Starting phenix.real_space_refine on Tue Jul 7 02:42:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jyo_36728/07_2026/8jyo_36728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jyo_36728/07_2026/8jyo_36728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jyo_36728/07_2026/8jyo_36728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jyo_36728/07_2026/8jyo_36728.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8jyo_36728/07_2026/8jyo_36728.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jyo_36728/07_2026/8jyo_36728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jyo_36728/07_2026/8jyo_36728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jyo_36728/07_2026/8jyo_36728.map" } resolution = 3.2 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9780 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 164 5.16 5 C 21831 2.51 5 N 5570 2.21 5 O 6668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34233 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7893 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 54, 'TRANS': 955} Chain breaks: 7 Chain: "B" Number of atoms: 7859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7859 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 53, 'TRANS': 951} Chain breaks: 7 Chain: "C" Number of atoms: 7717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7717 Classifications: {'peptide': 986} Link IDs: {'PTRANS': 52, 'TRANS': 933} Chain breaks: 8 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.05, per 1000 atoms: 0.21 Number of scatterers: 34233 At special positions: 0 Unit cell: (139.695, 158.79, 237.18, 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 164 16.00 O 6668 8.00 N 5570 7.00 C 21831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 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 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.02 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 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 331 " " NAG A1313 " - " ASN A 343 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 331 " " NAG B1312 " - " ASN B 343 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 331 " " NAG D 701 " - " ASN D 322 " " NAG D 702 " - " ASN D 432 " " NAG D 703 " - " ASN D 53 " " NAG E 701 " - " ASN E 322 " " NAG E 702 " - " ASN E 432 " " NAG E 703 " - " ASN E 53 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN C 165 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN C 801 " " NAG M 1 " - " ASN E 546 " " NAG N 1 " - " ASN E 90 " " NAG O 1 " - " ASN E 103 " " NAG P 1 " - " ASN D 546 " " NAG Q 1 " - " ASN D 90 " " NAG R 1 " - " ASN D 103 " Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.2 seconds 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7888 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 54 sheets defined 36.7% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.526A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.796A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 removed outlier: 3.700A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR A 827 " --> pdb=" O PHE A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.202A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.711A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.867A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.037A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.409A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.595A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.936A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.109A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.715A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.886A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.035A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.574A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.514A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.685A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.651A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.599A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.520A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.565A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.739A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.879A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.573A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.668A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'E' and resid 20 through 52 removed outlier: 3.707A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 80 Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.873A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE E 88 " --> pdb=" O LEU E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 88' Processing helix chain 'E' and resid 92 through 104 removed outlier: 3.629A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY E 104 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 130 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 194 removed outlier: 3.587A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.583A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 233 removed outlier: 3.859A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 252 removed outlier: 4.116A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 283 removed outlier: 4.429A pdb=" N SER E 280 " --> pdb=" O ASN E 277 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL E 283 " --> pdb=" O SER E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 318 removed outlier: 3.840A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.540A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.699A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 413 removed outlier: 4.337A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.651A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.376A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 