Starting phenix.real_space_refine on Tue Aug 26 22:08:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jyo_36728/08_2025/8jyo_36728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jyo_36728/08_2025/8jyo_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_36728/08_2025/8jyo_36728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jyo_36728/08_2025/8jyo_36728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jyo_36728/08_2025/8jyo_36728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jyo_36728/08_2025/8jyo_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-2.0-5787/lib/python3.9/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: 15 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: 15 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: 6.74, per 1000 atoms: 0.20 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: 2.73 Conformation dependent library (CDL) restraints added in 972.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.38 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: 6.53 Time building geometry restraints manager: 3.61 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: 20539 22.90 - 45.79: 1112 45.79 - 68.69: 97 68.69 - 91.59: 63 91.59 - 114.48: 22 Dihedral angle restraints: 21833 sinusoidal: 9587 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 21830 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: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 27.390 Find NCS groups from input model: 0.710 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 : 14.113 114.485 13813 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 aren 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 covalent geometry : bond 0.00462 (35052) covalent geometry : angle 0.59899 (47668) SS BOND : bond 0.00329 ( 44) SS BOND : angle 1.51372 ( 88) hydrogen bonds : bond 0.14446 ( 1407) hydrogen bonds : angle 5.95149 ( 3936) link_ALPHA1-3 : bond 0.00355 ( 2) link_ALPHA1-3 : angle 1.57621 ( 6) link_ALPHA1-6 : bond 0.00289 ( 2) link_ALPHA1-6 : angle 1.65695 ( 6) link_BETA1-4 : bond 0.00339 ( 17) link_BETA1-4 : angle 1.59590 ( 51) link_NAG-ASN : bond 0.00727 ( 55) link_NAG-ASN : angle 3.72528 ( 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 : 1.170 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: 0.1880 time to fit residues: 102.5273 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 : 1.314 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.156272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.099980 restraints weight = 86614.714| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 4.95 r_work: 0.2855 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35172 Z= 0.150 Angle : 0.625 18.116 47984 Z= 0.306 Chirality : 0.048 0.626 5513 Planarity : 0.004 0.058 6052 Dihedral : 9.203 101.785 6071 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.52 % Allowed : 5.95 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (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 covalent geometry : bond 0.00344 (35052) covalent geometry : angle 0.58189 (47668) SS BOND : bond 0.00366 ( 44) SS BOND : angle 1.42791 ( 88) hydrogen bonds : bond 0.05488 ( 1407) hydrogen bonds : angle 4.73496 ( 3936) link_ALPHA1-3 : bond 0.01306 ( 2) link_ALPHA1-3 : angle 2.05738 ( 6) link_ALPHA1-6 : bond 0.00306 ( 2) link_ALPHA1-6 : angle 2.20747 ( 6) link_BETA1-4 : bond 0.00718 ( 17) link_BETA1-4 : angle 1.83098 ( 51) link_NAG-ASN : bond 0.00700 ( 55) link_NAG-ASN : angle 3.65656 ( 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 217 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 1.380 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: 0.6304 (ppp) cc_final: 0.6074 (ppp) REVERT: A 189 LEU cc_start: 0.8323 (mm) cc_final: 0.8026 (mm) REVERT: A 238 PHE cc_start: 0.8227 (p90) cc_final: 0.7451 (p90) REVERT: A 351 TYR cc_start: 0.7903 (p90) cc_final: 0.7569 (p90) REVERT: A 378 LYS cc_start: 0.8901 (tppp) cc_final: 0.8657 (pttp) REVERT: A 452 LEU cc_start: 0.6933 (mt) cc_final: 0.6545 (mt) REVERT: B 133 PHE cc_start: 0.7215 (m-80) cc_final: 0.6858 (m-80) REVERT: B 157 PHE cc_start: 0.7927 (t80) cc_final: 0.7624 (t80) REVERT: B 365 TYR cc_start: 0.7980 (m-10) cc_final: 0.7639 (m-80) REVERT: C 110 LEU cc_start: 0.9233 (tp) cc_final: 0.9006 (tp) REVERT: C 200 TYR cc_start: 0.8875 (m-10) cc_final: 0.8566 (m-80) REVERT: C 823 PHE cc_start: 0.8619 (t80) cc_final: 0.8365 (t80) outliers start: 19 outliers final: 10 residues processed: 211 average time/residue: 0.1904 time to fit residues: 68.3123 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 : 1.020 ------------------------------------------------------------------------------- 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: 1.9990 chunk 229 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 408 optimal weight: 9.9990 chunk 354 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 197 optimal weight: 0.0020 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4396 r_free = 0.4396 target = 0.155935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.097801 restraints weight = 85327.845| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 5.45 r_work: 0.2855 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35172 Z= 0.149 Angle : 0.591 18.292 47984 Z= 0.289 Chirality : 0.046 0.613 5513 Planarity : 0.004 0.053 6052 Dihedral : 8.247 98.667 6071 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.68 % Allowed : 7.96 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.13), residues: 4139 helix: 1.82 (0.14), residues: 1414 sheet: 0.66 (0.19), residues: 727 loop : -1.01 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.023 0.001 TYR B1067 PHE 0.013 0.001 PHE C 400 TRP 0.010 0.001 TRP E 163 HIS 0.017 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00347 (35052) covalent geometry : angle 0.54929 (47668) SS BOND : bond 0.00302 ( 44) SS BOND : angle 1.48445 ( 88) hydrogen bonds : bond 0.05215 ( 1407) hydrogen bonds : angle 4.57265 ( 3936) link_ALPHA1-3 : bond 0.01272 ( 2) link_ALPHA1-3 : angle 1.87576 ( 6) link_ALPHA1-6 : bond 0.00546 ( 2) link_ALPHA1-6 : angle 2.02653 ( 6) link_BETA1-4 : bond 0.00428 ( 17) link_BETA1-4 : angle 1.65098 ( 51) link_NAG-ASN : bond 0.00647 ( 55) link_NAG-ASN : angle 3.47279 ( 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 209 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.214 Fit side-chains 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: 0.5992 (ppp) REVERT: A 189 LEU cc_start: 0.8368 (mm) cc_final: 0.8021 (mm) REVERT: A 211 ASN cc_start: 0.7827 (t0) cc_final: 0.7626 (t0) REVERT: A 238 PHE cc_start: 0.8296 (p90) cc_final: 0.7588 (p90) REVERT: A 351 TYR cc_start: 0.7734 (p90) cc_final: 0.7488 (p90) REVERT: A 378 LYS cc_start: 0.8902 (tppp) cc_final: 0.8695 (pttp) REVERT: A 392 PHE cc_start: 0.7855 (m-80) cc_final: 0.7527 (m-10) REVERT: A 452 LEU cc_start: 0.7210 (mt) cc_final: 0.6796 (mt) REVERT: B 133 PHE cc_start: 0.7214 (m-80) cc_final: 0.6860 (m-80) REVERT: B 157 PHE cc_start: 0.7821 (t80) cc_final: 0.7522 (t80) REVERT: B 365 TYR cc_start: 0.7996 (m-10) cc_final: 0.7588 (m-10) REVERT: B 392 PHE cc_start: 0.8170 (m-80) cc_final: 0.7880 (m-80) REVERT: C 200 TYR cc_start: 0.8915 (m-10) cc_final: 0.8575 (m-80) REVERT: C 207 HIS cc_start: 0.8566 (OUTLIER) cc_final: 0.8052 (p-80) outliers start: 25 outliers final: 10 residues processed: 205 average time/residue: 0.1808 time to fit residues: 64.2238 Evaluate side-chains 179 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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: 