Starting phenix.real_space_refine on Tue Jun 24 20:52:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g77_29799/06_2025/8g77_29799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g77_29799/06_2025/8g77_29799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g77_29799/06_2025/8g77_29799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g77_29799/06_2025/8g77_29799.map" model { file = "/net/cci-nas-00/data/ceres_data/8g77_29799/06_2025/8g77_29799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g77_29799/06_2025/8g77_29799.cif" } resolution = 2.8 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 18372 2.51 5 N 4777 2.21 5 O 5667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 1.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28942 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8447 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 58, 'TRANS': 1023} Chain breaks: 4 Chain: "B" Number of atoms: 8483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8483 Classifications: {'peptide': 1086} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 4 Chain: "D" Number of atoms: 8480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8480 Classifications: {'peptide': 1086} Link IDs: {'PTRANS': 59, 'TRANS': 1026} Chain breaks: 4 Chain: "G" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "K" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 195 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 15 Chain: "D" 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 Time building chain proxies: 17.08, per 1000 atoms: 0.59 Number of scatterers: 28942 At special positions: 0 Unit cell: (162.901, 169.099, 177.067, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 5667 8.00 N 4777 7.00 C 18372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=1.38 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=2.05 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 D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 94 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 94 " 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=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 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 Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A1134 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 74 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A 603 " " NAG A1312 " - " ASN A 122 " " NAG A1313 " - " ASN A 234 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 17 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 74 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 282 " " NAG B1314 " - " ASN B 122 " " NAG C 1 " - " ASN A 801 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 282 " " NAG D1304 " - " ASN D 331 " " NAG D1305 " - " ASN D 616 " " NAG D1306 " - " ASN D 657 " " NAG D1307 " - " ASN D 709 " " NAG D1308 " - " ASN D1074 " " NAG D1309 " - " ASN D 17 " " NAG D1310 " - " ASN D 165 " " NAG D1311 " - " ASN D 343 " " NAG D1312 " - " ASN D 603 " " NAG E 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN A 717 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN D 717 " " NAG N 1 " - " ASN D 801 " " NAG O 1 " - " ASN D1098 " " NAG P 1 " - " ASN D1134 " " NAG Q 1 " - " ASN A 17 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.15 Conformation dependent library (CDL) restraints added in 3.4 seconds 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6682 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 61 sheets defined 22.7% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.994A pdb=" N ALA A 260 " --> pdb=" O GLY A 257 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 261 " --> pdb=" O TRP A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 261' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.433A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.242A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.584A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.725A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.583A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.888A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.598A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.552A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 984 removed outlier: 3.500A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.149A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.589A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.452A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.965A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.679A 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 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.979A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 4.301A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.674A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 4.392A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.061A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.610A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.877A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.021A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.166A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 344 removed outlier: 3.893A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 371 removed outlier: 4.361A pdb=" N LEU D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 Processing helix chain 'D' and resid 404 through 411 removed outlier: 3.504A pdb=" N VAL D 407 " --> pdb=" O GLY D 404 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 619 through 623 Processing helix chain 'D' and resid 737 through 744 Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.611A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.673A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 909 Processing helix chain 'D' and resid 912 through 919 removed outlier: 4.051A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.957A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.208A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D1033 " --> pdb=" O MET D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 3.703A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 89 Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'K' and resid 85 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.041A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.698A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.743A pdb=" N PHE A 43 " --> pdb=" O ARG D 567 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU D 324 " --> pdb=" O ASN D 540 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASN D 542 " --> pdb=" O GLU D 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.552A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.680A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.178A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.861A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.777A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.008A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.582A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AB3, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.225A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.041A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.593A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 