Starting phenix.real_space_refine on Mon Aug 25 14:49:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g77_29799/08_2025/8g77_29799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g77_29799/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g77_29799/08_2025/8g77_29799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g77_29799/08_2025/8g77_29799.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g77_29799/08_2025/8g77_29799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g77_29799/08_2025/8g77_29799.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.047 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.83, per 1000 atoms: 0.24 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: 2.02 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.7 microseconds 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: 1.39 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: 7.75 Time building geometry restraints manager: 2.61 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 1308 or (resid 1309 an \ d (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or \ name C8 or name N2 or name O3 or name O5 or name O6 or 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 1312)) selection = (chain 'D' and (resid 14 through 624 or resid 634 through 676 or resid 690 throu \ gh 827 or resid 855 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 name C8 or name N2 or name O3 \ or name O5 or name O6 or name O7 )) or resid 1310 through 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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.590 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.020 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (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 ARG 0.017 0.001 ARG D 346 TYR 0.043 0.002 TYR D 160 PHE 0.042 0.002 PHE A1075 TRP 0.060 0.003 TRP D 258 HIS 0.036 0.002 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00571 (29610) covalent geometry : angle 0.86054 (40302) SS BOND : bond 0.09892 ( 44) SS BOND : angle 4.89781 ( 88) hydrogen bonds : bond 0.20782 ( 1028) hydrogen bonds : angle 8.04376 ( 2802) Misc. bond : bond 0.28620 ( 1) link_BETA1-4 : bond 0.00879 ( 11) link_BETA1-4 : angle 2.16822 ( 33) link_NAG-ASN : bond 0.03535 ( 50) link_NAG-ASN : angle 5.42309 ( 150) *********************** 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 : 1.091 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: 0.4774 time to fit residues: 162.7526 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 : 0.885 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0060 chunk 298 optimal weight: 4.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 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 K 71 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.218973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.168602 restraints weight = 31373.053| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.41 r_work: 0.3316 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0890 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= 0.132 Angle : 0.672 15.253 40573 Z= 0.332 Chirality : 0.049 0.794 4703 Planarity : 0.004 0.060 5153 Dihedral : 7.458 110.919 5196 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.92 % Favored : 95.97 % Rotamer: Outliers : 3.32 % Allowed : 16.72 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.14), residues: 3572 helix: 2.15 (0.20), residues: 691 sheet: -0.11 (0.17), residues: 858 loop : -1.45 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.022 0.001 TYR K 105 PHE 0.015 0.001 PHE A 497 TRP 0.018 0.001 TRP D 258 HIS 0.009 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00288 (29610) covalent geometry : angle 0.63154 (40302) SS BOND : bond 0.00480 ( 44) SS BOND : angle 1.32590 ( 88) hydrogen bonds : bond 0.05900 ( 1028) hydrogen bonds : angle 6.02168 ( 2802) Misc. bond : bond 0.00244 ( 1) link_BETA1-4 : bond 0.00584 ( 11) link_BETA1-4 : angle 1.73944 ( 33) link_NAG-ASN : bond 0.00667 ( 50) link_NAG-ASN : angle 3.66697 ( 150) *********************** 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 346 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 242 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7607 (pp) REVERT: A 619 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: A 690 GLN cc_start: 0.4138 (OUTLIER) cc_final: 0.3918 (mp10) REVERT: A 994 ASP cc_start: 0.8068 (m-30) cc_final: 0.7665 (m-30) REVERT: B 29 THR cc_start: 0.7788 (t) cc_final: 0.7455 (m) REVERT: B 74 ASN cc_start: 0.2429 (OUTLIER) cc_final: 0.2154 (m-40) REVERT: B 153 MET cc_start: 0.3786 (mmm) cc_final: 0.1089 (tmm) REVERT: B 206 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8063 (ttmt) REVERT: B 224 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: B 452 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5969 (mp) REVERT: B 556 ASN cc_start: 0.7218 (OUTLIER) cc_final: 0.6846 (p0) REVERT: B 675 GLN cc_start: 0.7056 (pp30) cc_final: 0.6023 (mt0) REVERT: B 856 ASN cc_start: 0.7418 (OUTLIER) cc_final: 0.7196 (m110) REVERT: B 994 ASP cc_start: 0.8175 (m-30) cc_final: 0.7972 (m-30) REVERT: D 133 PHE cc_start: 0.7183 (m-80) cc_final: 0.6064 (m-80) REVERT: D 144 TYR cc_start: 0.4951 (m-10) cc_final: 0.4719 (m-80) REVERT: D 456 PHE cc_start: 0.3298 (OUTLIER) cc_final: 0.3079 (p90) REVERT: D 787 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8257 (mt0) REVERT: G 33 MET cc_start: 0.5029 (tpt) cc_final: 0.3927 (ttt) outliers start: 104 outliers final: 40 residues processed: 326 average time/residue: 0.4291 time to fit residues: 174.6983 Evaluate side-chains 270 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 690 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1061 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 74 ASN 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 452 LEU 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 556 ASN 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 585 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 858 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 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 27 optimal weight: 0.1980 chunk 150 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 281 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 56 optimal weight: 0.0970 chunk 245 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A1101 HIS A1106 GLN 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** B1010 GLN D 245 HIS D1010 GLN G 97 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.217145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.166847 