Starting phenix.real_space_refine on Sat Jun 28 14:49:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wlo_37626/06_2025/8wlo_37626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wlo_37626/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wlo_37626/06_2025/8wlo_37626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wlo_37626/06_2025/8wlo_37626.map" model { file = "/net/cci-nas-00/data/ceres_data/8wlo_37626/06_2025/8wlo_37626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wlo_37626/06_2025/8wlo_37626.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.65, per 1000 atoms: 0.58 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: 7.78 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 4.26 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: 14.04 Time building geometry restraints manager: 9.20 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 1147 or resid 1301 thr \ ough 1306)) selection = (chain 'B' and (resid 14 through 141 or resid 154 through 176 or resid 188 throu \ gh 1147 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 141 or resid 154 through 176 or resid 188 throu \ gh 257 or resid 262 through 1147 or resid 1301 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.030 Extract box with map and model: 1.250 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 78.080 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.840 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (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 TRP 0.034 0.001 TRP B 436 HIS 0.004 0.000 HIS C 245 PHE 0.038 0.001 PHE C 168 TYR 0.039 0.001 TYR B 505 ARG 0.009 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00825 ( 37) link_NAG-ASN : angle 3.62780 ( 111) link_BETA1-4 : bond 0.00472 ( 12) link_BETA1-4 : angle 2.08923 ( 36) hydrogen bonds : bond 0.20109 ( 1151) hydrogen bonds : angle 7.34098 ( 3207) metal coordination : bond 0.01645 ( 2) SS BOND : bond 0.00223 ( 43) SS BOND : angle 1.01687 ( 86) covalent geometry : bond 0.00397 (31176) covalent geometry : angle 0.66373 (42431) *********************** 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 : 3.426 Fit side-chains revert: symmetry clash 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: 1.1341 time to fit residues: 161.3021 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 : 3.396 ------------------------------------------------------------------------------- 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 318 optimal weight: 8.9990 chunk 285 optimal weight: 0.0870 chunk 158 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 192 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 295 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 342 optimal weight: 0.0670 overall best weight: 1.6100 ------------------------------------------------------------------------------- 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 173 GLN B 218 GLN B 239 GLN B 354 ASN B 422 ASN B 439 ASN B 493 GLN 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 493 HIS E 524 GLN E 531 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.103842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.065624 restraints weight = 109864.481| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.06 r_work: 0.2801 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.680 31270 Z= 0.198 Angle : 0.637 13.295 42664 Z= 0.311 Chirality : 0.047 0.541 4905 Planarity : 0.004 0.069 5434 Dihedral : 9.498 106.032 5107 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.89 % Allowed : 21.12 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3740 helix: 1.71 (0.17), residues: 999 sheet: 0.44 (0.19), residues: 721 loop : -0.84 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 633 HIS 0.004 0.001 HIS E 373 PHE 0.018 0.001 PHE C 168 TYR 0.019 0.001 TYR B 369 ARG 0.006 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00715 ( 37) link_NAG-ASN : angle 3.11982 ( 111) link_BETA1-4 : bond 0.00544 ( 12) link_BETA1-4 : angle 2.00850 ( 36) hydrogen bonds : bond 0.05548 ( 1151) hydrogen bonds : angle 5.46661 ( 3207) metal coordination : bond 0.48057 ( 2) SS BOND : bond 0.00322 ( 43) SS BOND : angle 0.83392 ( 86) covalent geometry : bond 0.00343 (31176) covalent geometry : angle 0.61430 (42431) *********************** 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 171 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 75 time to evaluate : 3.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 LEU cc_start: 0.8871 (mt) cc_final: 0.8545 (tt) REVERT: A 586 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8633 (m-30) REVERT: A 675 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8666 (pp30) REVERT: B 153 MET cc_start: 0.5661 (OUTLIER) cc_final: 0.5360 (tpt) REVERT: B 335 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8948 (tm) REVERT: C 324 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8434 (pm20) REVERT: C 1038 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9274 (mmtm) REVERT: E 360 MET cc_start: 0.5330 (pmm) cc_final: 0.3270 (tpp) REVERT: E 579 MET cc_start: 0.6144 (mmp) cc_final: 0.4674 (tpt) outliers start: 96 outliers final: 24 residues processed: 159 average time/residue: 1.0725 time to fit residues: 214.4339 Evaluate side-chains 98 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 3.617 ------------------------------------------------------------------------------- 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 