714 through 715 removed outlier: 3.769A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.947A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC2, first strand: chain 'A' and resid 1076 through 1078 removed outlier: 3.842A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC4, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.116A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.730A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.718A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.854A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.982A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AD2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.666A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.670A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD6, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.788A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.175A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.902A pdb=" N ALA B 701 " --> pdb=" O ILE D 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.694A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.967A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.453A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.304A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 27 through 30 removed outlier: 4.365A pdb=" N ALA D 27 " --> pdb=" O TRP D 64 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N HIS D 207 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N ALA D 222 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.522A pdb=" N VAL D 47 " --> pdb=" O TYR D 279 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 68 through 69 removed outlier: 4.047A pdb=" N ARG D 78 " --> pdb=" O HIS D 69 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 84 through 85 removed outlier: 12.736A pdb=" N PHE D 135 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 12.414A pdb=" N THR D 240 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N ASN D 137 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N LEU D 242 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU D 244 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 10.589A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE D 140 " --> pdb=" O ARG D 158 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 158 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 154 " --> pdb=" O TYR D 144 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.552A pdb=" N ILE D 105 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.308A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR D 612 " --> pdb=" O CYS D 649 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE D 643 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AF2, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AF3, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.152A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.540A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 718 through 728 removed outlier: 5.895A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.532A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.669A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AF9, first strand: chain 'G' and resid 18 through 22 removed outlier: 3.597A pdb=" N LEU G 20 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL G 77 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 44 through 51 removed outlier: 5.671A pdb=" N LEU G 46 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ARG G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY G 34 " --> pdb=" O HIS G 95 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS G 95 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 90 through 92 removed outlier: 3.686A pdb=" N VAL G 114 " --> pdb=" O ALA G 90 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 19 through 21 Processing sheet with id=AG4, first strand: chain 'F' and resid 32 through 37 removed outlier: 3.627A pdb=" N ALA F 48 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU F 46 " --> pdb=" O ARG F 37 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 90 through 92 removed outlier: 3.677A pdb=" N ALA F 90 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL F 114 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 18 through 20 removed outlier: 3.917A pdb=" N LEU K 20 " --> pdb=" O LEU K 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU K 79 " --> pdb=" O LEU K 20 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 56 through 58 removed outlier: 5.821A pdb=" N LEU K 46 " --> pdb=" O ARG K 37 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE K 50 " --> pdb=" O MET K 33 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA K 90 " --> pdb=" O VAL K 114 " (cutoff:3.500A) 1034 hydrogen bonds defined for protein. 2802 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: 13.14 Time building geometry restraints manager: 8.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.19: 4 1.19 - 1.36: 9333 1.36 - 1.54: 19650 1.54 - 1.71: 461 1.71 - 1.89: 162 Bond restraints: 29610 Sorted by residual: bond pdb=" CG PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 1.503 1.017 0.486 3.40e-02 8.65e+02 2.05e+02 bond pdb=" C1 NAG B1311 " pdb=" O5 NAG B1311 " ideal model delta sigma weight residual 1.406 1.623 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C1 NAG D1312 " pdb=" O5 NAG D1312 " ideal model delta sigma weight residual 1.406 1.571 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.15e+01 bond pdb=" CG ASN D 603 " pdb=" OD1 ASN D 603 " ideal model delta sigma weight residual 1.231 1.130 0.101 1.90e-02 2.77e+03 2.82e+01 ... (remaining 29605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.84: 40292 11.84 - 23.67: 7 23.67 - 35.51: 1 35.51 - 47.34: 1 47.34 - 59.18: 1 Bond angle restraints: 40302 Sorted by residual: angle pdb=" CB ASN B 74 " pdb=" CG ASN B 74 " pdb=" ND2 ASN B 74 " ideal model delta sigma weight residual 116.40 70.42 45.98 1.50e+00 4.44e-01 9.40e+02 angle pdb=" CB ASN B 74 " pdb=" CG ASN B 74 " pdb=" OD1 ASN B 74 " ideal model delta sigma weight residual 120.80 179.98 -59.18 2.00e+00 2.50e-01 8.75e+02 angle pdb=" N PRO A 330 " pdb=" CD PRO A 330 " pdb=" CG PRO A 330 " ideal model delta sigma weight residual 103.20 73.13 30.07 1.50e+00 4.44e-01 4.02e+02 angle pdb=" OD1 ASN B 74 " pdb=" CG ASN B 74 " pdb=" ND2 ASN B 74 " ideal model delta sigma weight residual 122.60 109.60 13.00 1.00e+00 1.00e+00 1.69e+02 angle pdb=" CA PRO A 330 " pdb=" CB PRO A 330 " pdb=" CG PRO A 330 " ideal model delta sigma weight residual 104.50 81.12 23.38 1.90e+00 2.77e-01 1.51e+02 ... (remaining 40297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.30: 17248 25.30 - 50.59: 964 50.59 - 75.89: 139 75.89 - 101.18: 16 101.18 - 126.48: 1 Dihedral angle restraints: 18368 sinusoidal: 7931 harmonic: 10437 Sorted by residual: dihedral pdb=" CA VAL D1133 " pdb=" C VAL D1133 " pdb=" N ASN D1134 " pdb=" CA ASN D1134 " ideal model delta harmonic sigma weight residual -180.00 -133.22 -46.78 0 5.00e+00 4.00e-02 8.75e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 19.74 73.26 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CA THR D 602 " pdb=" C THR D 602 " pdb=" N ASN D 603 " pdb=" CA