restraints weight = 31226.721| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.39 r_work: 0.3304 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29716 Z= 0.145 Angle : 0.661 12.085 40573 Z= 0.326 Chirality : 0.048 0.399 4703 Planarity : 0.004 0.047 5153 Dihedral : 6.869 108.458 5172 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 3.84 % Allowed : 16.59 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.14), residues: 3572 helix: 2.12 (0.20), residues: 687 sheet: -0.18 (0.17), residues: 865 loop : -1.46 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.023 0.001 TYR K 105 PHE 0.015 0.002 PHE A 643 TRP 0.014 0.002 TRP D 353 HIS 0.013 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00336 (29610) covalent geometry : angle 0.62276 (40302) SS BOND : bond 0.00494 ( 44) SS BOND : angle 1.32292 ( 88) hydrogen bonds : bond 0.06072 ( 1028) hydrogen bonds : angle 5.66897 ( 2802) Misc. bond : bond 0.00724 ( 1) link_BETA1-4 : bond 0.00521 ( 11) link_BETA1-4 : angle 1.73221 ( 33) link_NAG-ASN : bond 0.00536 ( 50) link_NAG-ASN : angle 3.53031 ( 150) *********************** 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 361 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 241 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8364 (pp) REVERT: A 224 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: A 231 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7590 (pp) REVERT: A 357 ARG cc_start: 0.6659 (ttt-90) cc_final: 0.6323 (ttt-90) REVERT: A 613 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8563 (mt0) REVERT: A 619 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: A 787 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8406 (mt0) REVERT: A 994 ASP cc_start: 0.8204 (m-30) cc_final: 0.7742 (m-30) REVERT: A 1129 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7890 (t) REVERT: B 153 MET cc_start: 0.3627 (mmm) cc_final: 0.0951 (tmm) REVERT: B 224 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8180 (mt-10) REVERT: B 305 SER cc_start: 0.8968 (t) cc_final: 0.8635 (p) REVERT: B 675 GLN cc_start: 0.7170 (pp30) cc_final: 0.6059 (mt0) REVERT: B 740 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.7754 (tmm) REVERT: B 856 ASN cc_start: 0.7493 (OUTLIER) cc_final: 0.7250 (m110) REVERT: B 994 ASP cc_start: 0.8287 (m-30) cc_final: 0.8033 (m-30) REVERT: B 1111 GLU cc_start: 0.7934 (pp20) cc_final: 0.7690 (pp20) REVERT: D 52 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8340 (tp-100) REVERT: D 133 PHE cc_start: 0.7282 (m-80) cc_final: 0.6054 (m-80) REVERT: D 144 TYR cc_start: 0.4982 (m-10) cc_final: 0.4746 (m-80) REVERT: D 154 GLU cc_start: 0.4510 (OUTLIER) cc_final: 0.3998 (mm-30) REVERT: D 456 PHE cc_start: 0.3545 (OUTLIER) cc_final: 0.3283 (p90) REVERT: G 33 MET cc_start: 0.5040 (tpt) cc_final: 0.4024 (ttt) REVERT: K 81 MET cc_start: 0.2629 (tpp) cc_final: 0.2423 (tmm) outliers start: 120 outliers final: 61 residues processed: 327 average time/residue: 0.4405 time to fit residues: 178.5217 Evaluate side-chains 295 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 222 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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 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 565 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 619 GLU 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 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET 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 30 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 45 SER 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 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 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 740 MET Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain D residue 45 SER 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 349 SER Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 555 SER Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 624 ILE 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 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 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 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 23 VAL 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 344 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 143 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 296 optimal weight: 0.6980 chunk 310 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 388 ASN A 540 ASN A1101 HIS 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** B1010 GLN D 81 ASN D1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.218376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.168332 restraints weight = 31090.984| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.39 r_work: 0.3317 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1540 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= 0.116 Angle : 0.616 11.245 40573 Z= 0.302 Chirality : 0.046 0.384 4703 Planarity : 0.004 0.044 5153 Dihedral : 6.384 107.746 5172 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Rotamer: Outliers : 4.16 % Allowed : 16.91 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.14), residues: 3572 helix: 2.21 (0.20), residues: 687 sheet: -0.09 (0.17), residues: 845 loop : -1.40 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 983 TYR 0.025 0.001 TYR K 105 PHE 0.013 0.001 PHE B 32 TRP 0.012 0.001 TRP D 353 HIS 0.016 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00254 (29610) covalent geometry : angle 0.57775 (40302) SS BOND : bond 0.00489 ( 44) SS BOND : angle 1.15021 ( 88) hydrogen bonds : bond 0.05259 ( 1028) hydrogen bonds : angle 5.45567 ( 2802) Misc. bond : bond 0.00755 ( 1) link_BETA1-4 : bond 0.00545 ( 11) link_BETA1-4 : angle 1.62348 ( 33) link_NAG-ASN : bond 0.00533 ( 50) link_NAG-ASN : angle 3.42904 ( 150) *********************** 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 366 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 236 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.7732 (p) cc_final: 0.7394 (m) REVERT: A 48 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8165 (pp) REVERT: A 224 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: A 231 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7595 (pp) REVERT: A 245 HIS cc_start: 0.6660 (t70) cc_final: 0.6163 (m170) REVERT: A 619 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: A 655 HIS cc_start: 0.8638 (t-90) cc_final: 0.8435 (t70) REVERT: A 981 LEU cc_start: 0.8634 (mt) cc_final: 0.8391 (mt) REVERT: A 994 ASP cc_start: 0.8153 (m-30) cc_final: 0.7702 (m-30) REVERT: A 1129 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7962 (t) REVERT: B 153 MET cc_start: 0.3681 (mmm) cc_final: 0.0985 (tmm) REVERT: B 224 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: B 305 SER cc_start: 0.8969 (t) cc_final: 0.8657 (p) REVERT: B 675 GLN cc_start: 0.7193 (pp30) cc_final: 0.6098 (mt0) REVERT: B 856 ASN cc_start: 0.7506 (OUTLIER) cc_final: 0.7286 (m110) REVERT: B 994 ASP cc_start: 0.8243 (m-30) cc_final: 0.7981 (m-30) REVERT: B 1111 GLU cc_start: 0.8008 (pp20) cc_final: 0.7636 (pp20) REVERT: D 52 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8303 (tp-100) REVERT: D 133 PHE cc_start: 0.7360 (m-80) cc_final: 0.6133 (m-80) REVERT: D 144 TYR cc_start: 0.5014 (m-10) cc_final: 0.4778 (m-80) REVERT: D 153 MET cc_start: 0.6327 (mmt) cc_final: 0.5611 (mmm) REVERT: D 154 GLU cc_start: 0.4560 (OUTLIER) cc_final: 0.4083 (mm-30) REVERT: D 787 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8231 (mt0) REVERT: G 33 MET cc_start: 0.5027 (tpt) cc_final: 0.3993 (ttt) REVERT: G 45 GLU cc_start: 0.6584 (mp0) cc_final: 0.6366 (mp0) REVERT: G 81 MET cc_start: 0.1813 (ttt) cc_final: 0.0540 (ptt) REVERT: K 20 LEU cc_start: -0.0180 (OUTLIER) cc_final: -0.0773 (mt) outliers start: 130 outliers final: 67 residues processed: 337 average time/residue: 0.4859 time to fit residues: 204.0651 Evaluate side-chains 298 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 221 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 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 286 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 551 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 619 GLU 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 878 LEU 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 30 ASN Chi-restraints excluded: chain B residue 42 VAL 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 341 VAL 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 606 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain D residue 18 LEU 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 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 547 THR Chi-restraints excluded: chain D residue 555 SER Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 624 ILE 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 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 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 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 91 VAL Chi-restraints excluded: chain K residue 106 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 354 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 228 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 191 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 334 ASN A1101 HIS 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 804 GLN B1010 GLN D1010 GLN D1101 HIS D1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.213962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.162890 restraints weight = 30900.102| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.39 r_work: 0.3229 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29716 Z= 0.186 Angle : 0.691 12.726 40573 Z= 0.343 Chirality : 0.049 0.411 4703 Planarity : 0.005 0.052 5153 Dihedral : 6.354 106.064 5170 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 4.32 % Allowed : 17.39 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.14), residues: 3572 helix: 1.91 (0.20), residues: 692 sheet: -0.19 (0.18), residues: 821 loop : -1.44 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 983 TYR 0.028 0.002 TYR K 105 PHE 0.018 0.002 PHE A 643 TRP 0.017 0.002 TRP D 353 HIS 0.019 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00449 (29610) covalent geometry : angle 0.65540 (40302) SS BOND : bond 0.00505 ( 44) SS BOND : angle 1.50564 ( 88) hydrogen bonds : bond 0.06927 ( 1028) hydrogen bonds : angle 5.52944 ( 2802) Misc. bond : bond 0.00077 ( 1) link_BETA1-4 : bond 0.00527 ( 11) link_BETA1-4 : angle 1.67000 ( 33) link_NAG-ASN : bond 0.00437 ( 50) link_NAG-ASN : angle 3.42268 ( 150) *********************** 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 371 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 236 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8420 (pp) REVERT: A 224 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: A 231 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7649 (pp) REVERT: A 245 HIS cc_start: 0.6988 (t70) cc_final: 0.6430 (OUTLIER) REVERT: A 787 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8457 (mt0) REVERT: A 994 ASP cc_start: 0.8442 (m-30) cc_final: 0.7950 (m-30) REVERT: A 1119 ASN cc_start: 0.8617 (m110) cc_final: 0.8403 (m110) REVERT: A 1129 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7881 (t) REVERT: B 29 THR cc_start: 0.8018 (t) cc_final: 0.7605 (m) REVERT: B 80 ASP cc_start: 0.5829 (t0) cc_final: 0.5411 (t0) REVERT: B 153 MET cc_start: 0.3974 (mmm) cc_final: 0.1321 (tmm) REVERT: B 197 ILE cc_start: 0.7198 (OUTLIER) cc_final: 0.6730 (pt) REVERT: B 224 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8243 (mt-10) REVERT: B 305 SER cc_start: 0.8982 (t) cc_final: 0.8640 (p) REVERT: B 580 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: B 675 GLN cc_start: 0.7040 (pp30) cc_final: 0.6055 (mt0) REVERT: B 740 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7774 (tmm) REVERT: B 856 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7489 (m110) REVERT: B 994 ASP cc_start: 0.8399 (m-30) cc_final: 0.8101 (m-30) REVERT: B 1111 GLU cc_start: 0.8079 (pp20) cc_final: 0.7720 (pp20) REVERT: D 133 PHE cc_start: 0.7574 (m-80) cc_final: 0.6427 (m-80) REVERT: D 153 MET cc_start: 0.6325 (mmt) cc_final: 0.6068 (mmm) REVERT: D 456 PHE cc_start: 0.3772 (OUTLIER) cc_final: 0.3438 (p90) REVERT: D 620 VAL cc_start: 0.7307 (OUTLIER) cc_final: 0.7033 (m) REVERT: D 787 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8359 (mt0) REVERT: D 931 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8153 (mm) REVERT: D 1045 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7704 (tmtt) REVERT: D 1119 ASN cc_start: 0.8258 (m110) cc_final: 0.8025 (m-40) REVERT: G 33 MET cc_start: 0.4948 (tpt) cc_final: 0.4049 (ttt) REVERT: G 81 MET cc_start: 0.2390 (ttt) cc_final: 0.0787 (ptt) REVERT: G 106 ASP cc_start: 0.5076 (p0) cc_final: 0.4608 (p0) REVERT: F 5 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7310 (mm-40) REVERT: K 11 LEU cc_start: 0.2905 (OUTLIER) cc_final: 0.2088 (mm) outliers start: 135 outliers final: 74 residues processed: 336 average time/residue: 0.5237 time to fit residues: 216.0084 Evaluate side-chains 302 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 213 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 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 286 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 ASN 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 615 VAL Chi-restraints excluded: chain A residue 620 VAL 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 900 MET 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 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 341 VAL 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 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 D residue 18 LEU 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 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 547 THR 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 624 ILE 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 791 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 931 ILE 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 29 THR 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 11 LEU Chi-restraints excluded: chain K residue 12 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 351 optimal weight: 30.0000 chunk 89 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 163 optimal weight: 0.4980 chunk 340 optimal weight: 0.2980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 370 ASN A 394 ASN A1106 GLN B 52 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 564 GLN B1010 GLN D1010 GLN D1083 HIS D1101 HIS G 3 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.212848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.162085 restraints weight = 31074.026| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.38 r_work: 0.3219 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29716 Z= 0.194 Angle : 0.698 12.745 40573 Z= 0.346 Chirality : 0.050 0.413 4703 Planarity : 0.005 0.054 5153 Dihedral : 6.368 106.655 5170 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.74 % Rotamer: Outliers : 4.96 % Allowed : 17.26 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.14), residues: 3572 helix: 1.83 (0.20), residues: 687 sheet: -0.29 (0.17), residues: 840 loop : -1.47 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.031 0.002 TYR G 105 PHE 0.021 0.002 PHE A 643 TRP 0.018 0.002 TRP D 353 HIS 0.019 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00472 (29610) covalent geometry : angle 0.66094 (40302) SS BOND : bond 0.00581 ( 44) SS BOND : angle 1.64737 ( 88) hydrogen bonds : bond 0.06900 ( 1028) hydrogen bonds : angle 5.51242 ( 2802) Misc. bond : bond 0.00244 ( 1) link_BETA1-4 : bond 0.00552 ( 11) link_BETA1-4 : angle 1.66567 ( 33) link_NAG-ASN : bond 0.00443 ( 50) link_NAG-ASN : angle 3.47446 ( 150) *********************** 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: 155 poor density : 224 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8411 (pp) REVERT: A 224 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: A 231 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7675 (pp) REVERT: A 245 HIS cc_start: 0.7180 (t70) cc_final: 0.6566 (OUTLIER) REVERT: A 619 GLU cc_start: 0.7628 (mp0) cc_final: 0.7365 (mp0) REVERT: A 787 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8480 (mt0) REVERT: A 1119 ASN cc_start: 0.8598 (m110) cc_final: 0.8285 (m110) REVERT: A 1129 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7929 (t) REVERT: B 29 THR cc_start: 0.8015 (t) cc_final: 0.7784 (m) REVERT: B 80 ASP cc_start: 0.6027 (t0) cc_final: 0.5711 (t0) REVERT: B 153 MET cc_start: 0.3747 (mmm) cc_final: 0.1367 (tmm) REVERT: B 197 ILE cc_start: 0.7137 (OUTLIER) cc_final: 0.6697 (pt) REVERT: B 224 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8274 (mt-10) REVERT: B 580 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.6704 (mp10) REVERT: B 675 GLN cc_start: 0.6999 (pp30) cc_final: 0.6086 (mt0) REVERT: B 740 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.7823 (tmm) REVERT: B 856 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7565 (m110) REVERT: B 994 ASP cc_start: 0.8396 (m-30) cc_final: 0.8088 (m-30) REVERT: B 1111 GLU cc_start: 0.8147 (pp20) cc_final: 0.7677 (pp20) REVERT: B 1141 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6196 (tp) REVERT: D 133 PHE cc_start: 0.7587 (m-80) cc_final: 0.7053 (m-80) REVERT: D 144 TYR cc_start: 0.5276 (m-80) cc_final: 0.4888 (m-80) REVERT: D 153 MET cc_start: 0.6332 (mmt) cc_final: 0.5579 (mmm) REVERT: D 154 GLU cc_start: 0.4694 (OUTLIER) cc_final: 0.4355 (mm-30) REVERT: D 197 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.6535 (mp) REVERT: D 456 PHE cc_start: 0.3711 (OUTLIER) cc_final: 0.3158 (p90) REVERT: D 556 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7126 (m110) REVERT: D 740 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.7666 (tmm) REVERT: D 787 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8378 (mt0) REVERT: D 931 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8112 (mm) REVERT: D 988 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: D 1045 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7712 (tmtt) REVERT: D 1077 THR cc_start: 0.9379 (OUTLIER) cc_final: 0.9098 (p) REVERT: D 1139 ASP cc_start: 0.7101 (t0) cc_final: 0.6736 (t70) REVERT: G 33 MET cc_start: 0.5034 (tpt) cc_final: 0.4320 (ttt) REVERT: G 55 ASP cc_start: 0.4996 (OUTLIER) cc_final: 0.4402 (m-30) REVERT: G 81 MET cc_start: 0.2490 (ttt) cc_final: 0.0642 (ptt) REVERT: G 106 ASP cc_start: 0.4941 (p0) cc_final: 0.4380 (p0) REVERT: F 5 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7293 (mm-40) REVERT: K 11 LEU cc_start: 0.2749 (OUTLIER) cc_final: 0.2027 (mm) outliers start: 155 outliers final: 89 residues processed: 345 average time/residue: 0.4968 time to fit residues: 212.5227 Evaluate side-chains 318 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 207 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 118 LEU 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 286 THR Chi-restraints excluded: chain A residue 333 THR 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 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 643 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 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 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 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 