482 Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 4.305A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.682A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.671A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.850A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 92 through 104 removed outlier: 3.666A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.568A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.586A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 233 removed outlier: 3.845A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 4.109A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 283 removed outlier: 4.487A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL D 283 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.784A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.572A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.715A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.238A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.667A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.385A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.439A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.655A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 8.446A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.014A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.733A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.566A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.378A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.558A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.943A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.697A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.692A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.028A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.824A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.528A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.662A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.368A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.041A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.887A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 169 through 172 removed outlier: 5.087A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.108A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.966A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.311A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.714A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.699A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.236A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.762A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.610A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.023A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.272A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 169 through 172 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.003A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE5, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.829A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.073A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AE9, first strand: chain 'C' and resid 717 through 728 removed outlier: 5.972A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.734A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AF3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF4, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.572A pdb=" N VAL E 132 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.843A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'E' and resid 347 through 350 Processing sheet with id=AF7, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.556A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.845A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'D' and resid 347 through 350 1407 hydrogen bonds defined for protein. 3936 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: 7.74 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10825 1.35 - 1.47: 9106 1.47 - 1.60: 14888 1.60 - 1.72: 0 1.72 - 1.85: 233 Bond restraints: 35052 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" C1 MAN R 4 " pdb=" C2 MAN R 4 " ideal model delta sigma weight residual 1.526 1.562 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.27e+00 ... (remaining 35047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 46268 1.55 - 3.09: 1170 3.09 - 4.64: 177 4.64 - 6.18: 43 6.18 - 7.73: 10 Bond angle restraints: 47668 Sorted by residual: angle pdb=" N VAL B 130 " pdb=" CA VAL B 130 " pdb=" C VAL B 130 " ideal model delta sigma weight residual 111.91 106.09 5.82 8.90e-01 1.26e+00 4.28e+01 angle pdb=" C HIS D 34 " pdb=" N GLU D 35 " pdb=" CA GLU D 35 " ideal model delta sigma weight residual 120.29 115.53 4.76 1.42e+00 4.96e-01 1.12e+01 angle pdb=" N GLU D 35 " pdb=" CA GLU D 35 " pdb=" CB GLU D 35 " ideal model delta sigma weight residual 110.16 114.83 -4.67 1.48e+00 4.57e-01 9.97e+00 angle pdb=" C HIS E 34 " pdb=" N GLU E 35 " pdb=" CA GLU E 35 " ideal model delta sigma weight residual 120.29 115.84 4.45 1.42e+00 4.96e-01 9.83e+00 angle pdb=" N GLU E 35 " pdb=" CA GLU E 35 " pdb=" CB GLU E 35 " ideal model delta sigma weight residual 110.16 114.80 -4.64 1.48e+00 4.57e-01 9.81e+00 ... (remaining 47663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.90: 20463 22.90 - 45.79: 1112 45.79 - 68.69: 97 68.69 - 91.59: 63 91.59 - 114.48: 22 Dihedral angle restraints: 21757 sinusoidal: 9511 harmonic: 12246 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 7.67 85.33 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 36.53 56.47 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual 93.00 36.81 56.19 1 1.00e+01 1.00e-02 4.26e+01 ... (remaining 21754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 5466 0.134 - 0.269: 33 0.269 - 0.403: 