.4676 (OUTLIER) cc_final: 0.4052 (pmt) REVERT: C 231 ILE cc_start: 0.6020 (OUTLIER) cc_final: 0.5816 (mp) REVERT: C 787 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8656 (mt0) REVERT: C 1038 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9261 (mmtm) REVERT: C 1092 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8907 (pm20) REVERT: E 163 TRP cc_start: 0.7682 (OUTLIER) cc_final: 0.7202 (p-90) REVERT: E 360 MET cc_start: 0.5018 (pmm) cc_final: 0.3103 (ptp) REVERT: E 579 MET cc_start: 0.4523 (mmp) cc_final: 0.4268 (mmp) outliers start: 83 outliers final: 42 residues processed: 144 average time/residue: 0.4919 time to fit residues: 87.6304 Evaluate side-chains 126 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 68 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain E residue 163 TRP Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 438 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 201 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 313 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 330 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.101591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.059807 restraints weight = 104513.509| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.54 r_work: 0.2804 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31270 Z= 0.117 Angle : 0.572 15.119 42664 Z= 0.275 Chirality : 0.045 0.430 4905 Planarity : 0.004 0.063 5434 Dihedral : 6.611 95.890 5098 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.41 % Allowed : 19.83 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.14), residues: 3740 helix: 1.99 (0.17), residues: 1015 sheet: 0.52 (0.19), residues: 707 loop : -0.69 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 457 TYR 0.037 0.001 TYR B 505 PHE 0.018 0.001 PHE B 342 TRP 0.018 0.001 TRP A 633 HIS 0.005 0.000 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00267 (31176) covalent geometry : angle 0.54865 (42431) SS BOND : bond 0.00231 ( 43) SS BOND : angle 1.01622 ( 86) hydrogen bonds : bond 0.04527 ( 1151) hydrogen bonds : angle 4.59094 ( 3207) metal coordination : bond 0.01116 ( 2) link_BETA1-4 : bond 0.00380 ( 12) link_BETA1-4 : angle 1.79313 ( 36) link_NAG-ASN : bond 0.00473 ( 37) link_NAG-ASN : angle 2.98210 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 74 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 LEU cc_start: 0.8724 (mt) cc_final: 0.8396 (tt) REVERT: A 583 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8530 (pm20) REVERT: A 586 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8570 (m-30) REVERT: A 634 ARG cc_start: 0.7869 (pmt-80) cc_final: 0.7503 (ttp80) REVERT: A 645 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.9023 (p) REVERT: A 675 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8748 (pp30) REVERT: B 34 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8150 (mtp85) REVERT: B 153 MET cc_start: 0.5367 (OUTLIER) cc_final: 0.4996 (tpt) REVERT: B 335 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9018 (tm) REVERT: B 436 TRP cc_start: 0.8062 (t-100) cc_final: 0.7487 (t-100) REVERT: B 591 SER cc_start: 0.9235 (OUTLIER) cc_final: 0.8986 (p) REVERT: B 616 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7664 (t160) REVERT: B 825 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8794 (mmmt) REVERT: C 153 MET cc_start: 0.4687 (pmt) cc_final: 0.4091 (pmt) REVERT: C 787 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8643 (mt0) REVERT: C 1038 LYS cc_start: 0.9538 (OUTLIER) cc_final: 0.9267 (mmtm) REVERT: E 163 TRP cc_start: 0.7723 (OUTLIER) cc_final: 0.7194 (p-90) REVERT: E 579 MET cc_start: 0.4339 (mmp) cc_final: 0.4095 (mmp) outliers start: 80 outliers final: 46 residues processed: 144 average time/residue: 0.4604 time to fit residues: 82.9382 Evaluate side-chains 128 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 69 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain E residue 163 TRP Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 438 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 232 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 281 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 218 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 352 optimal weight: 7.9990 chunk 344 optimal weight: 30.0000 chunk 207 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 364 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 23 GLN B 188 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 487 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.098806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.056784 restraints weight = 103738.055| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 4.41 r_work: 0.2710 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.103 31270 Z= 0.457 Angle : 0.792 20.859 42664 Z= 0.393 Chirality : 0.053 0.539 4905 Planarity : 0.005 0.057 5434 Dihedral : 7.377 89.860 5097 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.65 % Allowed : 19.67 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.13), residues: 3740 helix: 1.59 (0.17), residues: 1035 sheet: 0.23 (0.19), residues: 724 loop : -1.01 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 357 TYR 0.030 0.002 TYR B 505 PHE 0.029 0.002 PHE A 823 TRP 0.035 0.002 TRP A 633 HIS 0.008 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.01088 (31176) covalent geometry : angle 0.76548 (42431) SS BOND : bond 0.00386 ( 43) SS BOND : angle 1.69304 ( 86) hydrogen bonds : bond 0.07303 ( 1151) hydrogen bonds : angle 5.23539 ( 3207) metal coordination : bond 0.01184 ( 2) link_BETA1-4 : bond 0.00771 ( 12) link_BETA1-4 : angle 2.33267 ( 36) link_NAG-ASN : bond 0.01023 ( 37) link_NAG-ASN : angle 3.65110 