ASN D 603 " ideal model delta harmonic sigma weight residual 180.00 139.58 40.42 0 5.00e+00 4.00e-02 6.53e+01 ... (remaining 18365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 4646 0.133 - 0.266: 46 0.266 - 0.398: 7 0.398 - 0.531: 2 0.531 - 0.664: 2 Chirality restraints: 4703 Sorted by residual: chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA ASN D 603 " pdb=" N ASN D 603 " pdb=" C ASN D 603 " pdb=" CB ASN D 603 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C1 NAG A1313 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1313 " pdb=" O5 NAG A1313 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.99e+00 ... (remaining 4700 not shown) Planarity restraints: 5203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 74 " -0.082 2.00e-02 2.50e+03 1.05e-01 1.37e+02 pdb=" CG ASN B 74 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B 74 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN B 74 " 0.187 2.00e-02 2.50e+03 pdb=" C1 NAG B1311 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 74 " 0.004 2.00e-02 2.50e+03 5.89e-02 4.33e+01 pdb=" CG ASN A 74 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN A 74 " 0.066 2.00e-02 2.50e+03 pdb=" ND2 ASN A 74 " -0.076 2.00e-02 2.50e+03 pdb=" C1 NAG A1309 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 891 " -0.099 5.00e-02 4.00e+02 1.39e-01 3.08e+01 pdb=" N PRO B 892 " 0.239 5.00e-02 4.00e+02 pdb=" CA PRO B 892 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO B 892 " -0.070 5.00e-02 4.00e+02 ... (remaining 5200 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 64 2.35 - 2.99: 15367 2.99 - 3.63: 39880 3.63 - 4.26: 63472 4.26 - 4.90: 108360 Nonbonded interactions: 227143 Sorted by model distance: nonbonded pdb=" CE1 PHE A 342 " pdb=" CG1 VAL A 511 " model vdw 1.714 3.760 nonbonded pdb=" O ASN B 87 " pdb=" OD1 ASN B 87 " model vdw 1.986 3.040 nonbonded pdb=" NZ LYS D 776 " pdb=" OE2 GLU D 780 " model vdw 2.027 3.120 nonbonded pdb=" OD1 ASN D1134 " pdb=" N2 NAG P 1 " model vdw 2.029 3.120 nonbonded pdb=" OG1 THR D 618 " pdb=" OE1 GLU D 619 " model vdw 2.037 3.040 ... (remaining 227138 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 178 or resid 184 through 1147 or resid 1301 thr \ ough 1308 or (resid 1309 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O5 or name O6 o \ r name O7 )) or resid 1310 through 1312)) selection = (chain 'B' and (resid 14 through 178 or resid 184 through 624 or resid 634 throu \ gh 676 or resid 690 through 827 or resid 855 through 1147 or resid 1301 through \ 1312)) selection = (chain 'D' and (resid 14 through 624 or resid 634 through 676 or resid 690 throu \ gh 827 or resid 855 through 1147 or resid 1301 through 1308 or (resid 1309 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or nam \ e C8 or name N2 or name O3 or name O5 or name O6 or name O7 )) or resid 1310 thr \ ough 1312)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.180 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 66.230 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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 : 0.007 0.656 29716 Z= 0.361 Angle : 0.949 59.177 40573 Z= 0.482 Chirality : 0.053 0.664 4703 Planarity : 0.006 0.139 5153 Dihedral : 14.505 126.478 11554 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.77 % Rotamer: Outliers : 1.28 % Allowed : 19.41 % Favored : 79.32 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.74 (0.14), residues: 3572 helix: 1.83 (0.20), residues: 708 sheet: -0.41 (0.17), residues: 871 loop : -1.44 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP D 258 HIS 0.036 0.002 HIS D 245 PHE 0.042 0.002 PHE A1075 TYR 0.043 0.002 TYR D 160 ARG 0.017 0.001 ARG D 346 Details of bonding type rmsd link_NAG-ASN : bond 0.03535 ( 50) link_NAG-ASN : angle 5.42309 ( 150) link_BETA1-4 : bond 0.00879 ( 11) link_BETA1-4 : angle 2.16822 ( 33) hydrogen bonds : bond 0.20782 ( 1028) hydrogen bonds : angle 8.04376 ( 2802) SS BOND : bond 0.09892 ( 44) SS BOND : angle 4.89781 ( 88) covalent geometry : bond 0.00571 (29610) covalent geometry : angle 0.86054 (40302) Misc. bond : bond 0.28620 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.4216 (mmm) cc_final: 0.1871 (tmm) REVERT: B 197 ILE cc_start: 0.6889 (OUTLIER) cc_final: 0.6577 (tt) REVERT: D 133 PHE cc_start: 0.7296 (m-80) cc_final: 0.7045 (m-80) REVERT: D 934 ILE cc_start: 0.6915 (OUTLIER) cc_final: 0.6708 (tp) outliers start: 40 outliers final: 24 residues processed: 277 average time/residue: 1.0407 time to fit residues: 356.5545 Evaluate side-chains 250 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 555 SER Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain K residue 29 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 150 optimal weight: 20.0000 chunk 92 optimal weight: 0.1980 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 279 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 324 optimal weight: 0.7980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 137 ASN A 580 GLN A 690 GLN A 914 ASN A1083 HIS A1101 HIS A1106 GLN B 30 ASN B 87 ASN B 99 ASN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1125 ASN D 69 HIS ** D 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN D 675 GLN D1010 GLN G 97 GLN K 71 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.217947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165975 restraints weight = 31148.289| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.33 r_work: 0.3287 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29716 Z= 0.142 Angle : 0.685 14.261 40573 Z= 0.339 Chirality : 0.049 0.498 4703 Planarity : 0.005 0.059 5153 Dihedral : 7.460 109.619 5196 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.12 % Favored : 95.77 % Rotamer: Outliers : 3.84 % Allowed : 16.30 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3572 helix: 2.12 (0.20), residues: 686 sheet: -0.15 (0.17), residues: 860 loop : -1.48 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 258 HIS 0.009 0.001 HIS B 245 PHE 0.015 0.001 PHE A 497 TYR 0.023 0.001 TYR B1067 ARG 0.014 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 50) link_NAG-ASN : angle 3.64156 ( 150) link_BETA1-4 : bond 0.00573 ( 11) link_BETA1-4 : angle 1.69403 ( 33) hydrogen bonds : bond 0.05968 ( 1028) hydrogen bonds : angle 5.94466 ( 2802) SS BOND : bond 0.00466 ( 44) SS BOND : angle 1.35443 ( 88) covalent geometry : bond 0.00318 (29610) covalent geometry : angle 0.64556 (40302) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 244 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6797 (pp) REVERT: A 231 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7614 (pp) REVERT: A 619 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: A 690 GLN cc_start: 0.4160 (OUTLIER) cc_final: 0.3941 (mp10) REVERT: A 994 ASP cc_start: 0.8164 (m-30) cc_final: 0.7734 (m-30) REVERT: B 29 THR cc_start: 0.7824 (t) cc_final: 0.7546 (m) REVERT: B 153 MET cc_start: 0.3608 (mmm) cc_final: 0.0981 (tmm) REVERT: B 206 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8000 (ttmt) REVERT: B 224 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: B 675 GLN cc_start: 0.7097 (pp30) cc_final: 0.6072 (mt0) REVERT: B 856 ASN cc_start: 0.7412 (OUTLIER) cc_final: 0.7206 (m110) REVERT: B 994 ASP cc_start: 0.8192 (m-30) cc_final: 