10 0.403 - 0.538: 2 0.538 - 0.672: 2 Chirality restraints: 5513 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.24e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN E 103 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.73e+00 ... (remaining 5510 not shown) Planarity restraints: 6107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO C 527 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 130 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C VAL C 130 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL C 130 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS C 131 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO B 561 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " 0.022 5.00e-02 4.00e+02 ... (remaining 6104 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 357 2.63 - 3.20: 30554 3.20 - 3.76: 49684 3.76 - 4.33: 67177 4.33 - 4.90: 114356 Nonbonded interactions: 262128 Sorted by model distance: nonbonded pdb=" NZ LYS B 811 " pdb=" OG SER B 813 " model vdw 2.061 3.120 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.134 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.148 3.040 nonbonded pdb=" OG SER A 746 " pdb=" OE1 GLU A 748 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR B 500 " pdb=" OH TYR E 41 " model vdw 2.242 3.040 ... (remaining 262123 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 25 through 65 or resid 86 through 177 or resid 188 through \ 470 or resid 490 through 620 or resid 640 through 675 or resid 690 through 827 \ or resid 855 through 1311)) selection = (chain 'B' and (resid 25 through 65 or resid 86 through 177 or resid 188 through \ 470 or resid 490 through 620 or resid 640 through 1311)) selection = (chain 'C' and (resid 25 through 65 or resid 86 through 675 or resid 690 through \ 827 or resid 855 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'O' selection = chain 'R' } 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 31.260 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 : 0.005 0.080 35172 Z= 0.207 Angle : 0.642 19.006 47984 Z= 0.311 Chirality : 0.050 0.672 5513 Planarity : 0.004 0.056 6052 Dihedral : 14.147 114.485 13737 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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 are not related in a simple way. whole: 0.32 (0.13), residues: 4139 helix: 1.79 (0.15), residues: 1368 sheet: 0.49 (0.19), residues: 708 loop : -1.00 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 460 TYR 0.015 0.001 TYR A1067 PHE 0.016 0.001 PHE C 906 TRP 0.025 0.001 TRP C 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (35052) covalent geometry : angle 0.59899 / 0.30 (47668) SS BOND : bond 0.00329 / 0.22 ( 44) SS BOND : angle 1.51372 / 1.00 ( 88) hydrogen bonds : bond 0.14446 / 9.61 ( 1407) hydrogen bonds : angle 5.95149 / 4.09 ( 3936) link_ALPHA1-3 : bond 0.00355 / 0.18 ( 2) link_ALPHA1-3 : angle 1.57621 / 0.87 ( 6) link_ALPHA1-6 : bond 0.00289 / 0.15 ( 2) link_ALPHA1-6 : angle 1.65695 / 0.89 ( 6) link_BETA1-4 : bond 0.00339 / 0.20 ( 17) link_BETA1-4 : angle 1.59590 / 0.94 ( 51) link_NAG-ASN : bond 0.00727 / 0.47 ( 55) link_NAG-ASN : angle 3.72528 / 2.24 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6260 (ppp) cc_final: 0.6059 (ppp) REVERT: A 189 LEU cc_start: 0.8300 (mm) cc_final: 0.8001 (mm) REVERT: A 238 PHE cc_start: 0.8519 (p90) cc_final: 0.7822 (p90) REVERT: B 133 PHE cc_start: 0.7332 (m-80) cc_final: 0.6804 (m-80) REVERT: B 157 PHE cc_start: 0.7889 (t80) cc_final: 0.7612 (t80) REVERT: B 1005 GLN cc_start: 0.8806 (tp40) cc_final: 0.8596 (mm-40) REVERT: C 110 LEU cc_start: 0.9117 (tp) cc_final: 0.8856 (tp) REVERT: C 200 TYR cc_start: 0.8703 (m-10) cc_final: 0.8486 (m-80) REVERT: C 358 ILE cc_start: 0.7839 (mm) cc_final: 0.7631 (mp) REVERT: C 532 ASN cc_start: 0.8912 (t0) cc_final: 0.8671 (t0) REVERT: C 571 ASP cc_start: 0.8000 (t0) cc_final: 0.7679 (t0) REVERT: E 548 THR cc_start: 0.3008 (p) cc_final: 0.2781 (t) REVERT: D 249 MET cc_start: 0.2345 (mmm) cc_final: 0.2050 (mmt) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2038 time to fit residues: 111.2790 Evaluate side-chains 179 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 HIS A 613 GLN B 901 GLN C 164 ASN C 207 HIS E 101 GLN E 345 HIS ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS D 472 GLN D 586 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.156303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.101758 restraints weight = 86727.725| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 4.40 r_work: 0.2893 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35172 Z= 0.152 Angle : 0.624 18.176 47984 Z= 0.306 Chirality : 0.048 0.624 5513 Planarity : 0.004 0.061 6052 Dihedral : 9.333 102.385 5995 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.49 % Allowed : 5.92 % Favored : 93.59 % 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 are not related in a simple way. whole: 0.44 (0.13), residues: 4139 helix: 1.86 (0.14), residues: 1406 sheet: 0.70 (0.19), residues: 717 loop : -1.04 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 177 TYR 0.024 0.001 TYR B1067 PHE 0.022 0.001 PHE A 168 TRP 0.017 0.001 TRP E 566 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (35052) covalent geometry : angle 0.58100 / 0.30 (47668) SS BOND : bond 0.00343 / 0.22 ( 44) SS BOND : angle 1.45509 / 1.07 ( 88) hydrogen bonds : bond 0.05537 / 3.62 ( 1407) hydrogen bonds : angle 4.74882 / 3.30 ( 3936) link_ALPHA1-3 : bond 0.01363 / 0.69 ( 2) link_ALPHA1-3 : angle 1.97257 / 1.11 ( 6) link_ALPHA1-6 : bond 0.00353 / 0.18 ( 2) link_ALPHA1-6 : angle 2.22464 / 1.13 ( 6) link_BETA1-4 : bond 0.00707 / 0.53 ( 17) link_BETA1-4 : angle 1.83115 / 1.07 ( 51) link_NAG-ASN : bond 0.00687 / 0.45 ( 55) link_NAG-ASN : angle 3.65778 / 2.22 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6299 (ppp) cc_final: 0.6098 (ppp) REVERT: A 189 LEU cc_start: 0.8272 (mm) cc_final: 0.8000 (mm) REVERT: A 238 PHE cc_start: 0.8297 (p90) cc_final: 0.7532 (p90) REVERT: A 351 TYR cc_start: 0.7809 (p90) cc_final: 0.7492 (p90) REVERT: A 378 LYS cc_start: 0.8897 (tppp) cc_final: 0.8660 (pttp) REVERT: A 452 LEU cc_start: 0.6922 (mt) cc_final: 0.6549 (mt) REVERT: B 133 PHE cc_start: 0.7199 (m-80) cc_final: 0.6865 (m-80) REVERT: B 157 PHE cc_start: 0.7830 (t80) cc_final: 0.7537 (t80) REVERT: B 365 TYR cc_start: 0.7951 (m-10) cc_final: 0.7608 (m-80) REVERT: C 110 LEU cc_start: 0.9227 (tp) cc_final: 0.9003 (tp) REVERT: C 200 TYR cc_start: 0.8880 (m-10) cc_final: 0.8570 (m-80) REVERT: C 358 ILE cc_start: 0.7533 (mm) cc_final: 0.7254 (mp) REVERT: C 823 PHE cc_start: 0.8618 (t80) cc_final: 0.8348 (t80) outliers start: 18 outliers final: 10 residues processed: 210 average time/residue: 0.2006 time to fit residues: 71.4134 Evaluate side-chains 180 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 433 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 214 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 229 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 408 optimal weight: 6.9990 chunk 354 optimal weight: 20.0000 chunk 81 optimal weight: 0.0770 chunk 197 optimal weight: 0.0070 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 505 HIS C 207 HIS ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.155794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.097965 restraints weight = 85314.667| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 5.29 r_work: 0.2858 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35172 Z= 0.157 Angle : 0.595 18.382 47984 Z= 0.292 Chirality : 0.047 0.622 5513 Planarity : 0.004 0.052 6052 Dihedral : 8.367 98.516 5995 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.71 % Allowed : 7.82 % Favored : 91.47 % 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 are not related in a simple way. whole: 0.42 (0.13), residues: 4139 helix: 1.82 (0.14), residues: 1414 sheet: 0.65 (0.19), residues: 727 loop : -1.03 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 245 TYR 0.024 0.001 TYR B1067 PHE 0.014 0.001 PHE C 133 TRP 0.010 0.001 TRP C 886 HIS 0.021 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (35052) covalent geometry : angle 0.55344 / 0.28 (47668) SS BOND : bond 0.00323 / 0.22 ( 44) SS BOND : angle 1.49311 / 1.09 ( 88) hydrogen bonds : bond 0.05306 / 3.45 ( 1407) hydrogen bonds : angle 4.59461 / 3.20 ( 3936) link_ALPHA1-3 : bond 0.01352 / 0.68 ( 2) link_ALPHA1-3 : angle 2.01068 / 1.07 ( 6) link_ALPHA1-6 : bond 0.00539 / 0.27 ( 2) link_ALPHA1-6 : angle 2.06448 / 1.06 ( 6) link_BETA1-4 : bond 0.00448 / 0.31 ( 17) link_BETA1-4 : angle 1.66279 / 1.02 ( 51) link_NAG-ASN : bond 0.00632 / 0.41 ( 55) link_NAG-ASN : angle 3.48473 / 2.08 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6270 (ppp) cc_final: 0.5996 (ppp) REVERT: A 189 LEU cc_start: 0.8360 (mm) cc_final: 0.8022 (mm) REVERT: A 238 PHE cc_start: 0.8321 (p90) cc_final: 0.7595 (p90) REVERT: A 351 TYR cc_start: 0.7734 (p90) cc_final: 0.7501 (p90) REVERT: A 378 LYS cc_start: 0.8903 (tppp) cc_final: 0.8692 (pttp) REVERT: A 392 PHE cc_start: 0.7855 (m-80) cc_final: 0.7520 (m-10) REVERT: A 452 LEU cc_start: 0.7210 (mt) cc_final: 0.6784 (mt) REVERT: B 133 PHE cc_start: 0.7219 (m-80) cc_final: 0.6897 (m-80) REVERT: B 157 PHE cc_start: 0.7780 (t80) cc_final: 0.7487 (t80) REVERT: B 365 TYR cc_start: 0.7999 (m-10) cc_final: 0.7601 (m-10) REVERT: B 392 PHE cc_start: 0.8161 (m-80) cc_final: 0.7922 (m-10) REVERT: C 110 LEU cc_start: 0.9306 (tp) cc_final: 0.9093 (tp) REVERT: C 200 TYR cc_start: 0.8912 (m-10) cc_final: 0.8595 (m-80) REVERT: C 207 HIS cc_start: 0.8572 (OUTLIER) cc_final: 0.8047 (p-80) REVERT: C 358 ILE cc_start: 0.7514 (mm) cc_final: 0.7229 (mp) outliers start: 26 outliers final: 10 residues processed: 207 average time/residue: 0.1985 time to fit residues: 70.3578 Evaluate side-chains 186 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain D residue 592 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 308 optimal weight: 30.0000 chunk 221 optimal weight: 0.6980 chunk 352 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 129 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 275 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 54 optimal weight: 0.0970 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 901 GLN B 439 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN D 524 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.156012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.098265 restraints weight = 84829.794| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 5.28 r_work: 0.2855 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35172 Z= 0.132 Angle : 0.580 18.033 47984 Z= 0.281 Chirality : 0.046 0.611 5513 Planarity : 0.004 0.053 6052 Dihedral : 7.586 95.453 5995 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.76 % Allowed : 9.29 % Favored : 89.95 % 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 are not related in a simple way. whole: 0.47 (0.13), residues: 4139 helix: 1.88 (0.14), residues: 1408 sheet: 0.67 (0.19), residues: 726 loop : -1.00 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 245 TYR 0.021 0.001 TYR B1067 PHE 0.014 0.001 PHE E 464 TRP 0.009 0.001 TRP E 163 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (35052) covalent geometry : angle 0.53900 / 0.27 (47668) SS BOND : bond 0.00290 / 0.20 ( 44) SS BOND : angle 1.28405 / 0.92 ( 88) hydrogen bonds : bond 0.04907 / 3.19 ( 1407) hydrogen bonds : angle 4.49861 / 3.13 ( 3936) link_ALPHA1-3 : bond 0.01205 / 0.59 ( 2) link_ALPHA1-3 : angle 1.90073 / 1.03 ( 6) link_ALPHA1-6 : bond 0.00588 / 0.30 ( 2) link_ALPHA1-6 : angle 1.87046 / 0.96 ( 6) link_BETA1-4 : bond 0.00405 / 0.27 ( 17) link_BETA1-4 : angle 1.57579 / 0.97 ( 51) link_NAG-ASN : bond 0.00635 / 