0.9990 chunk 352 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 129 optimal weight: 30.0000 chunk 17 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 275 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 54 optimal weight: 0.0170 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 901 GLN B 439 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN E 524 GLN D 524 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.156269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.100337 restraints weight = 86678.567| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 5.02 r_work: 0.2914 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35172 Z= 0.122 Angle : 0.573 17.770 47984 Z= 0.277 Chirality : 0.046 0.598 5513 Planarity : 0.004 0.053 6052 Dihedral : 7.418 95.707 6071 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.87 % Allowed : 9.26 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.13), residues: 4139 helix: 1.92 (0.14), residues: 1402 sheet: 0.70 (0.19), residues: 735 loop : -0.98 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 460 TYR 0.019 0.001 TYR B1067 PHE 0.016 0.001 PHE C 133 TRP 0.009 0.001 TRP E 163 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00275 (35052) covalent geometry : angle 0.53185 (47668) SS BOND : bond 0.00451 ( 44) SS BOND : angle 1.36620 ( 88) hydrogen bonds : bond 0.04726 ( 1407) hydrogen bonds : angle 4.47810 ( 3936) link_ALPHA1-3 : bond 0.01221 ( 2) link_ALPHA1-3 : angle 1.86611 ( 6) link_ALPHA1-6 : bond 0.00694 ( 2) link_ALPHA1-6 : angle 1.88713 ( 6) link_BETA1-4 : bond 0.00416 ( 17) link_BETA1-4 : angle 1.54473 ( 51) link_NAG-ASN : bond 0.00728 ( 55) link_NAG-ASN : angle 3.42828 ( 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 213 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6260 (ppp) cc_final: 0.5940 (ppp) REVERT: A 189 LEU cc_start: 0.8265 (mm) cc_final: 0.7960 (mm) REVERT: A 220 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6353 (t80) REVERT: A 238 PHE cc_start: 0.8336 (p90) cc_final: 0.7738 (p90) REVERT: A 240 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7319 (t) REVERT: A 392 PHE cc_start: 0.7886 (m-80) cc_final: 0.7630 (m-80) REVERT: A 452 LEU cc_start: 0.7394 (mt) cc_final: 0.6897 (mt) REVERT: B 133 PHE cc_start: 0.7124 (m-80) cc_final: 0.6743 (m-80) REVERT: B 157 PHE cc_start: 0.7556 (t80) cc_final: 0.7303 (t80) REVERT: B 365 TYR cc_start: 0.7925 (m-10) cc_final: 0.7613 (m-10) REVERT: B 563 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7397 (mp10) REVERT: C 200 TYR cc_start: 0.8818 (m-10) cc_final: 0.8527 (m-80) REVERT: C 351 TYR cc_start: 0.6382 (p90) cc_final: 0.6066 (p90) REVERT: E 480 MET cc_start: 0.5244 (mmt) cc_final: 0.5013 (mmm) REVERT: E 579 MET cc_start: 0.1267 (mtt) cc_final: 0.0790 (mmt) REVERT: D 237 TYR cc_start: 0.6197 (t80) cc_final: 0.4818 (m-80) REVERT: D 249 MET cc_start: 0.1051 (mmt) cc_final: 0.0818 (mmt) REVERT: D 516 TYR cc_start: 0.6950 (t80) cc_final: 0.6522 (m-80) outliers start: 32 outliers final: 12 residues processed: 204 average time/residue: 0.1951 time to fit residues: 68.1656 Evaluate side-chains 186 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 83 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 334 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 180 optimal weight: 3.9990 chunk 379 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 901 GLN B 901 GLN B1010 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4347 r_free = 0.4347 target = 0.152484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.092907 restraints weight = 84971.495| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 5.36 r_work: 0.2772 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.098 35172 Z= 0.386 