0.7971 (m-30) REVERT: D 52 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8310 (tp-100) REVERT: D 133 PHE cc_start: 0.7213 (m-80) cc_final: 0.6121 (m-80) REVERT: D 144 TYR cc_start: 0.4985 (m-10) cc_final: 0.4667 (m-10) REVERT: D 456 PHE cc_start: 0.3215 (OUTLIER) cc_final: 0.2977 (p90) REVERT: D 787 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8227 (mt0) REVERT: G 33 MET cc_start: 0.5041 (tpt) cc_final: 0.3984 (ttt) REVERT: F 5 GLN cc_start: 0.7474 (mm110) cc_final: 0.7272 (mm-40) outliers start: 120 outliers final: 47 residues processed: 340 average time/residue: 0.9407 time to fit residues: 402.2975 Evaluate side-chains 272 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 216 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 555 SER Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain D residue 1123 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain K residue 66 PHE Chi-restraints excluded: chain K residue 91 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 332 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 388 ASN A 690 GLN A1010 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 99 ASN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN D 81 ASN ** D 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN D1010 GLN D1119 ASN G 3 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.210888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.159554 restraints weight = 31110.172| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.34 r_work: 0.3190 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 29716 Z= 0.299 Angle : 0.840 13.567 40573 Z= 0.419 Chirality : 0.056 0.487 4703 Planarity : 0.006 0.054 5153 Dihedral : 7.401 107.791 5174 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.01 % Favored : 94.85 % Rotamer: Outliers : 5.21 % Allowed : 16.18 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 3572 helix: 1.45 (0.20), residues: 689 sheet: -0.37 (0.17), residues: 862 loop : -1.64 (0.12), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 353 HIS 0.011 0.002 HIS B 245 PHE 0.028 0.003 PHE A 643 TYR 0.034 0.002 TYR G 105 ARG 0.007 0.001 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 50) link_NAG-ASN : angle 3.95251 ( 150) link_BETA1-4 : bond 0.00566 ( 11) link_BETA1-4 : angle 2.00244 ( 33) hydrogen bonds : bond 0.08669 ( 1028) hydrogen bonds : angle 5.86979 ( 2802) SS BOND : bond 0.00647 ( 44) SS BOND : angle 2.14278 ( 88) covalent geometry : bond 0.00749 (29610) covalent geometry : angle 0.79896 (40302) Misc. bond : bond 0.00116 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 232 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8474 (pp) REVERT: A 197 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6802 (pp) REVERT: A 231 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7616 (pp) REVERT: A 245 HIS cc_start: 0.7038 (t70) cc_final: 0.6464 (m170) REVERT: A 330 PRO cc_start: 0.7401 (Cg_exo) cc_final: 0.7194 (Cg_endo) REVERT: A 619 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: A 787 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8451 (mt0) REVERT: A 1129 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7818 (t) REVERT: B 29 THR cc_start: 0.8063 (t) cc_final: 0.7653 (m) REVERT: B 74 ASN cc_start: 0.2087 (OUTLIER) cc_final: 0.1594 (m-40) REVERT: B 80 ASP cc_start: 0.5949 (t0) cc_final: 0.5459 (t0) REVERT: B 153 MET cc_start: 0.3669 (mmm) cc_final: 0.1134 (tmm) REVERT: B 197 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6754 (pt) REVERT: B 206 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8209 (ttmt) REVERT: B 216 LEU cc_start: 0.5660 (OUTLIER) cc_final: 0.5070 (pt) REVERT: B 224 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8258 (mt-10) REVERT: B 558 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7669 (mptt) REVERT: B 580 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.6712 (mp10) REVERT: B 675 GLN cc_start: 0.7064 (pp30) cc_final: 0.6032 (mt0) REVERT: B 740 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.7756 (tmm) REVERT: B 856 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.7464 (m110) REVERT: B 950 ASP cc_start: 0.8201 (m-30) cc_final: 0.7989 (m-30) REVERT: B 1111 GLU cc_start: 0.7995 (pp20) cc_final: 0.7758 (pp20) REVERT: D 80 ASP cc_start: 0.6411 (t0) cc_final: 0.6133 (t0) REVERT: D 133 PHE cc_start: 0.7606 (m-80) cc_final: 0.6476 (m-80) REVERT: D 153 MET cc_start: 0.6320 (mmt) cc_final: 0.5586 (mmm) REVERT: D 154 GLU cc_start: 0.4569 (OUTLIER) cc_final: 0.4217 (mm-30) REVERT: D 395 VAL cc_start: 0.8394 (t) cc_final: 0.7813 (p) REVERT: D 556 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7081 (m110) REVERT: D 619 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: D 787 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8307 (mt0) REVERT: D 931 ILE cc_start: 0.8444 (mt) cc_final: 0.8097 (mm) REVERT: D 1045 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7633 (tmtt) REVERT: D 1077 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.9070 (p) REVERT: D 1125 ASN cc_start: 0.7404 (t0) cc_final: 0.7142 (t0) REVERT: G 33 MET cc_start: 0.5195 (tpt) cc_final: 0.4354 (ttt) REVERT: G 81 MET cc_start: -0.0009 (OUTLIER) cc_final: -0.0392 (ttt) REVERT: G 106 ASP cc_start: 0.5089 (p0) cc_final: 0.4601 (p0) REVERT: F 5 GLN cc_start: 0.7731 (mm110) cc_final: 0.7273 (mm110) REVERT: K 81 MET cc_start: 0.2873 (tpp) cc_final: 0.2462 (tmm) outliers start: 163 outliers final: 82 residues processed: 366 average time/residue: 1.0332 time to fit residues: 469.5848 Evaluate side-chains 312 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 209 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 555 SER Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 790 LYS Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1045 LYS Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 66 PHE Chi-restraints excluded: chain K residue 91 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 2 optimal weight: 0.7980 chunk 319 optimal weight: 0.5980 chunk 329 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 185 optimal weight: 0.9980 chunk 268 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 293 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 314 GLN A 394 ASN A 613 GLN A1101 HIS A1106 GLN B 99 ASN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1010 GLN D 245 HIS D1010 GLN D1083 HIS D1101 HIS D1119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.214678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.163300 restraints weight = 31232.563| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.37 r_work: 0.3268 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29716 Z= 0.133 Angle : 0.653 11.856 40573 Z= 0.323 Chirality : 0.047 0.422 4703 Planarity : 0.004 0.051 5153 Dihedral : 6.645 108.842 5174 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.58 % Favored : 96.30 % Rotamer: Outliers : 4.60 % Allowed : 17.42 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3572 helix: 1.83 (0.20), residues: 690 sheet: -0.24 (0.17), residues: 850 loop : -1.53 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 633 HIS 0.017 0.001 HIS B 245 PHE 0.015 0.001 PHE D 456 TYR 0.028 0.001 TYR K 105 ARG 0.005 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 50) link_NAG-ASN : angle 3.51450 ( 150) link_BETA1-4 : bond 0.00538 ( 11) link_BETA1-4 : angle 1.66148 ( 33) hydrogen bonds : bond 0.05988 ( 1028) hydrogen bonds : angle 5.55212 ( 2802) SS BOND : bond 0.00496 ( 44) SS BOND : angle 1.46922 ( 88) covalent geometry : bond 0.00301 (29610) covalent geometry : angle 0.61365 (40302) Misc. bond : bond 0.00201 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 239 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8378 (pp) REVERT: A 197 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6787 (pp) REVERT: A 231 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7519 (pp) REVERT: A 245 HIS cc_start: 0.6916 (t70) cc_final: 0.6465 (m170) REVERT: A 281 GLU cc_start: 0.7586 (pm20) cc_final: 0.7384 (pm20) REVERT: A 330 PRO cc_start: 0.7222 (Cg_exo) cc_final: 0.7000 (Cg_endo) REVERT: A 576 VAL cc_start: 0.8790 (m) cc_final: 0.8566 (p) REVERT: A 585 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6994 (mt) REVERT: A 613 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8580 (mt0) REVERT: A 1129 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7949 (t) REVERT: B 29 THR cc_start: 0.7985 (t) cc_final: 0.7735 (m) REVERT: B 74 ASN cc_start: 0.1857 (OUTLIER) cc_final: 0.1234 (m-40) REVERT: B 80 ASP cc_start: 0.5822 (t0) cc_final: 0.5354 (t0) REVERT: B 153 MET cc_start: 0.3989 (mmm) cc_final: 0.1449 (tmm) REVERT: B 224 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: B 558 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7630 (mptt) REVERT: B 580 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.6656 (mp10) REVERT: B 675 GLN cc_start: 0.6940 (pp30) cc_final: 0.5978 (mt0) REVERT: B 856 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7562 (m110) REVERT: B 1111 GLU cc_start: 0.8036 (pp20) cc_final: 0.7716 (pp20) REVERT: D 80 ASP cc_start: 0.6361 (t0) cc_final: 0.6108 (t0) REVERT: D 96 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8050 (pt0) REVERT: D 133 PHE cc_start: 0.7546 (m-80) cc_final: 0.6520 (m-80) REVERT: D 224 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: D 456 PHE cc_start: 0.3628 (OUTLIER) cc_final: 0.3153 (p90) REVERT: D 620 VAL cc_start: 0.7241 (OUTLIER) cc_final: 0.6965 (m) REVERT: D 787 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8238 (mt0) REVERT: D 1077 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9014 (p) REVERT: D 1119 ASN cc_start: 0.8429 (m-40) cc_final: 0.8091 (m110) REVERT: G 33 MET cc_start: 0.5137 (tpt) cc_final: 0.4259 (ttt) REVERT: G 55 ASP cc_start: 0.4970 (OUTLIER) cc_final: 0.4406 (m-30) REVERT: G 106 ASP cc_start: 0.4786 (p0) cc_final: 0.4395 (p0) REVERT: F 5 GLN cc_start: 0.7676 (mm110) cc_final: 0.7261 (mm-40) REVERT: K 20 LEU cc_start: -0.0096 (OUTLIER) cc_final: -0.0785 (mt) REVERT: K 81 MET cc_start: 0.2893 (tpp) cc_final: 0.2458 (tmm) outliers start: 144 outliers final: 69 residues processed: 350 average time/residue: 1.0322 time to fit residues: 447.4267 Evaluate side-chains 301 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 214 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 555 SER Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 66 PHE Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 108 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 314 optimal weight: 0.8980 chunk 104 optimal weight: 0.0570 chunk 69 optimal weight: 1.9990 chunk 326 optimal weight: 0.9980 chunk 290 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 394 ASN A 540 ASN A 613 GLN A1101 HIS A1119 ASN B 99 ASN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN D1010 GLN D1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.213625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.162143 restraints weight = 31043.202| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.37 r_work: 0.3248 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29716 Z= 0.149 Angle : 0.658 11.476 40573 Z= 0.325 Chirality : 0.048 0.407 4703 Planarity : 0.004 0.054 5153 Dihedral : 6.378 107.874 5174 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.42 % Favored : 95.46 % Rotamer: Outliers : 4.92 % Allowed : 17.49 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3572 helix: 1.88 (0.20), residues: 692 sheet: -0.22 (0.17), residues: 851 loop : -1.52 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 353 HIS 0.019 0.001 HIS B 245 PHE 0.015 0.002 PHE A 643 TYR 0.027 0.001 TYR G 105 ARG 0.008 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 50) link_NAG-ASN : angle 3.39718 ( 150) link_BETA1-4 : bond 0.00539 ( 11) link_BETA1-4 : angle 1.63958 ( 33) hydrogen bonds : bond 0.06242 ( 1028) hydrogen bonds : angle 5.47174 ( 2802) SS BOND : bond 0.00526 ( 44) SS BOND : angle 1.50082 ( 88) covalent geometry : bond 0.00352 (29610) covalent geometry : angle 0.62122 (40302) Misc. bond : bond 0.00398 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 223 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8353 (pp) REVERT: A 197 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6788 (pp) REVERT: A 224 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: A 231 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7537 (pp) REVERT: A 245 HIS cc_start: 0.6958 (t70) cc_final: 0.6519 (OUTLIER) REVERT: A 281 GLU cc_start: 0.7674 (pm20) cc_final: 0.7411 (pm20) REVERT: A 787 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8459 (mt0) REVERT: A 1068 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8682 (t) REVERT: A 1119 ASN cc_start: 0.8530 (m-40) cc_final: 0.7898 (m110) REVERT: A 1129 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7934 (t) REVERT: B 29 THR cc_start: 0.8042 (t) cc_final: 0.7795 (m) REVERT: B 74 ASN cc_start: 0.2226 (OUTLIER) cc_final: 0.1564 (m-40) REVERT: B 80 ASP cc_start: 0.5919 (t0) cc_final: 0.5655 (t0) REVERT: B 153 MET cc_start: 0.3755 (mmm) cc_final: 0.1319 (tmm) REVERT: B 224 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8238 (mt-10) REVERT: B 529 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7763 (ttpp) REVERT: B 580 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.6667 (mp10) REVERT: B 675 GLN cc_start: 0.6972 (pp30) cc_final: 0.6021 (mt0) REVERT: B 740 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.7791 (tmm) REVERT: B 856 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7557 (m110) REVERT: B 994 ASP cc_start: 0.8352 (m-30) cc_final: 0.8067 (m-30) REVERT: B 1038 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8587 (ttmm) REVERT: B 1111 GLU cc_start: 0.8094 (pp20) cc_final: 0.7680 (pp20) REVERT: D 80 ASP cc_start: 0.6513 (t0) cc_final: 0.6256 (t0) REVERT: D 96 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: D 133 PHE cc_start: 0.7576 (m-80) cc_final: 0.6515 (m-80) REVERT: D 787 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: D 1077 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9011 (p) REVERT: G 33 MET cc_start: 0.5217 (tpt) cc_final: 0.4487 (ttt) REVERT: G 81 MET cc_start: 0.2280 (ttt) cc_final: 0.0632 (ptt) REVERT: G 106 ASP cc_start: 0.4890 (p0) cc_final: 0.4500 (p0) REVERT: F 5 GLN cc_start: 0.7800 (mm110) cc_final: 0.7377 (mm110) REVERT: K 81 MET cc_start: 0.2830 (tpp) cc_final: 0.2393 (tmm) outliers start: 154 outliers final: 87 residues processed: 345 average time/residue: 1.0070 time to fit residues: 438.2481 Evaluate side-chains 317 