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 341 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 395 VAL 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 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 856 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 154 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 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 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 791 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 931 ILE Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 988 GLU 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 29 THR Chi-restraints excluded: chain G residue 55 ASP 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 11 LEU 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 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 33 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 284 optimal weight: 0.9990 chunk 297 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 170 optimal weight: 0.4980 chunk 231 optimal weight: 8.9990 chunk 319 optimal weight: 0.7980 chunk 339 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 613 GLN A1125 ASN B 52 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** B1010 GLN D 245 HIS D1010 GLN D1101 HIS D1119 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.215767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.166799 restraints weight = 31025.099| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.29 r_work: 0.3292 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29716 Z= 0.117 Angle : 0.626 18.528 40573 Z= 0.309 Chirality : 0.046 0.382 4703 Planarity : 0.004 0.049 5153 Dihedral : 5.949 107.224 5169 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 3.84 % Allowed : 18.51 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.14), residues: 3572 helix: 2.08 (0.20), residues: 691 sheet: -0.16 (0.18), residues: 816 loop : -1.37 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 357 TYR 0.028 0.001 TYR K 105 PHE 0.015 0.001 PHE D 456 TRP 0.013 0.001 TRP D 633 HIS 0.019 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00255 (29610) covalent geometry : angle 0.59134 (40302) SS BOND : bond 0.00671 ( 44) SS BOND : angle 1.97582 ( 88) hydrogen bonds : bond 0.05331 ( 1028) hydrogen bonds : angle 5.36032 ( 2802) Misc. bond : bond 0.00125 ( 1) link_BETA1-4 : bond 0.00554 ( 11) link_BETA1-4 : angle 1.57228 ( 33) link_NAG-ASN : bond 0.00499 ( 50) link_NAG-ASN : angle 3.06190 ( 150) *********************** 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 335 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 215 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8279 (pp) REVERT: A 224 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: A 231 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7694 (pp) REVERT: A 245 HIS cc_start: 0.7074 (t70) cc_final: 0.6504 (OUTLIER) REVERT: A 613 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8499 (mt0) REVERT: A 787 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8464 (mt0) REVERT: A 1129 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.7988 (t) REVERT: B 29 THR cc_start: 0.8045 (t) cc_final: 0.7793 (m) REVERT: B 80 ASP cc_start: 0.5919 (t0) cc_final: 0.5682 (t0) REVERT: B 153 MET cc_start: 0.4008 (mmm) cc_final: 0.1343 (tmm) REVERT: B 197 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6632 (pt) REVERT: B 200 TYR cc_start: 0.7607 (m-80) cc_final: 0.7383 (m-80) REVERT: B 224 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8186 (mt-10) REVERT: B 305 SER cc_start: 0.8994 (t) cc_final: 0.8660 (p) REVERT: B 558 LYS cc_start: 0.8011 (mmtt) cc_final: 0.7642 (mppt) REVERT: B 580 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.6632 (mp10) REVERT: B 675 GLN cc_start: 0.6987 (pp30) cc_final: 0.6616 (pt0) REVERT: B 856 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7549 (m110) REVERT: B 994 ASP cc_start: 0.8245 (m-30) cc_final: 0.7960 (m-30) REVERT: B 1111 GLU cc_start: 0.8098 (pp20) cc_final: 0.7495 (pp20) REVERT: B 1141 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6177 (tp) REVERT: D 153 MET cc_start: 0.6476 (mmt) cc_final: 0.6217 (mmm) REVERT: D 197 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.6831 (tt) REVERT: D 357 ARG cc_start: 0.7272 (mtp85) cc_final: 0.7002 (mtm180) REVERT: D 456 PHE cc_start: 0.3822 (OUTLIER) cc_final: 0.3381 (p90) REVERT: D 787 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8284 (mt0) REVERT: D 1077 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9000 (p) REVERT: D 1139 ASP cc_start: 0.7017 (t0) cc_final: 0.6679 (t70) REVERT: G 33 MET cc_start: 0.4941 (tpt) cc_final: 0.4274 (ttt) REVERT: G 55 ASP cc_start: 0.4945 (OUTLIER) cc_final: 0.4395 (m-30) REVERT: G 81 MET cc_start: 0.2405 (ttt) cc_final: 0.0595 (ptt) REVERT: G 106 ASP cc_start: 0.4843 (p0) cc_final: 0.4419 (p0) REVERT: F 5 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7343 (mm-40) REVERT: K 11 LEU cc_start: 0.2696 (OUTLIER) cc_final: 0.1959 (mm) REVERT: K 20 LEU cc_start: 0.0098 (OUTLIER) cc_final: -0.0924 (mt) REVERT: K 55 ASP cc_start: 0.4786 (OUTLIER) cc_final: 0.4381 (m-30) REVERT: K 81 MET cc_start: 0.2732 (tpp) cc_final: 0.2419 (tmm) outliers start: 120 outliers final: 66 residues processed: 312 average time/residue: 0.4612 time to fit residues: 178.5473 Evaluate side-chains 286 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 202 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 177 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 613 GLN 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 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 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 84 LEU 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 478 THR 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 734 THR 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 1001 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 79 PHE 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 456 PHE Chi-restraints excluded: chain D residue 529 LYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 585 LEU 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 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 G residue 2 VAL Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain F residue 67 THR 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 55 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 249 optimal weight: 8.9990 chunk 336 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 