Angle : 0.797 21.990 47984 Z= 0.395 Chirality : 0.054 0.805 5513 Planarity : 0.005 0.054 6052 Dihedral : 7.501 74.719 6071 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.11 % Allowed : 11.57 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.13), residues: 4139 helix: 1.50 (0.14), residues: 1401 sheet: 0.27 (0.19), residues: 724 loop : -1.33 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 214 TYR 0.034 0.002 TYR B1067 PHE 0.022 0.002 PHE D 315 TRP 0.014 0.002 TRP C 886 HIS 0.009 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00946 (35052) covalent geometry : angle 0.75668 (47668) SS BOND : bond 0.00828 ( 44) SS BOND : angle 2.30561 ( 88) hydrogen bonds : bond 0.07336 ( 1407) hydrogen bonds : angle 4.97702 ( 3936) link_ALPHA1-3 : bond 0.01415 ( 2) link_ALPHA1-3 : angle 1.96693 ( 6) link_ALPHA1-6 : bond 0.00638 ( 2) link_ALPHA1-6 : angle 1.93126 ( 6) link_BETA1-4 : bond 0.00474 ( 17) link_BETA1-4 : angle 1.86936 ( 51) link_NAG-ASN : bond 0.00680 ( 55) link_NAG-ASN : angle 3.90719 ( 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 204 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6617 (ppp) cc_final: 0.6140 (ppp) REVERT: A 196 ASN cc_start: 0.8166 (t0) cc_final: 0.7575 (m-40) REVERT: A 238 PHE cc_start: 0.8227 (p90) cc_final: 0.7498 (p90) REVERT: A 392 PHE cc_start: 0.7854 (m-80) cc_final: 0.7549 (m-10) REVERT: A 855 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7582 (p90) REVERT: B 119 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7487 (mp) REVERT: B 133 PHE cc_start: 0.7244 (m-80) cc_final: 0.6768 (m-80) REVERT: B 563 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7281 (mt0) REVERT: C 351 TYR cc_start: 0.6301 (p90) cc_final: 0.5882 (p90) REVERT: C 358 ILE cc_start: 0.7695 (mm) cc_final: 0.7470 (mp) REVERT: E 383 MET cc_start: 0.4973 (ttp) cc_final: 0.4568 (ppp) REVERT: E 562 LYS cc_start: 0.3241 (mtpt) cc_final: 0.2799 (tttt) REVERT: E 579 MET cc_start: 0.4604 (mtt) cc_final: 0.4301 (mmt) REVERT: D 123 MET cc_start: 0.4398 (tpp) cc_final: 0.4017 (ptp) REVERT: D 249 MET cc_start: 0.2048 (mmt) cc_final: 0.1637 (mmt) REVERT: D 332 MET cc_start: 0.4829 (ppp) cc_final: 0.4530 (ptp) REVERT: D 516 TYR cc_start: 0.7441 (t80) cc_final: 0.6888 (m-80) outliers start: 41 outliers final: 23 residues processed: 196 average time/residue: 0.1929 time to fit residues: 64.5885 Evaluate side-chains 178 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 TYR 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 379 CYS 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 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 1096 VAL 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: 3.9990 chunk 93 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 416 optimal weight: 30.0000 chunk 21 optimal weight: 2.9990 chunk 402 optimal weight: 6.9990 chunk 195 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 283 optimal weight: 0.8980 chunk 334 optimal weight: 30.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 901 GLN E 42 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.154760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.097118 restraints weight = 84697.755| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 6.13 r_work: 0.2812 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 35172 Z= 0.136 Angle : 0.610 18.856 47984 Z= 0.296 Chirality : 0.046 0.655 5513 Planarity : 0.004 0.046 6052 Dihedral : 6.700 66.850 6071 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.11 % Allowed : 12.69 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.13), residues: 4139 helix: 1.77 (0.14), residues: 1396 sheet: 0.47 (0.20), residues: 689 loop : -1.11 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.020 0.001 TYR B1067 PHE 