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 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 800 PHE 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 231 optimal weight: 10.0000 chunk 373 optimal weight: 30.0000 chunk 161 optimal weight: 6.9990 chunk 357 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 212 optimal weight: 10.0000 chunk 266 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 102 optimal weight: 0.0000 chunk 332 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 853 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 = 0.4091 r_free = 0.4091 target = 0.102442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.062986 restraints weight = 103580.711| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.45 r_work: 0.2813 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 31270 Z= 0.131 Angle : 0.595 12.790 42664 Z= 0.289 Chirality : 0.046 0.502 4905 Planarity : 0.004 0.056 5434 Dihedral : 8.065 105.163 5100 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.68 % Allowed : 20.40 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3740 helix: 1.72 (0.17), residues: 1010 sheet: 0.54 (0.19), residues: 701 loop : -0.80 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 633 HIS 0.010 0.001 HIS E 374 PHE 0.032 0.001 PHE C 168 TYR 0.015 0.001 TYR B 369 ARG 0.005 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 37) link_NAG-ASN : angle 2.91353 ( 111) link_BETA1-4 : bond 0.00473 ( 12) link_BETA1-4 : angle 1.92657 ( 36) hydrogen bonds : bond 0.05029 ( 1151) hydrogen bonds : angle 5.07599 ( 3207) metal coordination : bond 0.03547 ( 2) SS BOND : bond 0.00285 ( 43) SS BOND : angle 1.47711 ( 86) covalent geometry : bond 0.00297 (31176) covalent geometry : angle 0.57067 (42431) *********************** 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 158 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 69 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8602 (m-30) REVERT: A 645 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8888 (p) REVERT: A 675 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8649 (pp30) REVERT: A 1043 CYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8984 (m) REVERT: B 34 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7657 (mtp85) REVERT: B 153 MET cc_start: 0.5472 (OUTLIER) cc_final: 0.5130 (tpt) REVERT: B 335 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8961 (tm) REVERT: B 591 SER cc_start: 0.9256 (OUTLIER) cc_final: 0.9022 (p) REVERT: C 153 MET cc_start: 0.4873 (pmt) cc_final: 0.4359 (pmt) REVERT: C 324 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8396 (pm20) REVERT: C 801 ASN cc_start: 0.6058 (OUTLIER) cc_final: 0.5612 (m-40) REVERT: E 323 MET cc_start: 0.5811 (mmm) cc_final: 0.5610 (tpt) REVERT: E 579 MET cc_start: 0.3625 (mmp) cc_final: 0.3211 (mmp) outliers start: 89 outliers final: 36 residues processed: 149 average time/residue: 0.9744 time to fit residues: 184.2168 Evaluate side-chains 112 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 66 time to evaluate : 3.284 ------------------------------------------------------------------------------- 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 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 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 553 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 638 THR 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 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 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 801 ASN 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 E residue 522 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 182 optimal weight: 5.9990 chunk 322 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 235 optimal weight: 8.9990 chunk 226 optimal weight: 30.0000 chunk 81 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 346 optimal weight: 20.0000 chunk 340 optimal weight: 50.0000 chunk 153 optimal weight: 20.0000 chunk 254 optimal weight: 0.4980 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 501 ASN B1135 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 245 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.101437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.062005 restraints weight = 103509.614| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.45 r_work: 0.2755 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 31270 Z= 0.206 Angle : 0.619 13.239 42664 Z= 0.301 Chirality : 0.047 0.521 4905 Planarity : 0.004 0.056 5434 Dihedral : 7.600 102.667 5100 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.01 % Allowed : 19.64 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3740 helix: 1.73 (0.17), residues: 1016 sheet: 0.40 (0.19), residues: 727 loop : -0.81 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 633 HIS 0.007 0.001 HIS E 374 PHE 0.019 0.001 PHE C 800 TYR 0.016 0.001 TYR A1067 ARG 0.004 0.000 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 37) link_NAG-ASN : angle 2.98034 ( 111) link_BETA1-4 : bond 0.00471 ( 12) link_BETA1-4 : angle 1.97595 ( 36) hydrogen bonds : bond 0.05658 ( 1151) hydrogen bonds : angle 5.03406 ( 3207) metal coordination : bond 0.01912 ( 2) SS BOND : bond 0.00285 ( 43) SS BOND : angle 1.42953 ( 86) covalent geometry : bond 0.00489 (31176) covalent geometry : angle 0.59528 (42431) *********************** 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 