256 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 351 optimal weight: 0.0060 chunk 247 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- 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 613 GLN A1119 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 Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.212641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.161675 restraints weight = 30977.152| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.34 r_work: 0.3235 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 29716 Z= 0.186 Angle : 0.702 16.843 40573 Z= 0.349 Chirality : 0.049 0.394 4703 Planarity : 0.005 0.053 5153 Dihedral : 5.976 102.943 5166 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.13 % Rotamer: Outliers : 4.44 % Allowed : 18.35 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.14), residues: 3572 helix: 1.88 (0.20), residues: 686 sheet: -0.23 (0.17), residues: 838 loop : -1.42 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 983 TYR 0.031 0.002 TYR G 105 PHE 0.021 0.002 PHE A 643 TRP 0.018 0.002 TRP D 353 HIS 0.022 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00452 (29610) covalent geometry : angle 0.66425 (40302) SS BOND : bond 0.00550 ( 44) SS BOND : angle 2.58019 ( 88) hydrogen bonds : bond 0.06789 ( 1028) hydrogen bonds : angle 5.46122 ( 2802) Misc. bond : bond 0.00167 ( 1) link_BETA1-4 : bond 0.00540 ( 11) link_BETA1-4 : angle 1.62822 ( 33) link_NAG-ASN : bond 0.00439 ( 50) link_NAG-ASN : angle 3.22519 ( 150) *********************** 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 353 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 214 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8363 (pp) REVERT: A 224 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: A 231 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7733 (pp) REVERT: A 245 HIS cc_start: 0.7340 (t70) cc_final: 0.6725 (OUTLIER) REVERT: A 619 GLU cc_start: 0.7696 (mp0) cc_final: 0.7490 (mp0) REVERT: A 740 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.7778 (tmm) REVERT: A 787 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8463 (mt0) REVERT: A 1119 ASN cc_start: 0.8521 (m-40) cc_final: 0.7996 (m110) REVERT: A 1129 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.7927 (t) REVERT: B 29 THR cc_start: 0.8081 (t) cc_final: 0.7849 (m) REVERT: B 80 ASP cc_start: 0.6177 (t0) cc_final: 0.5843 (t0) REVERT: B 153 MET cc_start: 0.3791 (mmm) cc_final: 0.1289 (tmm) REVERT: B 170 TYR cc_start: 0.7421 (t80) cc_final: 0.7140 (t80) REVERT: B 197 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6695 (pt) REVERT: B 200 TYR cc_start: 0.7629 (m-80) cc_final: 0.7360 (m-80) REVERT: B 224 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8261 (mt-10) REVERT: B 305 SER cc_start: 0.8985 (t) cc_final: 0.8632 (p) REVERT: B 558 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7670 (mppt) REVERT: B 580 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.6655 (mp10) REVERT: B 675 GLN cc_start: 0.6754 (pp30) cc_final: 0.6481 (pt0) REVERT: B 740 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7820 (tmm) REVERT: B 856 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7605 (m110) REVERT: B 994 ASP cc_start: 0.8385 (m-30) cc_final: 0.8084 (m-30) REVERT: B 1111 GLU cc_start: 0.8178 (pp20) cc_final: 0.7603 (pp20) REVERT: B 1141 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6197 (tp) REVERT: D 81 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7171 (p0) REVERT: D 96 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8063 (pt0) REVERT: D 153 MET cc_start: 0.6588 (mmt) cc_final: 0.6334 (mmm) REVERT: D 592 PHE cc_start: 0.7858 (p90) cc_final: 0.7475 (p90) REVERT: D 619 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: D 787 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8375 (mt0) REVERT: D 1077 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9125 (p) REVERT: D 1139 ASP cc_start: 0.7066 (t0) cc_final: 0.6705 (t70) REVERT: G 33 MET cc_start: 0.5006 (tpt) cc_final: 0.4558 (ttt) REVERT: G 55 ASP cc_start: 0.4975 (OUTLIER) cc_final: 0.4379 (m-30) REVERT: F 5 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7378 (mm-40) REVERT: K 11 LEU cc_start: 0.2725 (OUTLIER) cc_final: 0.1986 (mm) outliers start: 139 outliers final: 81 residues processed: 325 average time/residue: 0.4400 time to fit residues: 177.6345 Evaluate side-chains 310 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 211 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 118 LEU 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 385 THR Chi-restraints excluded: chain A residue 394 ASN 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 546 LEU Chi-restraints excluded: chain A residue 551 VAL 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 734 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 957 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1054 GLN 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 84 LEU 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 341 VAL Chi-restraints excluded: chain B residue 385 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 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 646 ARG 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 740 MET 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 1001 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 18 LEU 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 565 PHE Chi-restraints excluded: chain D residue 585 LEU 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 735 SER 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 G residue 2 VAL Chi-restraints excluded: chain G residue 55 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 185 optimal weight: 0.6980 chunk 216 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 344 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 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** B1010 GLN D1010 GLN D1101 HIS ** F 49 GLN ** 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 = 0.4288 r_free = 0.4288 target = 0.211780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.159059 restraints weight = 30832.998| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.35 r_work: 0.3209 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2665 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= 0.194 Angle : 0.711 16.155 40573 Z= 0.354 Chirality : 0.050 0.404 4703 Planarity : 0.005 0.054 5153 Dihedral : 6.075 103.059 5166 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 