0.016 0.001 PHE D 555 TRP 0.008 0.001 TRP A 104 HIS 0.006 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00311 (35052) covalent geometry : angle 0.56508 (47668) SS BOND : bond 0.00436 ( 44) SS BOND : angle 1.72648 ( 88) hydrogen bonds : bond 0.05132 ( 1407) hydrogen bonds : angle 4.63088 ( 3936) link_ALPHA1-3 : bond 0.01166 ( 2) link_ALPHA1-3 : angle 1.73103 ( 6) link_ALPHA1-6 : bond 0.00734 ( 2) link_ALPHA1-6 : angle 1.63315 ( 6) link_BETA1-4 : bond 0.00454 ( 17) link_BETA1-4 : angle 1.46208 ( 51) link_NAG-ASN : bond 0.00615 ( 55) link_NAG-ASN : angle 3.66833 ( 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 206 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 1.344 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: 0.6491 (ppp) cc_final: 0.5992 (ppp) REVERT: A 189 LEU cc_start: 0.8532 (mm) cc_final: 0.8172 (mm) REVERT: A 196 ASN cc_start: 0.8122 (t0) cc_final: 0.7482 (m-40) REVERT: A 238 PHE cc_start: 0.8268 (p90) cc_final: 0.7576 (p90) REVERT: A 240 THR cc_start: 0.7436 (OUTLIER) cc_final: 0.7040 (t) REVERT: A 392 PHE cc_start: 0.7831 (m-80) cc_final: 0.7557 (m-10) REVERT: A 855 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7255 (p90) REVERT: B 133 PHE cc_start: 0.7208 (m-80) cc_final: 0.6737 (m-80) REVERT: B 177 MET cc_start: 0.6885 (tmm) cc_final: 0.6644 (tmm) REVERT: B 365 TYR cc_start: 0.7732 (m-10) cc_final: 0.7376 (m-10) REVERT: B 563 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7348 (mp10) REVERT: C 207 HIS cc_start: 0.8605 (OUTLIER) cc_final: 0.8258 (p90) REVERT: C 338 PHE cc_start: 0.8649 (m-80) cc_final: 0.8436 (m-80) REVERT: C 351 TYR cc_start: 0.6293 (p90) cc_final: 0.5877 (p90) REVERT: C 358 ILE cc_start: 0.7592 (mm) cc_final: 0.7305 (mp) REVERT: E 225 ASP cc_start: 0.2665 (m-30) cc_final: 0.2408 (t70) REVERT: E 562 LYS cc_start: 0.3177 (mtpt) cc_final: 0.2658 (tttt) REVERT: E 579 MET cc_start: 0.3630 (mtt) cc_final: 0.2869 (mmt) REVERT: D 152 MET cc_start: 0.2681 (ptp) cc_final: 0.2339 (ptp) REVERT: D 249 MET cc_start: 0.1617 (mmt) cc_final: 0.1194 (mmt) REVERT: D 332 MET cc_start: 0.4496 (ppp) cc_final: 0.4230 (ptp) REVERT: D 516 TYR cc_start: 0.7578 (t80) cc_final: 0.6981 (m-80) outliers start: 41 outliers final: 21 residues processed: 200 average time/residue: 0.1966 time to fit residues: 67.9392 Evaluate side-chains 182 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 A residue 1136 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 576 VAL 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 525 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 976 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 103 optimal weight: 0.1980 chunk 413 optimal weight: 20.0000 chunk 325 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 359 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 373 optimal weight: 8.9990 chunk 294 optimal weight: 0.8980 chunk 343 optimal weight: 30.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 563 GLN A 901 GLN E 42 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.153840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.098553 restraints weight = 87084.276| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 4.97 r_work: 0.2845 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 35172 Z= 0.205 Angle : 0.645 19.558 47984 Z= 0.315 Chirality : 0.047 0.675 5513 Planarity : 0.004 0.047 6052 Dihedral : 6.443 59.685 6071 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.09 % Allowed : 13.15 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.13), residues: 4139 helix: 1.72 (0.14), residues: 1401 sheet: 0.45 (0.20), residues: 702 loop : -1.16 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 514 TYR 0.027 0.001 TYR B1067 PHE 0.019 0.002 PHE D 555 