0.41 ( 55) link_NAG-ASN : angle 3.47385 / 2.08 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6242 (ppp) cc_final: 0.5870 (ppp) REVERT: A 189 LEU cc_start: 0.8383 (mm) cc_final: 0.8043 (mm) REVERT: A 211 ASN cc_start: 0.7560 (t0) cc_final: 0.7354 (t0) REVERT: A 220 PHE cc_start: 0.7035 (OUTLIER) cc_final: 0.6320 (t80) REVERT: A 238 PHE cc_start: 0.8285 (p90) cc_final: 0.7604 (p90) REVERT: A 240 THR cc_start: 0.7522 (OUTLIER) cc_final: 0.7162 (t) REVERT: A 351 TYR cc_start: 0.7735 (p90) cc_final: 0.7525 (p90) REVERT: A 378 LYS cc_start: 0.8902 (tppp) cc_final: 0.8691 (pttp) REVERT: A 392 PHE cc_start: 0.7830 (m-80) cc_final: 0.7552 (m-80) REVERT: A 452 LEU cc_start: 0.7237 (mt) cc_final: 0.6845 (mt) REVERT: B 133 PHE cc_start: 0.7119 (m-80) cc_final: 0.6742 (m-80) REVERT: B 157 PHE cc_start: 0.7837 (t80) cc_final: 0.7533 (t80) REVERT: B 365 TYR cc_start: 0.7942 (m-10) cc_final: 0.7606 (m-10) REVERT: B 563 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7327 (mp10) REVERT: C 200 TYR cc_start: 0.8848 (m-10) cc_final: 0.8556 (m-80) REVERT: C 351 TYR cc_start: 0.6424 (p90) cc_final: 0.6027 (p90) REVERT: E 579 MET cc_start: 0.3562 (mtt) cc_final: 0.3083 (mmt) REVERT: D 237 TYR cc_start: 0.6371 (t80) cc_final: 0.4747 (m-80) outliers start: 28 outliers final: 13 residues processed: 199 average time/residue: 0.2050 time to fit residues: 69.8333 Evaluate side-chains 185 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 592 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 338 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 102 optimal weight: 0.0030 chunk 334 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 chunk 379 optimal weight: 30.0000 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 901 GLN B1010 GLN C 334 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.153544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.096589 restraints weight = 85039.797| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 5.01 r_work: 0.2807 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 35172 Z= 0.281 Angle : 0.700 20.568 47984 Z= 0.345 Chirality : 0.050 0.730 5513 Planarity : 0.004 0.055 6052 Dihedral : 7.259 80.011 5995 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.14 % Allowed : 11.00 % Favored : 87.86 % 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 are not related in a simple way. whole: 0.13 (0.13), residues: 4139 helix: 1.66 (0.14), residues: 1405 sheet: 0.35 (0.19), residues: 727 loop : -1.19 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 24 TYR 0.032 0.002 TYR B1067 PHE 0.030 0.002 PHE D 315 TRP 0.011 0.001 TRP C 886 HIS 0.007 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.28 (35052) covalent geometry : angle 0.66026 / 0.34 (47668) SS BOND : bond 0.00556 / 0.32 ( 44) SS BOND : angle 1.74752 / 1.24 ( 88) hydrogen bonds : bond 0.06517 / 4.20 ( 1407) hydrogen bonds : angle 4.76843 / 3.31 ( 3936) link_ALPHA1-3 : bond 0.01342 / 0.67 ( 2) link_ALPHA1-3 : angle 1.92671 / 1.02 ( 6) link_ALPHA1-6 : bond 0.00678 / 0.34 ( 2) link_ALPHA1-6 : angle 1.79662 / 0.96 ( 6) link_BETA1-4 : bond 0.00430 / 0.30 ( 17) link_BETA1-4 : angle 1.73671 / 1.04 ( 51) link_NAG-ASN : bond 0.00612 / 0.39 ( 55) link_NAG-ASN : angle 3.71414 / 2.25 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6495 (ppp) cc_final: 0.6042 (ppp) REVERT: A 189 LEU cc_start: 0.8353 (mm) cc_final: 0.7987 (mm) REVERT: A 196 ASN cc_start: 0.8129 (t0) cc_final: 0.7510 (m-40) REVERT: A 211 ASN cc_start: 0.7521 (t0) cc_final: 0.7268 (t0) REVERT: A 238 PHE cc_start: 0.8271 (p90) cc_final: 0.7568 (p90) REVERT: A 240 THR cc_start: 0.7415 (OUTLIER) cc_final: 0.6997 (t) REVERT: A 378 LYS cc_start: 0.8886 (tppp) cc_final: 0.8653 (pttp) REVERT: A 392 PHE cc_start: 0.7898 (m-80) cc_final: 0.7621 (m-10) REVERT: A 452 LEU cc_start: 0.7253 (mt) cc_final: 0.6835 (mt) REVERT: A 855 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7527 (p90) REVERT: B 119 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7526 (mp) REVERT: B 133 PHE cc_start: 0.7197 (m-80) cc_final: 0.6705 (m-80) REVERT: B 157 PHE cc_start: 0.7900 (t80) cc_final: 0.7651 (t80) REVERT: B 365 TYR cc_start: 0.8105 (m-10) cc_final: 0.7771 (m-10) REVERT: B 562 PHE cc_start: 0.8005 (p90) cc_final: 0.7742 (p90) REVERT: B 563 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7272 (mt0) REVERT: C 351 TYR cc_start: 0.6372 (p90) cc_final: 0.5935 (p90) REVERT: E 383 MET cc_start: 0.5027 (ttp) cc_final: 0.4468 (ppp) REVERT: E 562 LYS cc_start: 0.3203 (mtpt) cc_final: 0.2674 (tttt) REVERT: E 579 MET cc_start: 0.2928 (mtt) cc_final: 0.2428 (mmt) REVERT: D 123 MET cc_start: 0.4546 (tpp) cc_final: 0.4008 (ptp) REVERT: D 249 MET cc_start: 0.1656 (mmt) cc_final: 0.1450 (mmt) REVERT: D 516 TYR cc_start: 0.7425 (t80) cc_final: 0.6829 (m-80) outliers start: 42 outliers final: 22 residues processed: 201 average time/residue: 0.1972 time to fit residues: 68.1168 Evaluate side-chains 182 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 592 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 14 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 252 optimal weight: 0.9980 chunk 251 optimal weight: 4.9990 chunk 416 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 402 optimal weight: 8.9990 chunk 195 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 334 optimal weight: 40.