168 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 68 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8519 (pm20) REVERT: A 586 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8598 (m-30) REVERT: A 645 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8839 (p) REVERT: A 675 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8729 (pp30) REVERT: A 995 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8663 (ptp-170) REVERT: B 14 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8185 (pp30) REVERT: B 34 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.7970 (mtp85) REVERT: B 153 MET cc_start: 0.5577 (OUTLIER) cc_final: 0.5241 (tpt) REVERT: B 335 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9005 (tm) REVERT: B 825 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8783 (mmmt) REVERT: C 153 MET cc_start: 0.4800 (OUTLIER) cc_final: 0.4251 (pmt) REVERT: C 324 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: C 619 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8135 (mp0) REVERT: C 1038 LYS cc_start: 0.9561 (OUTLIER) cc_final: 0.9287 (mmtm) REVERT: E 360 MET cc_start: 0.5167 (pmm) cc_final: 0.2985 (tpt) REVERT: E 579 MET cc_start: 0.5946 (mmp) cc_final: 0.5608 (mmp) outliers start: 100 outliers final: 42 residues processed: 155 average time/residue: 1.2172 time to fit residues: 233.5229 Evaluate side-chains 123 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 67 time to evaluate : 3.829 ------------------------------------------------------------------------------- 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 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 995 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 14 GLN 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 582 LEU 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 153 MET Chi-restraints excluded: chain C residue 167 THR 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 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 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 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 261 CYS Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 205 optimal weight: 3.9990 chunk 262 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 39 optimal weight: 30.0000 chunk 343 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 369 optimal weight: 9.9990 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 188 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 239 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.101355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059350 restraints weight = 103079.624| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 4.47 r_work: 0.2780 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 31270 Z= 0.190 Angle : 0.606 12.937 42664 Z= 0.294 Chirality : 0.047 0.530 4905 Planarity : 0.004 0.055 5434 Dihedral : 7.312 101.228 5097 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.22 % Allowed : 19.28 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3740 helix: 1.77 (0.17), residues: 1017 sheet: 0.40 (0.19), residues: 724 loop : -0.82 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 633 HIS 0.006 0.001 HIS E 374 PHE 0.017 0.001 PHE C 800 TYR 0.014 0.001 TYR C1067 ARG 0.003 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 37) link_NAG-ASN : angle 2.95336 ( 111) link_BETA1-4 : bond 0.00438 ( 12) link_BETA1-4 : angle 1.94666 ( 36) hydrogen bonds : bond 0.05476 ( 1151) hydrogen bonds : angle 4.91553 ( 3207) metal coordination : bond 0.01358 ( 2) SS BOND : bond 0.00327 ( 43) SS BOND : angle 1.23638 ( 86) covalent geometry : bond 0.00451 (31176) covalent geometry : angle 0.58321 (42431) *********************** 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 175 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 68 time to evaluate : 3.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8799 (p90) REVERT: A 583 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8528 (pm20) REVERT: A 586 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8631 (m-30) REVERT: A 645 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8930 (p) REVERT: A 675 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8746 (pp30) REVERT: A 995 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8681 (ptp-170) REVERT: B 34 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8095 (mtp85) REVERT: B 153 MET cc_start: 0.5608 (OUTLIER) cc_final: 0.5282 (tpt) REVERT: B 335 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9034 (tm) REVERT: B 591 SER cc_start: 0.9283 (OUTLIER) cc_final: 0.9055 (p) REVERT: B 616 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7642 (t160) REVERT: B 825 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8834 (mmmt) REVERT: C 153 MET cc_start: 0.4763 (OUTLIER) cc_final: 0.4185 (pmt) REVERT: C 324 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: C 1038 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9288 (mmtm) REVERT: E 579 MET cc_start: 0.3168 (mmp) cc_final: 0.2773 (mmp) outliers start: 107 outliers final: 47 residues processed: 161 average time/residue: 1.1219 time to fit residues: 223.7750 Evaluate side-chains 129 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 67 time to evaluate : 3.889 ------------------------------------------------------------------------------- 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 