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 63 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.8849 (p90) REVERT: A 583 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8560 (pm20) REVERT: A 586 ASP cc_start: 0.9044 (OUTLIER) cc_final: 0.8602 (m-30) REVERT: A 645 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8839 (p) REVERT: A 675 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8745 (pp30) REVERT: B 153 MET cc_start: 0.5434 (OUTLIER) cc_final: 0.5141 (tpt) REVERT: B 335 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9034 (tm) REVERT: B 436 TRP cc_start: 0.8076 (t-100) cc_final: 0.7431 (t-100) REVERT: B 591 SER cc_start: 0.9234 (OUTLIER) cc_final: 0.8974 (p) REVERT: B 616 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7788 (t160) REVERT: B 825 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8886 (mmmm) REVERT: C 153 MET cc_start: 0.4920 (OUTLIER) cc_final: 0.4257 (pmt) REVERT: C 787 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8754 (mt0) REVERT: C 1038 LYS cc_start: 0.9548 (OUTLIER) cc_final: 0.9295 (mmtm) REVERT: E 360 MET cc_start: 0.4876 (pmm) cc_final: 0.3052 (ptp) REVERT: E 579 MET cc_start: 0.4440 (mmp) cc_final: 0.3906 (mmt) outliers start: 88 outliers final: 43 residues processed: 138 average time/residue: 0.4443 time to fit residues: 76.7069 Evaluate side-chains 116 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 60 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 438 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 210 optimal weight: 1.9990 chunk 340 optimal weight: 50.0000 chunk 371 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 300 optimal weight: 0.5980 chunk 192 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 150 optimal weight: 20.0000 chunk 358 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.101158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.059242 restraints weight = 102408.469| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.47 r_work: 0.2794 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31270 Z= 0.119 Angle : 0.609 15.577 42664 Z= 0.295 Chirality : 0.046 0.540 4905 Planarity : 0.004 0.061 5434 Dihedral : 6.716 87.692 5097 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.54 % Allowed : 20.52 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.14), residues: 3740 helix: 1.81 (0.17), residues: 1027 sheet: 0.42 (0.19), residues: 717 loop : -0.83 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 457 TYR 0.030 0.001 TYR B 505 PHE 0.014 0.001 PHE B 456 TRP 0.020 0.001 TRP A 633 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00268 (31176) covalent geometry : angle 0.58377 (42431) SS BOND : bond 0.00451 ( 43) SS BOND : angle 1.17524 ( 86) hydrogen bonds : bond 0.04907 ( 1151) hydrogen bonds : angle 4.72946 ( 3207) metal coordination : bond 0.01163 ( 2) link_BETA1-4 : bond 0.00521 ( 12) link_BETA1-4 : angle 1.91040 ( 36) link_NAG-ASN : bond 0.00600 ( 37) link_NAG-ASN : angle 3.14620 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 66 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8593 (pm20) REVERT: A 586 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8585 (m-30) REVERT: A 645 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8974 (p) REVERT: A 675 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8725 (pp30) REVERT: B 153 MET cc_start: 0.5407 (OUTLIER) cc_final: 0.4959 (tpt) REVERT: B 335 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9075 (tm) REVERT: B 436 TRP cc_start: 0.8026 (t-100) cc_final: 0.7449 (t-100) REVERT: B 591 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8936 (p) REVERT: B 825 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8753 (mmmt) REVERT: C 153 MET cc_start: 0.4718 (pmt) cc_final: 0.4063 (pmt) REVERT: C 1038 LYS cc_start: 0.9527 (OUTLIER) cc_final: 0.9280 (mmtm) REVERT: E 360 MET cc_start: 0.4842 (pmm) cc_final: 0.3066 (ptp) outliers start: 51 outliers final: 33 residues processed: 114 average time/residue: 0.4986 time to fit residues: 70.6277 Evaluate side-chains 105 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 63 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 455 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 65 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 345 optimal weight: 9.9990 chunk 260 optimal weight: 3.9990 chunk 369 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 283 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.100811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.058845 restraints weight = 103684.455| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 4.55 r_work: 0.2765 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 31270 Z= 0.158 Angle : 0.614 15.330 42664 Z= 0.297 Chirality : 0.046 0.553 4905 Planarity : 0.004 0.058 5434 Dihedral : 6.568 81.160 5097 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.63 % Allowed : 20.46 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.14), residues: 3740 helix: 1.87 (0.17), residues: 1028 sheet: 0.45 (0.19), residues: 714 loop : -0.82 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 457 TYR 0.030 0.001 TYR B 505 PHE 0.019 0.001 PHE C 168 TRP 0.022 0.001 TRP A 633 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00373 (31176) covalent geometry : angle 0.58911 (42431) SS BOND : bond 0.00276 ( 43) SS BOND : angle 1.21557 ( 86) hydrogen bonds : bond 0.05126 ( 1151) hydrogen bonds : angle 4.70665 ( 3207) metal coordination : bond 0.01117 ( 2) link_BETA1-4 : bond 0.00456 ( 12) link_BETA1-4 : angle 1.91223 ( 36) link_NAG-ASN : bond 0.00486 ( 37) link_NAG-ASN : angle 3.17011 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14871.03 seconds wall clock time: 252 minutes 21.24 seconds (15141.24 seconds total)