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN E 42 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.155727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.096875 restraints weight = 84800.494| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 5.54 r_work: 0.2862 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 35172 Z= 0.112 Angle : 0.575 17.977 47984 Z= 0.278 Chirality : 0.045 0.599 5513 Planarity : 0.004 0.053 6052 Dihedral : 6.432 71.689 5995 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.84 % Allowed : 11.95 % Favored : 87.20 % 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 are not related in a simple way. whole: 0.45 (0.13), residues: 4139 helix: 1.91 (0.14), residues: 1390 sheet: 0.61 (0.20), residues: 696 loop : -0.97 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 454 TYR 0.017 0.001 TYR B1067 PHE 0.017 0.001 PHE D 555 TRP 0.009 0.001 TRP D 168 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (35052) covalent geometry : angle 0.53044 / 0.27 (47668) SS BOND : bond 0.00357 / 0.24 ( 44) SS BOND : angle 1.58240 / 1.06 ( 88) hydrogen bonds : bond 0.04554 / 2.97 ( 1407) hydrogen bonds : angle 4.47208 / 3.11 ( 3936) link_ALPHA1-3 : bond 0.01203 / 0.60 ( 2) link_ALPHA1-3 : angle 1.77811 / 0.99 ( 6) link_ALPHA1-6 : bond 0.00788 / 0.40 ( 2) link_ALPHA1-6 : angle 1.57382 / 0.83 ( 6) link_BETA1-4 : bond 0.00443 / 0.29 ( 17) link_BETA1-4 : angle 1.40033 / 0.84 ( 51) link_NAG-ASN : bond 0.00637 / 0.42 ( 55) link_NAG-ASN : angle 3.55166 / 2.16 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6447 (ppp) cc_final: 0.6014 (ppp) REVERT: A 189 LEU cc_start: 0.8456 (mm) cc_final: 0.8123 (mm) REVERT: A 196 ASN cc_start: 0.8079 (t0) cc_final: 0.7429 (m-40) REVERT: A 211 ASN cc_start: 0.7397 (t0) cc_final: 0.7188 (t0) REVERT: A 238 PHE cc_start: 0.8265 (p90) cc_final: 0.7648 (p90) REVERT: A 240 THR cc_start: 0.7451 (OUTLIER) cc_final: 0.7157 (t) REVERT: A 378 LYS cc_start: 0.8864 (tppp) cc_final: 0.8641 (pttp) REVERT: A 392 PHE cc_start: 0.7797 (m-80) cc_final: 0.7524 (m-10) REVERT: A 855 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7420 (p90) REVERT: B 133 PHE cc_start: 0.7172 (m-80) cc_final: 0.6768 (m-80) REVERT: B 157 PHE cc_start: 0.7813 (t80) cc_final: 0.7518 (t80) REVERT: B 365 TYR cc_start: 0.7971 (m-10) cc_final: 0.7592 (m-10) REVERT: B 563 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7381 (mp10) REVERT: C 200 TYR cc_start: 0.8963 (m-10) cc_final: 0.8607 (m-80) REVERT: C 207 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.8146 (p90) REVERT: C 338 PHE cc_start: 0.8619 (m-80) cc_final: 0.8353 (m-80) REVERT: C 351 TYR cc_start: 0.6412 (p90) cc_final: 0.5996 (p90) REVERT: E 225 ASP cc_start: 0.2676 (m-30) cc_final: 0.2416 (t70) REVERT: E 408 MET cc_start: 0.2244 (pmm) cc_final: 0.2027 (ppp) REVERT: E 579 MET cc_start: 0.3472 (mtt) cc_final: 0.2791 (mmt) REVERT: D 249 MET cc_start: 0.1834 (mmt) cc_final: 0.1467 (mmt) REVERT: D 516 TYR cc_start: 0.7429 (t80) cc_final: 0.6814 (m-80) outliers start: 31 outliers final: 16 residues processed: 197 average time/residue: 0.2055 time to fit residues: 69.6665 Evaluate side-chains 183 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 520 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 103 optimal weight: 0.0980 chunk 413 optimal weight: 0.0020 chunk 325 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 359 optimal weight: 20.0000 chunk 253 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 373 optimal weight: 0.0000 chunk 294 optimal weight: 0.4980 chunk 343 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 755 GLN E 42 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.157746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.103844 restraints weight = 86197.386| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 6.12 r_work: 0.2888 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.092 35172 Z= 0.105 Angle : 0.563 17.458 47984 Z= 0.271 Chirality : 0.045 0.567 5513 Planarity : 0.004 0.049 6052 Dihedral : 5.963 61.309 5995 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.84 % Allowed : 12.31 % Favored : 86.85 % 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 are not related in a simple way. whole: 0.56 (0.13), residues: 4139 helix: 1.91 (0.14), residues: 1401 sheet: 0.73 (0.20), residues: 713 loop : -0.90 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 514 TYR 0.022 0.001 TYR A 453 PHE 0.023 0.001 PHE B 374 TRP 0.008 0.001 TRP D 461 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (35052) covalent geometry : angle 0.52115 / 0.26 (47668) SS BOND : bond 0.00343 / 0.23 ( 44) SS BOND : angle 1.51612 / 1.03 ( 88) hydrogen bonds : bond 0.04186 / 2.72 ( 1407) hydrogen bonds : angle 4.38923 / 3.06 ( 3936) link_ALPHA1-3 : bond 0.01083 / 0.54 ( 2) link_ALPHA1-3 : angle 1.79047 / 0.98 ( 6) link_ALPHA1-6 : bond 0.00808 / 0.41 ( 2) link_ALPHA1-6 : angle 1.53965 / 0.81 ( 6) link_BETA1-4 : bond 0.00455 / 0.30 ( 17) link_BETA1-4 : angle 1.38438 / 0.83 ( 51) link_NAG-ASN : bond 0.00613 / 0.40 ( 55) link_NAG-ASN : angle 3.43420 / 2.10 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6424 (ppp) cc_final: 0.5983 (ppp) REVERT: A 189 LEU cc_start: 0.8529 (mm) cc_final: 0.8154 (mm) REVERT: A 196 ASN cc_start: 0.8143 (t0) cc_final: 0.7493 (m-40) REVERT: A 238 PHE cc_start: 0.8280 (p90) cc_final: 0.7699 (p90) REVERT: A 240 THR cc_start: 0.7374 (OUTLIER) cc_final: 0.7129 (t) REVERT: A 378 LYS cc_start: 0.8850 (tppp) cc_final: 0.8622 (pttp) REVERT: A 392 PHE cc_start: 0.7776 (m-80) cc_final: 0.7493 (m-10) REVERT: A 855 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7161 (p90) REVERT: B 133 PHE cc_start: 0.7166 (m-80) cc_final: 0.6934 (m-80) REVERT: B 157 PHE cc_start: 0.7703 (t80) cc_final: 0.7467 (t80) REVERT: B 365 TYR cc_start: 0.8137 (m-10) cc_final: 0.7763 (m-10) REVERT: B 563 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7349 (mt0) REVERT: C 200 TYR cc_start: 0.8928 (m-10) cc_final: 0.8580 (m-80) REVERT: C 207 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.8180 (p90) REVERT: C 351 TYR cc_start: 0.6379 (p90) cc_final: 0.5990 (p90) REVERT: E 579 MET cc_start: 0.3751 (mtt) cc_final: 0.3107 (mmt) REVERT: D 249 MET cc_start: 0.2049 (mmt) cc_final: 0.1758 (mmt) REVERT: D 332 MET cc_start: 0.4988 (ppp) cc_final: 0.4214 (pmm) outliers start: 31 outliers final: 16 residues processed: 199 average time/residue: 