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 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 430 THR 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 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 88 ASP 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 167 THR 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 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 740 MET 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 Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 179 optimal weight: 0.9990 chunk 240 optimal weight: 0.0370 chunk 30 optimal weight: 0.9990 chunk 233 optimal weight: 9.9990 chunk 345 optimal weight: 3.9990 chunk 364 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 369 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.101495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.059869 restraints weight = 103370.147| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.46 r_work: 0.2787 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1891 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 : 0.593 12.540 42664 Z= 0.287 Chirality : 0.046 0.517 4905 Planarity : 0.004 0.065 5434 Dihedral : 7.094 99.833 5097 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.68 % Allowed : 19.61 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3740 helix: 1.86 (0.17), residues: 1016 sheet: 0.46 (0.19), residues: 714 loop : -0.77 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 633 HIS 0.005 0.001 HIS E 374 PHE 0.019 0.001 PHE A 79 TYR 0.015 0.001 TYR C1067 ARG 0.007 0.000 ARG A 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 37) link_NAG-ASN : angle 2.92128 ( 111) link_BETA1-4 : bond 0.00401 ( 12) link_BETA1-4 : angle 1.90255 ( 36) hydrogen bonds : bond 0.05176 ( 1151) hydrogen bonds : angle 4.80393 ( 3207) metal coordination : bond 0.01138 ( 2) SS BOND : bond 0.00245 ( 43) SS BOND : angle 1.17721 ( 86) covalent geometry : bond 0.00373 (31176) covalent geometry : angle 0.57017 (42431) *********************** 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 160 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 71 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8818 (p90) REVERT: A 583 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8534 (pm20) REVERT: A 586 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8585 (m-30) REVERT: A 645 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8977 (p) REVERT: A 675 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8742 (pp30) REVERT: A 995 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8657 (ptp-170) REVERT: B 34 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8174 (mtp85) REVERT: B 153 MET cc_start: 0.5609 (OUTLIER) cc_final: 0.5287 (tpt) REVERT: B 335 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9044 (tm) REVERT: B 591 SER cc_start: 0.9280 (OUTLIER) cc_final: 0.9048 (p) REVERT: B 616 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7579 (t160) REVERT: B 825 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8830 (mmmt) REVERT: C 153 MET cc_start: 0.4780 (pmt) cc_final: 0.4195 (pmt) REVERT: C 1038 LYS cc_start: 0.9541 (OUTLIER) cc_final: 0.9292 (mmtm) REVERT: E 360 MET cc_start: 0.4968 (pmm) cc_final: 0.3118 (ptp) REVERT: E 579 MET cc_start: 0.4260 (mmp) cc_final: 0.3817 (mmp) outliers start: 89 outliers final: 49 residues processed: 148 average time/residue: 1.1318 time to fit residues: 209.0571 Evaluate side-chains 128 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 66 time to evaluate : 3.457 ------------------------------------------------------------------------------- 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 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 900 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 995 ARG 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 41 LYS 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 414 GLN 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 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 130 VAL Chi-restraints excluded: chain C residue 131 CYS 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 515 PHE Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 740 MET 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 Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 226 optimal weight: 20.0000 chunk 178 optimal weight: 0.0370 chunk 277 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 223 optimal weight: 0.7980 chunk 260 optimal weight: 9.9990 chunk 274 optimal weight: 1.9990 chunk 321 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.101385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.061043 restraints weight = 103174.943| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 5.15 r_work: 0.2756 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31270 Z= 0.155 Angle : 0.590 12.924 42664 Z= 0.286 Chirality : 0.046 0.512 4905 Planarity : 0.004 0.056 5434 Dihedral : 6.964 98.574 5097 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.62 % Allowed : 19.