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 214 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 555 SER Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 66 PHE Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 108 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 242 optimal weight: 5.9990 chunk 104 optimal weight: 0.0870 chunk 221 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 290 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 394 ASN A 540 ASN A1125 ASN B 99 ASN B 137 ASN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN D1010 GLN D1101 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.211360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.159775 restraints weight = 31078.029| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.39 r_work: 0.3213 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 29716 Z= 0.201 Angle : 0.707 12.116 40573 Z= 0.352 Chirality : 0.050 0.424 4703 Planarity : 0.005 0.059 5153 Dihedral : 6.421 107.716 5173 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % Rotamer: Outliers : 4.99 % Allowed : 18.06 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3572 helix: 1.72 (0.20), residues: 692 sheet: -0.33 (0.17), residues: 869 loop : -1.56 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 353 HIS 0.021 0.001 HIS B 245 PHE 0.020 0.002 PHE A 643 TYR 0.032 0.002 TYR G 105 ARG 0.004 0.001 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 50) link_NAG-ASN : angle 3.44911 ( 150) link_BETA1-4 : bond 0.00567 ( 11) link_BETA1-4 : angle 1.68289 ( 33) hydrogen bonds : bond 0.07149 ( 1028) hydrogen bonds : angle 5.52688 ( 2802) SS BOND : bond 0.00556 ( 44) SS BOND : angle 1.64301 ( 88) covalent geometry : bond 0.00495 (29610) covalent geometry : angle 0.67092 (40302) Misc. bond : bond 0.00148 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 223 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8427 (pp) REVERT: A 197 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6831 (pp) REVERT: A 224 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: A 231 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7634 (pp) REVERT: A 245 HIS cc_start: 0.7144 (t70) cc_final: 0.6644 (OUTLIER) REVERT: A 740 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.7742 (tmm) REVERT: A 787 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8463 (mt0) REVERT: A 1129 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7902 (t) REVERT: B 29 THR cc_start: 0.8075 (t) cc_final: 0.7842 (m) REVERT: B 74 ASN cc_start: 0.2048 (OUTLIER) cc_final: 0.1195 (p0) REVERT: B 80 ASP cc_start: 0.6240 (t0) cc_final: 0.5851 (t0) REVERT: B 153 MET cc_start: 0.3745 (mmm) cc_final: 0.1158 (tmm) REVERT: B 197 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6717 (pt) REVERT: B 224 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8223 (mt-10) REVERT: B 529 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7730 (ttpp) REVERT: B 558 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7644 (mppt) REVERT: B 580 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.6637 (mp10) REVERT: B 675 GLN cc_start: 0.6842 (pp30) cc_final: 0.6509 (pt0) REVERT: B 740 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.7803 (tmm) REVERT: B 856 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7642 (m110) REVERT: B 1038 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8530 (ttmm) REVERT: B 1111 GLU cc_start: 0.8158 (pp20) cc_final: 0.7797 (pp20) REVERT: B 1141 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6191 (tp) REVERT: D 80 ASP cc_start: 0.6550 (t0) cc_final: 0.6284 (t0) REVERT: D 96 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8096 (pt0) REVERT: D 133 PHE cc_start: 0.7640 (m-80) cc_final: 0.6617 (m-80) REVERT: D 144 TYR cc_start: 0.5224 (m-80) cc_final: 0.4856 (m-80) REVERT: D 197 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.6547 (mp) REVERT: D 456 PHE cc_start: 0.3832 (OUTLIER) cc_final: 0.3264 (p90) REVERT: D 619 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: D 787 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8346 (mt0) REVERT: D 1045 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7714 (tmtt) REVERT: D 1077 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.9079 (p) REVERT: G 33 MET cc_start: 0.5121 (tpt) cc_final: 0.4692 (ttt) REVERT: G 55 ASP cc_start: 0.4817 (OUTLIER) cc_final: 0.4204 (m-30) REVERT: G 81 MET cc_start: 0.2617 (ttt) cc_final: 0.0701 (ptt) REVERT: G 106 ASP cc_start: 0.5050 (p0) cc_final: 0.4501 (p0) REVERT: F 5 GLN cc_start: 0.7839 (mm110) cc_final: 0.7212 (mm110) REVERT: K 11 LEU cc_start: 0.3156 (OUTLIER) cc_final: 0.2329 (mm) outliers start: 156 outliers final: 87 residues processed: 349 average time/residue: 1.0307 time to fit residues: 449.7827 Evaluate side-chains 323 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 212 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 555 SER Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 619 GLU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1045 LYS Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 95 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 66 PHE Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 108 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 329 optimal weight: 30.0000 chunk 264 optimal weight: 6.9990 chunk 317 optimal weight: 0.5980 chunk 343 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 282 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 540 ASN B 99 ASN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1101 HIS ** D 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN D1101 HIS ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.213399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.178680 restraints weight = 30874.880| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.58 r_work: 0.3580 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29716 Z= 0.191 Angle : 0.694 11.966 40573 Z= 0.346 Chirality : 0.050 0.418 4703 Planarity : 0.005 0.056 5153 Dihedral : 6.365 107.534 5173 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.13 % Rotamer: Outliers : 5.08 % Allowed : 18.41 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3572 helix: 1.74 (0.20), residues: 693 sheet: -0.29 (0.17), residues: 854 loop : -1.54 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 353 HIS 0.021 0.001 HIS B 245 PHE 0.021 0.002 PHE A 643 TYR 0.033 0.002 TYR G 105 ARG 0.007 0.001 ARG F 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 50) link_NAG-ASN : angle 3.37467 ( 150) link_BETA1-4 : bond 0.00514 ( 11) link_BETA1-4 : angle 1.65301 ( 33) hydrogen bonds : bond 0.06913 ( 1028) hydrogen bonds : angle 5.50190 ( 2802) SS BOND : bond 0.00539 ( 44) SS BOND : angle 1.69909 ( 88) covalent geometry : bond 0.00466 (29610) covalent geometry : angle 0.65894 (40302) Misc. bond : bond 0.00163 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 222 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8422 (pp) REVERT: A 177 MET cc_start: 0.4275 (OUTLIER) cc_final: 0.3667 (mpt) REVERT: A 224 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: A 231 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7846 (pp) REVERT: A 245 HIS cc_start: 0.7577 (t70) cc_final: 0.7234 (OUTLIER) REVERT: A 585 