0.2070 time to fit residues: 70.4323 Evaluate side-chains 182 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 520 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 201 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 257 optimal weight: 4.9990 chunk 396 optimal weight: 0.0670 chunk 77 optimal weight: 0.8980 chunk 280 optimal weight: 0.0970 chunk 400 optimal weight: 30.0000 chunk 229 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.155765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.098928 restraints weight = 85668.005| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 5.01 r_work: 0.2882 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 35172 Z= 0.134 Angle : 0.585 17.809 47984 Z= 0.283 Chirality : 0.045 0.598 5513 Planarity : 0.004 0.046 6052 Dihedral : 5.805 58.866 5995 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.92 % Allowed : 12.66 % Favored : 86.42 % 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 are not related in a simple way. whole: 0.53 (0.13), residues: 4139 helix: 1.90 (0.14), residues: 1403 sheet: 0.68 (0.19), residues: 711 loop : -0.90 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 983 TYR 0.021 0.001 TYR B1067 PHE 0.020 0.001 PHE D 555 TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (35052) covalent geometry : angle 0.54429 / 0.27 (47668) SS BOND : bond 0.00371 / 0.25 ( 44) SS BOND : angle 1.58775 / 1.09 ( 88) hydrogen bonds : bond 0.04618 / 2.99 ( 1407) hydrogen bonds : angle 4.42150 / 3.08 ( 3936) link_ALPHA1-3 : bond 0.01026 / 0.51 ( 2) link_ALPHA1-3 : angle 1.84390 / 1.02 ( 6) link_ALPHA1-6 : bond 0.00787 / 0.39 ( 2) link_ALPHA1-6 : angle 1.51503 / 0.81 ( 6) link_BETA1-4 : bond 0.00444 / 0.30 ( 17) link_BETA1-4 : angle 1.38832 / 0.83 ( 51) link_NAG-ASN : bond 0.00572 / 0.37 ( 55) link_NAG-ASN : angle 3.41692 / 2.07 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6459 (ppp) cc_final: 0.6019 (ppp) REVERT: A 189 LEU cc_start: 0.8510 (mm) cc_final: 0.8130 (mm) REVERT: A 196 ASN cc_start: 0.8172 (t0) cc_final: 0.7516 (m-40) REVERT: A 238 PHE cc_start: 0.8233 (p90) cc_final: 0.7645 (p90) REVERT: A 240 THR cc_start: 0.7364 (OUTLIER) cc_final: 0.7135 (t) REVERT: A 378 LYS cc_start: 0.8818 (tppp) cc_final: 0.8575 (pttp) REVERT: A 392 PHE cc_start: 0.7901 (m-80) cc_final: 0.7634 (m-10) REVERT: A 855 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7244 (p90) REVERT: B 133 PHE cc_start: 0.7140 (m-80) cc_final: 0.6887 (m-80) REVERT: B 157 PHE cc_start: 0.7779 (t80) cc_final: 0.7514 (t80) REVERT: B 365 TYR cc_start: 0.8198 (m-10) cc_final: 0.7827 (m-80) REVERT: B 563 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7372 (mt0) REVERT: C 200 TYR cc_start: 0.8959 (m-10) cc_final: 0.8608 (m-80) REVERT: C 207 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.8261 (p90) REVERT: C 351 TYR cc_start: 0.6395 (p90) cc_final: 0.5988 (p90) REVERT: E 562 LYS cc_start: 0.3039 (mtpt) cc_final: 0.2519 (tttt) REVERT: E 579 MET cc_start: 0.3580 (mtt) cc_final: 0.3123 (mmt) REVERT: D 249 MET cc_start: 0.1938 (mmt) cc_final: 0.1637 (mmt) REVERT: D 332 MET cc_start: 0.5086 (ppp) cc_final: 0.4346 (pmm) REVERT: D 516 TYR cc_start: 0.7241 (t80) cc_final: 0.6622 (m-80) outliers start: 34 outliers final: 18 residues processed: 192 average time/residue: 0.1964 time to fit residues: 64.3624 Evaluate side-chains 182 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 518 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 167 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 397 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 307 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.155151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.098959 restraints weight = 87750.106| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.67 r_work: 0.2889 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 35172 Z= 0.142 Angle : 0.593 17.908 47984 Z= 0.288 Chirality : 0.045 0.612 5513 Planarity : 0.004 0.058 6052 Dihedral : 5.709 58.562 5995 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.62 % Allowed : 13.31 % Favored : 86.06 % 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 are not related in a simple way. whole: 0.51 (0.13), residues: 4139 helix: 1.88 (0.14), residues: 1403 sheet: 0.66 (0.19), residues: 711 loop : -0.92 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 983 TYR 0.022 0.001 TYR A 453 PHE 0.022 0.001 PHE D 555 TRP 0.011 0.001 TRP D 478 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (35052) covalent geometry : angle 0.55299 / 0.28 (47668) SS BOND : bond 0.00365 / 0.24 ( 44) SS BOND : angle 1.56110 / 1.07 ( 88) hydrogen bonds : bond 0.04720 / 3.05 ( 1407) hydrogen bonds : angle 4.43339 / 3.08 ( 3936) link_ALPHA1-3 : bond 0.00977 / 0.49 ( 2) link_ALPHA1-3 : angle 1.90331 / 1.07 ( 6) link_ALPHA1-6 : bond 0.00733 / 0.36 ( 2) link_ALPHA1-6 : angle 1.46586 / 0.78 ( 6) link_BETA1-4 : bond 0.00430 / 0.29 ( 17) link_BETA1-4 : angle 1.39587 / 0.84 ( 51) link_NAG-ASN : bond 0.00552 / 0.35 ( 55) link_NAG-ASN : angle 3.41583 / 2.07 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6438 (ppp) cc_final: 0.5982 (ppp) REVERT: A 189 LEU cc_start: 0.8529 (mm) cc_final: 0.8165 (mm) REVERT: A 196 ASN cc_start: 0.8191 (t0) cc_final: 0.7541 (m-40) REVERT: A 238 PHE cc_start: 0.8237 (p90) cc_final: 0.7633 (p90) REVERT: A 240 THR cc_start: 0.7526 (OUTLIER) cc_final: 0.7318 (t) REVERT: A 378 LYS cc_start: 0.8799 (tppp) cc_final: 0.8577 (pttp) REVERT: A 392 PHE cc_start: 0.7780 (m-80) cc_final: 0.7503 (m-10) REVERT: A 855 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.6917 (p90) REVERT: B 157 PHE cc_start: 0.7683 (t80) cc_final: 0.7463 (t80) REVERT: B 177 MET cc_start: 0.6897 (tmm) cc_final: 0.6681 (tmm) REVERT: B 365 TYR cc_start: 0.8067 (m-10) cc_final: 0.7681 (m-80) REVERT: B 563 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7404 (mt0) REVERT: C 200 TYR