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3740 helix: 1.91 (0.17), residues: 1015 sheet: 0.48 (0.19), residues: 714 loop : -0.77 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 633 HIS 0.005 0.001 HIS E 374 PHE 0.017 0.001 PHE B 342 TYR 0.015 0.001 TYR C1067 ARG 0.004 0.000 ARG A 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 37) link_NAG-ASN : angle 2.96739 ( 111) link_BETA1-4 : bond 0.00422 ( 12) link_BETA1-4 : angle 1.89072 ( 36) hydrogen bonds : bond 0.05099 ( 1151) hydrogen bonds : angle 4.75550 ( 3207) metal coordination : bond 0.01038 ( 2) SS BOND : bond 0.00236 ( 43) SS BOND : angle 1.29994 ( 86) covalent geometry : bond 0.00365 (31176) covalent geometry : angle 0.56655 (42431) *********************** 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 158 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 71 time to evaluate : 3.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8770 (p90) REVERT: A 583 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8529 (pm20) REVERT: A 586 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8588 (m-30) REVERT: A 645 THR cc_start: 0.9241 (OUTLIER) cc_final: 0.8983 (p) REVERT: A 675 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8750 (pp30) REVERT: A 995 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8664 (ptp-170) REVERT: B 34 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8190 (mtp85) REVERT: B 153 MET cc_start: 0.5506 (OUTLIER) cc_final: 0.5193 (tpt) REVERT: B 214 ARG cc_start: 0.8453 (ptp-170) cc_final: 0.8176 (pmm-80) REVERT: B 335 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9009 (tm) REVERT: B 591 SER cc_start: 0.9268 (OUTLIER) cc_final: 0.9031 (p) REVERT: B 616 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7637 (t160) REVERT: B 825 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8813 (mmmt) REVERT: C 153 MET cc_start: 0.4742 (pmt) cc_final: 0.4136 (pmt) REVERT: C 324 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8419 (pm20) REVERT: C 787 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8655 (mt0) REVERT: C 1038 LYS cc_start: 0.9555 (OUTLIER) cc_final: 0.9296 (mmtm) REVERT: C 1092 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.8973 (pm20) REVERT: E 163 TRP cc_start: 0.7613 (OUTLIER) cc_final: 0.7156 (p-90) REVERT: E 323 MET cc_start: 0.5647 (tpt) cc_final: 0.3584 (pmm) REVERT: E 360 MET cc_start: 0.4989 (pmm) cc_final: 0.3071 (ptp) REVERT: E 579 MET cc_start: 0.5137 (mmp) cc_final: 0.4777 (mmp) outliers start: 87 outliers final: 51 residues processed: 147 average time/residue: 1.2097 time to fit residues: 220.3208 Evaluate side-chains 137 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 69 time to evaluate : 3.623 ------------------------------------------------------------------------------- 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 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 900 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 995 ARG 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 41 LYS 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 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 88 ASP 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 167 THR 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 515 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 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 163 TRP Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 7.9990 chunk 353 optimal weight: 9.9990 chunk 288 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 330 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 246 optimal weight: 9.9990 chunk 348 optimal weight: 20.0000 chunk 226 optimal weight: 9.9990 chunk 276 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 115 GLN B 121 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 487 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.099189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.057469 restraints weight = 103731.275| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.25 r_work: 0.2728 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 31270 Z= 0.353 Angle : 0.724 17.213 42664 Z= 0.357 Chirality : 0.052 0.646 4905 Planarity : 0.005 0.065 5434 Dihedral : 7.347 92.144 5096 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.01 % Allowed : 19.49 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 3740 helix: 1.65 (0.17), residues: 1033 sheet: 0.26 (0.19), residues: 729 loop : -0.97 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 633 HIS 0.006 0.001 HIS C1064 PHE 0.024 0.002 PHE A 823 TYR 0.040 0.002 TYR B 505 ARG 0.006 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 37) link_NAG-ASN : angle 3.55355 ( 111) link_BETA1-4 : bond 0.00717 ( 12) link_BETA1-4 : angle 2.20957 ( 36) hydrogen bonds : bond 0.06808 ( 1151) hydrogen bonds : angle 5.15899 ( 3207) metal coordination : bond 0.01145 ( 2) SS BOND : bond 0.00333 ( 43) SS BOND : angle 1.55080 ( 86) covalent geometry : bond 0.00844 (31176) covalent geometry : angle 0.69643 (42431) *********************** 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 168 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 68 time to evaluate : 3.