4.35 % Allowed : 18.41 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.14), residues: 3572 helix: 1.77 (0.20), residues: 684 sheet: -0.25 (0.17), residues: 872 loop : -1.51 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 509 TYR 0.031 0.002 TYR G 105 PHE 0.020 0.002 PHE A 643 TRP 0.019 0.002 TRP D 353 HIS 0.025 0.002 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00477 (29610) covalent geometry : angle 0.67349 (40302) SS BOND : bond 0.00528 ( 44) SS BOND : angle 2.52377 ( 88) hydrogen bonds : bond 0.06894 ( 1028) hydrogen bonds : angle 5.46775 ( 2802) Misc. bond : bond 0.00066 ( 1) link_BETA1-4 : bond 0.00520 ( 11) link_BETA1-4 : angle 1.62891 ( 33) link_NAG-ASN : bond 0.00445 ( 50) link_NAG-ASN : angle 3.23503 ( 150) *********************** 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 349 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 213 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8397 (pp) REVERT: A 177 MET cc_start: 0.3769 (OUTLIER) cc_final: 0.3135 (mpt) REVERT: A 224 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: A 231 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7734 (pp) REVERT: A 245 HIS cc_start: 0.7527 (t70) cc_final: 0.6835 (OUTLIER) REVERT: A 585 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7109 (mt) REVERT: A 740 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.7859 (tmm) REVERT: A 787 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8490 (mt0) REVERT: A 1129 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.7972 (t) REVERT: B 29 THR cc_start: 0.8168 (t) cc_final: 0.7921 (m) REVERT: B 80 ASP cc_start: 0.6154 (t0) cc_final: 0.5886 (t0) REVERT: B 153 MET cc_start: 0.3987 (mmm) cc_final: 0.1433 (tmm) REVERT: B 170 TYR cc_start: 0.7512 (t80) cc_final: 0.7253 (t80) REVERT: B 224 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8227 (mt-10) REVERT: B 558 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7526 (mmmt) REVERT: B 580 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.6718 (mp10) REVERT: B 616 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.7387 (m-40) REVERT: B 675 GLN cc_start: 0.6786 (pp30) cc_final: 0.6508 (pt0) REVERT: B 740 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.7877 (tmm) REVERT: B 856 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7652 (m110) REVERT: B 994 ASP cc_start: 0.8415 (m-30) cc_final: 0.8112 (m-30) REVERT: B 1111 GLU cc_start: 0.8175 (pp20) cc_final: 0.7580 (pp20) REVERT: B 1141 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6236 (tp) REVERT: D 81 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7211 (p0) REVERT: D 144 TYR cc_start: 0.5279 (m-80) cc_final: 0.5032 (m-80) REVERT: D 153 MET cc_start: 0.6660 (mmt) cc_final: 0.6404 (mmm) REVERT: D 619 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: D 787 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8414 (mt0) REVERT: D 1045 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7736 (tmtt) REVERT: D 1077 THR cc_start: 0.9383 (OUTLIER) cc_final: 0.9135 (p) REVERT: D 1139 ASP cc_start: 0.7152 (t0) cc_final: 0.6789 (t70) REVERT: G 33 MET cc_start: 0.5272 (tpt) cc_final: 0.4858 (ttt) REVERT: G 55 ASP cc_start: 0.4881 (OUTLIER) cc_final: 0.4310 (m-30) REVERT: G 81 MET cc_start: 0.3114 (ttt) cc_final: 0.0949 (ptt) REVERT: F 5 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7306 (mm110) REVERT: K 11 LEU cc_start: 0.2942 (OUTLIER) cc_final: 0.2118 (mm) REVERT: K 81 MET cc_start: 0.3037 (tpp) cc_final: 0.2566 (tmm) outliers start: 136 outliers final: 87 residues processed: 322 average time/residue: 0.4508 time to fit residues: 181.5514 Evaluate side-chains 314 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 207 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 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 333 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 394 ASN 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 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU 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 734 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 791 THR Chi-restraints excluded: chain A residue 868 GLU 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 1129 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 84 LEU 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 503 VAL Chi-restraints excluded: chain B residue 524 VAL 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 616 ASN Chi-restraints excluded: chain B residue 646 ARG 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 740 MET 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 1001 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 79 PHE 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 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 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 735 SER 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 G residue 2 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain F residue 50 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 118 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 21 optimal weight: 0.0470 chunk 310 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 305 optimal weight: 5.9990 chunk 344 optimal weight: 1.9990 chunk 328 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 323 optimal weight: 6.9990 chunk 230 optimal weight: 7.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- 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 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** B1010 GLN B1101 HIS ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN D1101 HIS D1125 ASN ** 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 = 0.4292 r_free = 0.4292 target = 0.212163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.161392 restraints weight = 30700.379| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.33 r_work: 0.3220 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 29716 Z= 0.187 Angle : 0.821 59.199 40573 Z= 0.439 Chirality : 0.050 0.473 4703 Planarity : 0.005 0.138 5153 Dihedral : 6.082 103.156 5166 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.68 % Favored : 95.18 % Rotamer: Outliers : 3.71 % Allowed : 19.21 % Favored : 77.