cc_start: 0.8982 (m-10) cc_final: 0.8604 (m-80) REVERT: C 338 PHE cc_start: 0.8804 (m-80) cc_final: 0.8580 (m-10) REVERT: C 351 TYR cc_start: 0.6269 (p90) cc_final: 0.5874 (p90) REVERT: E 562 LYS cc_start: 0.2996 (mtpt) cc_final: 0.2455 (tttt) REVERT: E 579 MET cc_start: 0.3067 (mtt) cc_final: 0.2524 (mmt) REVERT: D 152 MET cc_start: 0.3831 (ptt) cc_final: 0.3129 (ptm) REVERT: D 249 MET cc_start: 0.1542 (mmt) cc_final: 0.1168 (mmt) REVERT: D 332 MET cc_start: 0.4784 (ppp) cc_final: 0.4473 (ptp) REVERT: D 516 TYR cc_start: 0.7307 (t80) cc_final: 0.6853 (m-80) outliers start: 23 outliers final: 17 residues processed: 181 average time/residue: 0.1889 time to fit residues: 59.0947 Evaluate side-chains 176 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 336 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 150 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 chunk 238 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 372 optimal weight: 30.0000 chunk 267 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.155176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.101147 restraints weight = 85802.967| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 6.81 r_work: 0.2810 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35172 Z= 0.159 Angle : 0.605 18.339 47984 Z= 0.295 Chirality : 0.046 0.637 5513 Planarity : 0.004 0.047 6052 Dihedral : 5.728 58.495 5995 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.68 % Allowed : 13.37 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.13), residues: 4139 helix: 1.87 (0.14), residues: 1401 sheet: 0.73 (0.19), residues: 720 loop : -0.98 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 983 TYR 0.024 0.001 TYR B1067 PHE 0.022 0.001 PHE D 555 TRP 0.015 0.001 TRP D 271 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (35052) covalent geometry : angle 0.56597 / 0.29 (47668) SS BOND : bond 0.00379 / 0.25 ( 44) SS BOND : angle 1.61995 / 1.11 ( 88) hydrogen bonds : bond 0.04961 / 3.21 ( 1407) hydrogen bonds : angle 4.47187 / 3.11 ( 3936) link_ALPHA1-3 : bond 0.00948 / 0.48 ( 2) link_ALPHA1-3 : angle 1.92014 / 1.10 ( 6) link_ALPHA1-6 : bond 0.00663 / 0.33 ( 2) link_ALPHA1-6 : angle 1.39985 / 0.74 ( 6) link_BETA1-4 : bond 0.00446 / 0.31 ( 17) link_BETA1-4 : angle 1.40315 / 0.84 ( 51) link_NAG-ASN : bond 0.00546 / 0.35 ( 55) link_NAG-ASN : angle 3.44007 / 2.08 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8278 Ramachandran restraints generated. 4139 Oldfield, 0 Emsley, 4139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6480 (ppp) cc_final: 0.5973 (ppp) REVERT: A 196 ASN cc_start: 0.8232 (t0) cc_final: 0.7588 (m-40) REVERT: A 238 PHE cc_start: 0.8231 (p90) cc_final: 0.7641 (p90) REVERT: A 240 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.7238 (t) REVERT: A 378 LYS cc_start: 0.8789 (tppp) cc_final: 0.8564 (pttp) REVERT: A 392 PHE cc_start: 0.7855 (m-80) cc_final: 0.7526 (m-10) REVERT: A 517 LEU cc_start: 0.6614 (mm) cc_final: 0.6401 (mm) REVERT: A 855 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.6960 (p90) REVERT: B 157 PHE cc_start: 0.7852 (t80) cc_final: 0.7606 (t80) REVERT: B 365 TYR cc_start: 0.8081 (m-10) cc_final: 0.7686 (m-80) REVERT: B 563 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7357 (mt0) REVERT: C 200 TYR cc_start: 0.8976 (m-10) cc_final: 0.8611 (m-80) REVERT: C 207 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.8302 (p90) REVERT: C 338 PHE cc_start: 0.8824 (m-80) cc_final: 0.8579 (m-10) REVERT: C 351 TYR cc_start: 0.6193 (p90) cc_final: 0.5773 (p90) REVERT: E 360 MET cc_start: -0.2221 (ttp) cc_final: -0.2513 (ptp) REVERT: E 562 LYS cc_start: 0.2944 (mtpt) cc_final: 0.2373 (tttt) REVERT: E 579 MET cc_start: 0.2429 (mtt) cc_final: 0.2080 (mmm) REVERT: D 249 MET cc_start: 0.1319 (mmt) cc_final: 0.0922 (mmt) REVERT: D 332 MET cc_start: 0.4524 (ppp) cc_final: 0.4144 (ptp) outliers start: 25 outliers final: 18 residues processed: 181 average time/residue: 0.1855 time to fit residues: 58.2669 Evaluate side-chains 179 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 359 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 302 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 226 optimal weight: 0.7980 chunk 199 optimal weight: 0.0670 chunk 385 optimal weight: 0.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.156063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.099235 restraints weight = 85845.785| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 4.79 r_work: 0.2923 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 35172 Z= 0.102 Angle : 0.565 17.004 47984 Z= 0.274 Chirality : 0.044 0.561 5513 Planarity : 0.004 0.047 6052 Dihedral : 5.453 58.003 5995 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.54 % Allowed : 13.45 % Favored : 86.01 % 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 are not related in a simple way. whole: 0.63 (0.13), residues: 4139 helix: 1.93 (0.14), residues: 1400 sheet: 0.81 (0.19), residues: 724 loop : -0.86 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 518 TYR 0.031 0.001 TYR A 453 PHE 0.018 0.001 PHE C 133 TRP 0.009 0.001 TRP E 165 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (35052) covalent geometry : angle 0.52720 / 0.27 (47668) SS BOND : bond 0.00368 / 0.25 ( 44) SS BOND : angle 1.36401 / 0.93 ( 88) hydrogen bonds : bond 0.03994 / 2.59 ( 1407) hydrogen bonds : angle 4.32345 / 3.01 ( 3936) link_ALPHA1-3 : bond 0.00779 / 0.40 ( 2) link_ALPHA1-3 : angle 1.63953 / 0.91 ( 6) link_ALPHA1-6 : bond 0.00657 / 0.33 ( 2) link_ALPHA1-6 : angle 1.35557 / 0.71 ( 6) link_BETA1-4 : bond 0.00471 / 0.32 ( 17) link_BETA1-4 : angle 1.32026 / 0.80 ( 51) link_NAG-ASN : bond 0.00598 / 0.39 ( 55) link_NAG-ASN : angle 3.26951 / 1.97 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12092.10 seconds wall clock time: 206 minutes 30.85 seconds (12390.85 seconds total)