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8562 (p90) REVERT: A 583 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8539 (pm20) REVERT: A 586 ASP cc_start: 0.9038 (OUTLIER) cc_final: 0.8591 (m-30) REVERT: A 645 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8846 (p) REVERT: A 675 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8731 (pp30) REVERT: B 34 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8387 (mtp85) REVERT: B 153 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.5135 (tpt) REVERT: B 335 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9056 (tm) REVERT: B 436 TRP cc_start: 0.8111 (t-100) cc_final: 0.7495 (t-100) REVERT: B 616 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7734 (t160) REVERT: C 153 MET cc_start: 0.4832 (OUTLIER) cc_final: 0.4185 (pmt) REVERT: C 324 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8307 (pm20) REVERT: C 787 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8712 (mt0) REVERT: C 1038 LYS cc_start: 0.9546 (OUTLIER) cc_final: 0.9290 (mmtm) REVERT: E 323 MET cc_start: 0.5410 (tpt) cc_final: 0.3537 (pmm) REVERT: E 579 MET cc_start: 0.5818 (mmp) cc_final: 0.5591 (mmp) outliers start: 100 outliers final: 49 residues processed: 157 average time/residue: 1.1479 time to fit residues: 224.7046 Evaluate side-chains 130 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 68 time to evaluate : 3.706 ------------------------------------------------------------------------------- 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 188 ASN Chi-restraints excluded: chain A residue 241 LEU 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 1141 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 41 LYS 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 345 THR 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 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 858 LEU 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 117 LEU 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 167 THR 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 510 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 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 974 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 328 optimal weight: 6.9990 chunk 12 optimal weight: 0.0570 chunk 264 optimal weight: 7.9990 chunk 258 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 329 optimal weight: 20.0000 chunk 281 optimal weight: 0.9990 chunk 322 optimal weight: 2.9990 chunk 356 optimal weight: 50.0000 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 245 HIS ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.099556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.057749 restraints weight = 103279.060| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 4.36 r_work: 0.2755 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 31270 Z= 0.216 Angle : 0.646 17.994 42664 Z= 0.316 Chirality : 0.048 0.602 4905 Planarity : 0.004 0.059 5434 Dihedral : 7.088 89.352 5096 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.32 % Allowed : 19.83 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3740 helix: 1.74 (0.17), residues: 1027 sheet: 0.28 (0.18), residues: 747 loop : -0.94 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 633 HIS 0.005 0.001 HIS B 519 PHE 0.018 0.001 PHE B 342 TYR 0.030 0.001 TYR B 505 ARG 0.005 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 37) link_NAG-ASN : angle 3.43217 ( 111) link_BETA1-4 : bond 0.00538 ( 12) link_BETA1-4 : angle 1.99737 ( 36) hydrogen bonds : bond 0.05738 ( 1151) hydrogen bonds : angle 4.93274 ( 3207) metal coordination : bond 0.01102 ( 2) SS BOND : bond 0.00358 ( 43) SS BOND : angle 1.37800 ( 86) covalent geometry : bond 0.00513 (31176) covalent geometry : angle 0.61795 (42431) *********************** 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 148 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 71 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.8048 (t80) REVERT: A 318 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8571 (p90) REVERT: A 583 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8589 (pm20) REVERT: A 586 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8597 (m-30) REVERT: A 645 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8938 (p) REVERT: A 675 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8709 (pp30) REVERT: B 34 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8375 (mtp85) REVERT: B 153 MET cc_start: 0.5315 (OUTLIER) cc_final: 0.4918 (tpt) REVERT: B 214 ARG cc_start: 0.8351 (ptp-170) cc_final: 0.8145 (pmm-80) REVERT: B 335 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9038 (tm) REVERT: B 436 TRP cc_start: 0.8150 (t-100) cc_final: 0.7544 (t-100) REVERT: B 591 SER cc_start: 0.9227 (OUTLIER) cc_final: 0.8954 (p) REVERT: C 153 MET cc_start: 0.4722 (OUTLIER) cc_final: 0.4051 (pmt) REVERT: C 324 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8316 (pm20) REVERT: C 1038 LYS cc_start: 0.9534 (OUTLIER) cc_final: 0.9284 (mmtm) REVERT: E 163 TRP cc_start: 0.7715 (OUTLIER) cc_final: 0.6842 (p-90) REVERT: E 323 MET cc_start: 0.5540 (tpt) cc_final: 0.3560 (pmm) REVERT: E 360 MET cc_start: 0.4918 (pmm) cc_final: 0.3090 (ptp) outliers start: 77 outliers final: 45 residues processed: 141 average time/residue: 1.1201 time to fit residues: 196.2835 Evaluate side-chains 124 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 65 time to evaluate : 3.324 ------------------------------------------------------------------------------- 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 200 TYR Chi-restraints excluded: chain A residue 241 LEU 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 1141 LEU 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 335 LEU Chi-restraints excluded: chain B residue 430 THR 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 620 VAL Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 858 LEU 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 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 167 THR 