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7503 (mt) REVERT: A 740 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8025 (tmm) REVERT: A 787 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8409 (mt0) REVERT: A 1119 ASN cc_start: 0.8512 (m-40) cc_final: 0.7829 (m110) REVERT: A 1129 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8148 (t) REVERT: B 74 ASN cc_start: 0.1207 (OUTLIER) cc_final: 0.0681 (p0) REVERT: B 153 MET cc_start: 0.4485 (mmm) cc_final: 0.2338 (tmm) REVERT: B 197 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.6795 (pt) REVERT: B 224 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: B 529 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7745 (ttpp) REVERT: B 558 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7841 (mmmt) REVERT: B 580 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.7174 (mp10) REVERT: B 675 GLN cc_start: 0.6850 (pp30) cc_final: 0.6591 (pt0) REVERT: B 740 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.7900 (tmm) REVERT: B 856 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7645 (m110) REVERT: B 1038 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8248 (ttmm) REVERT: B 1111 GLU cc_start: 0.8092 (pp20) cc_final: 0.7814 (pp20) REVERT: B 1141 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7064 (tp) REVERT: D 81 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7297 (p0) REVERT: D 96 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7955 (pt0) REVERT: D 176 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.4876 (pp) REVERT: D 552 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7656 (pp) REVERT: D 787 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8256 (mt0) REVERT: D 1045 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7801 (tmtt) REVERT: F 5 GLN cc_start: 0.8096 (mm110) cc_final: 0.7677 (mm110) REVERT: K 11 LEU cc_start: 0.2387 (OUTLIER) cc_final: 0.1735 (mm) REVERT: K 81 MET cc_start: 0.4399 (OUTLIER) cc_final: 0.3891 (tmm) outliers start: 159 outliers final: 94 residues processed: 346 average time/residue: 0.9874 time to fit residues: 430.5304 Evaluate side-chains 325 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 207 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1045 LYS Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 66 PHE Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 108 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 235 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 304 optimal weight: 0.5980 chunk 239 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 232 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 179 optimal weight: 0.6980 chunk 236 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 540 ASN B 99 ASN B 211 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1101 HIS D 245 HIS D1010 GLN D1125 ASN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.216322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.182275 restraints weight = 31011.150| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 1.57 r_work: 0.3629 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29716 Z= 0.122 Angle : 0.622 11.686 40573 Z= 0.308 Chirality : 0.046 0.381 4703 Planarity : 0.004 0.044 5153 Dihedral : 5.944 106.402 5170 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.74 % Rotamer: Outliers : 3.87 % Allowed : 20.08 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3572 helix: 2.02 (0.20), residues: 688 sheet: -0.15 (0.18), residues: 830 loop : -1.46 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 633 HIS 0.024 0.001 HIS B 245 PHE 0.022 0.001 PHE D 456 TYR 0.028 0.001 TYR G 105 ARG 0.004 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 50) link_NAG-ASN : angle 3.12762 ( 150) link_BETA1-4 : bond 0.00476 ( 11) link_BETA1-4 : angle 1.58312 ( 33) hydrogen bonds : bond 0.05451 ( 1028) hydrogen bonds : angle 5.36249 ( 2802) SS BOND : bond 0.00525 ( 44) SS BOND : angle 1.27428 ( 88) covalent geometry : bond 0.00272 (29610) covalent geometry : angle 0.58915 (40302) Misc. bond : bond 0.00471 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 211 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8304 (pp) REVERT: A 224 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: A 585 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7531 (mt) REVERT: A 619 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: A 787 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8359 (mt0) REVERT: B 74 ASN cc_start: 0.1184 (OUTLIER) cc_final: 0.0519 (p0) REVERT: B 153 MET cc_start: 0.4437 (mmm) cc_final: 0.2269 (tmm) REVERT: B 197 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.6758 (pt) REVERT: B 224 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: B 529 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7728 (ttpp) REVERT: B 580 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: B 675 GLN cc_start: 0.6749 (pp30) cc_final: 0.6518 (pt0) REVERT: B 856 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7569 (m110) REVERT: B 994 ASP cc_start: 0.8109 (m-30) cc_final: 0.7858 (m-30) REVERT: B 1038 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8270 (ttmm) REVERT: B 1111 GLU cc_start: 0.8039 (pp20) cc_final: 0.7817 (pp20) REVERT: B 1141 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.6999 (tp) REVERT: D 81 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7404 (p0) REVERT: D 96 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7924 (pt0) REVERT: D 104 TRP cc_start: 0.8215 (OUTLIER) cc_final: 0.7894 (m-90) REVERT: D 197 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7167 (tt) REVERT: D 456 PHE cc_start: 0.4130 (OUTLIER) cc_final: 0.3772 (p90) REVERT: D 787 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: F 5 GLN cc_start: 0.8037 (mm110) cc_final: 0.7612 (mm110) REVERT: F 6 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: K 11 LEU cc_start: 0.2060 (OUTLIER) cc_final: 0.1342 (mm) REVERT: K 81 MET cc_start: 0.4359 (OUTLIER) cc_final: 0.3861 (tmm) outliers start: 121 outliers final: 66 residues processed: 310 average time/residue: 0.9845 time to fit residues: 380.5713 Evaluate side-chains 290 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 202 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 104 TRP Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 66 PHE Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 108 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 245 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 303 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 273 optimal weight: 6.9990 chunk 40 optimal weight: 40.0000 chunk 272 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 245 HIS A 394 ASN A 540 ASN B 99 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1101 HIS D 115 GLN D1010 GLN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.216681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.182812 restraints weight = 30907.354| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.55 r_work: 0.3628 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 29716 Z= 0.120 Angle : 0.619 11.560 40573 Z= 0.306 Chirality : 0.046 0.367 4703 Planarity : 0.004 0.043 5153 Dihedral : 5.750 106.158 5170 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.37 % Favored : 95.52 % Rotamer: Outliers : 3.52 % Allowed : 20.40 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3572 helix: 2.08 (0.20), residues: 684 sheet: -0.16 (0.17), residues: 856 loop : -1.40 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.025 0.001 HIS B 245 PHE 0.017 0.001 PHE D 456 TYR 0.031 0.001 TYR G 105 ARG 0.006 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 50) link_NAG-ASN : angle 3.08982 ( 150) link_BETA1-4 : bond 0.00600 ( 11) link_BETA1-4 : angle 1.51455 ( 33) hydrogen bonds : bond 0.05298 ( 1028) hydrogen bonds : angle 5.32336 ( 2802) SS BOND : bond 0.00458 ( 44) SS BOND : angle 1.68395 ( 88) covalent geometry : bond 0.00271 (29610) covalent geometry : angle 0.58452 (40302) Misc. bond : bond 0.00085 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 208 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 787 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8365 (mt0) REVERT: B 74 ASN cc_start: 0.1241 (OUTLIER) cc_final: 0.0503 (p0) REVERT: B 153 MET cc_start: 0.4580 (mmm) cc_final: 0.2349 (tmm) REVERT: B 197 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.6683 (pt) REVERT: B 224 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: B 529 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7756 (ttpp) REVERT: B 580 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7141 (mp10) REVERT: B 675 GLN cc_start: 0.6824 (pp30) cc_final: 0.6594 (pt0) REVERT: B 740 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7891 (tmm) REVERT: B 856 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7605 (m110) REVERT: B 994 ASP cc_start: 0.8125 (m-30) cc_final: 0.7870 (m-30) REVERT: B 1111 GLU cc_start: 0.8031 (pp20) cc_final: 0.7775 (pp20) REVERT: B 1141 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.6986 (tp) REVERT: D 81 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7442 (p0) REVERT: D 197 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7209 (tt) REVERT: D 592 PHE cc_start: 0.8189 (p90) cc_final: 0.7792 (p90) REVERT: F 5 GLN cc_start: 0.8006 (mm110) cc_final: 0.7567 (mm110) REVERT: F 6 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: K 11 LEU cc_start: 0.1914 (OUTLIER) cc_final: 0.1195 (mm) outliers start: 110 outliers final: 69 residues processed: 298 average time/residue: 1.0308 time to fit residues: 388.6627 Evaluate side-chains 285 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 203 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 108 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 264 optimal weight: 2.9990 chunk 245 optimal weight: 0.0980 chunk 0 optimal weight: 9.9990 chunk 201 optimal weight: 0.7980 chunk 305 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 245 HIS A1125 ASN B 99 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1101 HIS D1010 GLN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.213746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.178824 restraints weight = 30813.885| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.59 r_work: 0.3589 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 29716 Z= 0.186 Angle : 0.692 11.323 40573 Z= 0.345 Chirality : 0.049 0.380 4703 Planarity : 0.005 0.044 5153 Dihedral : 5.925 105.470 5166 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.96 % Favored : 94.93 % Rotamer: Outliers : 3.07 % Allowed : 21.00 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3572 helix: 1.78 (0.20), residues: 694 sheet: -0.25 (0.17), residues: 852 loop : -1.47 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 64 HIS 0.027 0.001 HIS B 245 PHE 0.021 0.002 PHE A 643 TYR 0.033 0.002 TYR G 105 ARG 0.006 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 50) link_NAG-ASN : angle 3.20376 ( 150) link_BETA1-4 : bond 0.00511 ( 11) link_BETA1-4 : angle 1.57695 ( 33) hydrogen bonds : bond 0.06738 ( 1028) hydrogen bonds : angle 5.40469 ( 2802) SS BOND : bond 0.00542 ( 44) SS BOND : angle 2.06551 ( 88) covalent geometry : bond 0.00455 (29610) covalent geometry : angle 0.65715 (40302) Misc. bond : bond 0.00183 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 202 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.7944 (tmm) REVERT: A 787 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8326 (mt0) REVERT: B 74 ASN cc_start: 0.1357 (OUTLIER) cc_final: 0.0620 (p0) REVERT: B 153 MET cc_start: 0.4580 (mmm) cc_final: 0.3612 (tmm) REVERT: B 200 TYR cc_start: 0.7272 (m-80) cc_final: 0.7062 (t80) REVERT: B 224 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: B 529 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7704 (ttpp) REVERT: B 580 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7041 (mp10) REVERT: B 740 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7924 (tmm) REVERT: B 856 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7563 (m110) REVERT: B 994 ASP cc_start: 0.8067 (m-30) cc_final: 0.7790 (m-30) REVERT: B 1111 GLU cc_start: 0.7853 (pp20) cc_final: 0.7568 (pp20) REVERT: D 81 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7584 (p0) REVERT: D 1045 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7551 (tmtt) REVERT: F 5 GLN cc_start: 0.7949 (mm110) cc_final: 0.7539 (mm110) REVERT: K 11 LEU cc_start: 0.1888 (OUTLIER) cc_final: 0.1227 (mm) outliers start: 96 outliers final: 70 residues processed: 277 average time/residue: 1.0230 time to fit residues: 353.6077 Evaluate side-chains 278 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 197 time to evaluate : 3.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1045 LYS Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 108 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 269 optimal weight: 0.9980 chunk 104 optimal weight: 0.0170 chunk 116 optimal weight: 4.9990 chunk 262 optimal weight: 0.0770 chunk 304 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 352 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 99 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1101 HIS D 644 GLN D1010 GLN D1125 ASN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.216337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.182588 restraints weight = 31009.644| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.54 r_work: 0.3633 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29716 Z= 0.120 Angle : 0.612 11.752 40573 Z= 0.303 Chirality : 0.046 0.364 4703 Planarity : 0.004 0.042 5153 Dihedral : 5.659 105.527 5166 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.09 % Favored : 95.80 % Rotamer: Outliers : 2.94 % Allowed : 21.39 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3572 helix: 2.04 (0.20), residues: 677 sheet: -0.22 (0.18), residues: 847 loop : -1.36 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 64 HIS 0.026 0.001 HIS B 245 PHE 0.016 0.001 PHE D 456 TYR 0.028 0.001 TYR G 105 ARG 0.005 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 50) link_NAG-ASN : angle 2.96761 ( 150) link_BETA1-4 : bond 0.00516 ( 11) link_BETA1-4 : angle 1.49614 ( 33) hydrogen bonds : bond 0.05286 ( 1028) hydrogen bonds : angle 5.28215 ( 2802) SS BOND : bond 0.00464 ( 44) SS BOND : angle 1.56365 ( 88) covalent geometry : bond 0.00271 (29610) covalent geometry : angle 0.58113 (40302) Misc. bond : bond 0.00116 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24428.55 seconds wall clock time: 419 minutes 47.02 seconds (25187.02 seconds total)