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.14), residues: 3572 helix: 1.78 (0.20), residues: 684 sheet: -0.26 (0.17), residues: 872 loop : -1.51 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 65 TYR 0.032 0.001 TYR G 105 PHE 0.020 0.002 PHE B 456 TRP 0.018 0.002 TRP D 353 HIS 0.023 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00426 (29610) covalent geometry : angle 0.78867 (40302) SS BOND : bond 0.00767 ( 44) SS BOND : angle 2.70866 ( 88) hydrogen bonds : bond 0.06662 ( 1028) hydrogen bonds : angle 5.47094 ( 2802) Misc. bond : bond 0.00161 ( 1) link_BETA1-4 : bond 0.00665 ( 11) link_BETA1-4 : angle 1.69707 ( 33) link_NAG-ASN : bond 0.00421 ( 50) link_NAG-ASN : angle 3.23288 ( 150) ********************** 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 322 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 206 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8367 (pp) REVERT: A 177 MET cc_start: 0.3703 (OUTLIER) cc_final: 0.3078 (mpt) REVERT: A 224 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: A 231 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7705 (pp) REVERT: A 245 HIS cc_start: 0.7491 (t70) cc_final: 0.6800 (OUTLIER) REVERT: A 585 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7039 (mt) REVERT: A 740 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.7786 (tmm) REVERT: A 787 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8471 (mt0) REVERT: A 1129 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7919 (t) REVERT: B 28 TYR cc_start: 0.8047 (m-10) cc_final: 0.7843 (m-10) REVERT: B 29 THR cc_start: 0.8025 (t) cc_final: 0.7813 (m) REVERT: B 80 ASP cc_start: 0.6200 (t0) cc_final: 0.5822 (t0) REVERT: B 153 MET cc_start: 0.3944 (mmm) cc_final: 0.1425 (tmm) REVERT: B 170 TYR cc_start: 0.7475 (t80) cc_final: 0.7178 (t80) REVERT: B 224 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: B 558 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7485 (mmmt) REVERT: B 580 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.6638 (mp10) REVERT: B 616 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7352 (m-40) REVERT: B 675 GLN cc_start: 0.6758 (pp30) cc_final: 0.6482 (pt0) REVERT: B 740 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.7810 (tmm) REVERT: B 856 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7646 (m110) REVERT: B 994 ASP cc_start: 0.8390 (m-30) cc_final: 0.8081 (m-30) REVERT: B 1111 GLU cc_start: 0.8148 (pp20) cc_final: 0.7547 (pp20) REVERT: B 1141 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6170 (tp) REVERT: D 81 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7198 (p0) REVERT: D 144 TYR cc_start: 0.5236 (m-80) cc_final: 0.4993 (m-80) REVERT: D 153 MET cc_start: 0.6609 (mmt) cc_final: 0.6352 (mmm) REVERT: D 619 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: D 787 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8386 (mt0) REVERT: D 1045 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7718 (tmtt) REVERT: D 1077 THR cc_start: 0.9383 (OUTLIER) cc_final: 0.9122 (p) REVERT: D 1139 ASP cc_start: 0.7089 (t0) cc_final: 0.6736 (t70) REVERT: G 33 MET cc_start: 0.5256 (tpt) cc_final: 0.4856 (ttt) REVERT: G 55 ASP cc_start: 0.4908 (OUTLIER) cc_final: 0.4321 (m-30) REVERT: G 81 MET cc_start: 0.3068 (ttt) cc_final: 0.0913 (ptt) REVERT: F 5 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7240 (mm110) REVERT: K 11 LEU cc_start: 0.2968 (OUTLIER) cc_final: 0.2145 (mm) REVERT: K 81 MET cc_start: 0.2991 (tpp) cc_final: 0.2528 (tmm) outliers start: 116 outliers final: 87 residues processed: 296 average time/residue: 0.4564 time to fit residues: 168.4470 Evaluate side-chains 312 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 205 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 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 333 THR Chi-restraints excluded: chain A residue 385 THR 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 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU 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 734 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 791 THR Chi-restraints excluded: chain A residue 868 GLU 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 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 84 LEU 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 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 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 574 ASP 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 616 ASN Chi-restraints excluded: chain B residue 646 ARG 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 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 1001 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 79 PHE 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 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 547 THR 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 735 SER 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 G residue 2 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain F residue 50 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 184 optimal weight: 0.8980 chunk 198 optimal weight: 0.4980 chunk 176 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 352 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 147 optimal weight: 0.0170 chunk 343 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 211 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B1010 GLN B1101 HIS D1010 GLN D1101 HIS ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.215253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.166093 restraints weight = 31156.437| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.33 r_work: 0.3280 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29716 Z= 0.117 Angle : 0.627 13.074 40573 Z= 0.311 Chirality : 0.046 0.382 4703 Planarity : 0.004 0.050 5153 Dihedral : 5.713 103.388 5166 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 2.75 % Allowed : 20.24 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.14), residues: 3572 helix: 2.03 (0.20), residues: 686 sheet: -0.17 (0.17), residues: 855 loop : -1.40 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 577 TYR 0.028 0.001 TYR G 105 PHE 0.022 0.001 PHE D 456 TRP 0.013 0.001 TRP D 633 HIS 0.024 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00251 (29610) covalent geometry : angle 0.59245 (40302) SS BOND : bond 0.00454 ( 44) SS BOND : angle 2.10076 ( 88) hydrogen bonds : bond 0.05267 ( 1028) hydrogen bonds : angle 5.34149 ( 2802) Misc. bond : bond 0.00131 ( 1) link_BETA1-4 : bond 0.00545 ( 11) link_BETA1-4 : angle 1.55111 ( 33) link_NAG-ASN : bond 0.00455 ( 50) link_NAG-ASN : angle 2.98377 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12430.65 seconds wall clock time: 211 minutes 50.25 seconds (12710.25 seconds total)