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 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 740 MET 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 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 283 VAL Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 305 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 363 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 225 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 256 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 564 GLN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.101269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.059475 restraints weight = 103606.529| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 4.51 r_work: 0.2798 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31270 Z= 0.115 Angle : 0.607 15.482 42664 Z= 0.290 Chirality : 0.046 0.561 4905 Planarity : 0.004 0.060 5434 Dihedral : 6.584 83.974 5096 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.69 % Allowed : 20.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3740 helix: 1.90 (0.17), residues: 1015 sheet: 0.50 (0.19), residues: 711 loop : -0.80 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 633 HIS 0.005 0.001 HIS E 374 PHE 0.017 0.001 PHE C 168 TYR 0.032 0.001 TYR B 505 ARG 0.004 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 37) link_NAG-ASN : angle 3.25221 ( 111) link_BETA1-4 : bond 0.00491 ( 12) link_BETA1-4 : angle 1.87902 ( 36) hydrogen bonds : bond 0.04567 ( 1151) hydrogen bonds : angle 4.66679 ( 3207) metal coordination : bond 0.01212 ( 2) SS BOND : bond 0.00268 ( 43) SS BOND : angle 1.12308 ( 86) covalent geometry : bond 0.00262 (31176) covalent geometry : angle 0.58103 (42431) ********************** 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 129 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 73 time to evaluate : 3.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.8073 (t80) REVERT: A 318 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8769 (p90) REVERT: A 583 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8592 (pm20) REVERT: A 586 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8592 (m-30) REVERT: A 645 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.9009 (p) REVERT: A 675 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8747 (pp30) REVERT: B 153 MET cc_start: 0.5273 (OUTLIER) cc_final: 0.5014 (tpt) REVERT: B 335 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9116 (tm) REVERT: B 402 ILE cc_start: 0.7349 (OUTLIER) cc_final: 0.6826 (tt) REVERT: B 436 TRP cc_start: 0.8036 (t-100) cc_final: 0.7505 (t-100) REVERT: B 591 SER cc_start: 0.9239 (OUTLIER) cc_final: 0.8992 (p) REVERT: C 153 MET cc_start: 0.4751 (pmt) cc_final: 0.4083 (pmt) REVERT: C 1038 LYS cc_start: 0.9548 (OUTLIER) cc_final: 0.9294 (mmtm) REVERT: E 163 TRP cc_start: 0.7577 (OUTLIER) cc_final: 0.6853 (p-90) REVERT: E 323 MET cc_start: 0.6104 (tpt) cc_final: 0.3889 (pmm) REVERT: E 360 MET cc_start: 0.4687 (pmm) cc_final: 0.2960 (ptp) REVERT: E 579 MET cc_start: 0.4322 (mmp) cc_final: 0.3150 (tpt) outliers start: 56 outliers final: 38 residues processed: 126 average time/residue: 1.2556 time to fit residues: 196.8168 Evaluate side-chains 117 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 67 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 318 PHE 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 208 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 576 VAL 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 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 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 640 SER 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 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 438 PHE Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 212 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 74 optimal weight: 0.0870 chunk 363 optimal weight: 20.0000 chunk 239 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 186 optimal weight: 0.6980 chunk 195 optimal weight: 4.9990 chunk 241 optimal weight: 6.9990 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.099757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.058318 restraints weight = 103588.586| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 4.40 r_work: 0.2763 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 31270 Z= 0.193 Angle : 0.632 15.837 42664 Z= 0.306 Chirality : 0.047 0.560 4905 Planarity : 0.004 0.058 5434 Dihedral : 6.629 78.026 5096 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.84 % Allowed : 20.55 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3740 helix: 1.89 (0.17), residues: 1028 sheet: 0.42 (0.19), residues: 724 loop : -0.86 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 633 HIS 0.005 0.001 HIS E 374 PHE 0.019 0.001 PHE B 342 TYR 0.030 0.001 TYR B 505 ARG 0.003 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 37) link_NAG-ASN : angle 3.20142 ( 111) link_BETA1-4 : bond 0.00465 ( 12) link_BETA1-4 : angle 1.90860 ( 36) hydrogen bonds : bond 0.05327 ( 1151) hydrogen bonds : angle 4.75674 ( 3207) metal coordination : bond 0.01133 ( 2) SS BOND : bond 0.00265 ( 43) SS BOND : angle 1.23866 ( 86) covalent geometry : bond 0.00457 (31176) covalent geometry : angle 0.60736 (42431) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33484.31 seconds wall clock time: 571 minutes 3.56 seconds (34263.56 seconds total)