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00502 (35052) covalent geometry : angle 0.60242 (47668) SS BOND : bond 0.00383 ( 44) SS BOND : angle 1.83487 ( 88) hydrogen bonds : bond 0.05619 ( 1407) hydrogen bonds : angle 4.65995 ( 3936) link_ALPHA1-3 : bond 0.01115 ( 2) link_ALPHA1-3 : angle 1.75865 ( 6) link_ALPHA1-6 : bond 0.00931 ( 2) link_ALPHA1-6 : angle 1.69983 ( 6) link_BETA1-4 : bond 0.00406 ( 17) link_BETA1-4 : angle 1.53408 ( 51) link_NAG-ASN : bond 0.00581 ( 55) link_NAG-ASN : angle 3.68130 ( 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 199 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 1.307 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: 0.6567 (ppp) cc_final: 0.6056 (ppp) REVERT: A 196 ASN cc_start: 0.8114 (t0) cc_final: 0.7513 (m-40) REVERT: A 238 PHE cc_start: 0.8290 (p90) cc_final: 0.7619 (p90) REVERT: A 240 THR cc_start: 0.7360 (OUTLIER) cc_final: 0.6991 (t) REVERT: A 392 PHE cc_start: 0.7766 (m-80) cc_final: 0.7497 (m-10) REVERT: A 855 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7262 (p90) REVERT: B 133 PHE cc_start: 0.7246 (m-80) cc_final: 0.6846 (m-80) REVERT: B 365 TYR cc_start: 0.7838 (m-10) cc_final: 0.7416 (m-10) REVERT: B 563 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7327 (mt0) REVERT: C 338 PHE cc_start: 0.8687 (m-80) cc_final: 0.8472 (m-80) REVERT: C 351 TYR cc_start: 0.6320 (p90) cc_final: 0.5914 (p90) REVERT: C 358 ILE cc_start: 0.7647 (mm) cc_final: 0.7341 (mp) REVERT: E 562 LYS cc_start: 0.3036 (mtpt) cc_final: 0.2554 (tttt) REVERT: E 579 MET cc_start: 0.3205 (mtt) cc_final: 0.2456 (mmt) REVERT: D 123 MET cc_start: 0.4506 (tpp) cc_final: 0.4047 (ptp) REVERT: D 249 MET cc_start: 0.1282 (mmt) cc_final: 0.0796 (mmt) REVERT: D 332 MET cc_start: 0.4447 (ppp) cc_final: 0.4085 (ptp) REVERT: D 516 TYR cc_start: 0.7469 (t80) cc_final: 0.6876 (m-80) outliers start: 40 outliers final: 25 residues processed: 191 average time/residue: 0.1752 time to fit residues: 58.3666 Evaluate side-chains 182 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 242 LEU 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 B residue 576 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 130 VAL 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 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 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: 10.0000 chunk 7 optimal weight: 20.0000 chunk 174 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 257 optimal weight: 0.8980 chunk 396 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 280 optimal weight: 0.9990 chunk 400 optimal weight: 20.0000 chunk 229 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 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 = 0.4374 r_free = 0.4374 target = 0.154489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098786 restraints weight = 87371.603| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.78 r_work: 0.2880 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2598 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= 0.149 Angle : 0.603 18.741 47984 Z= 0.293 Chirality : 0.046 0.634 5513 Planarity : 0.004 0.046 6052 Dihedral : 6.115 58.994 6071 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.01 % Allowed : 13.31 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.13), residues: 4139 helix: 1.76 (0.14), residues: 1404 sheet: 0.55 (0.20), residues: 694 loop : -1.09 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 514 TYR 0.021 0.001 TYR B1067 PHE 0.020 0.001 PHE B 374 TRP 0.008 0.001 TRP B 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00354 (35052) covalent geometry : angle 0.55975 (47668) SS BOND : bond 0.00396 ( 44) SS BOND : angle 1.67178 ( 88) hydrogen bonds : bond 0.04967 ( 1407) hydrogen bonds : angle 4.54772 ( 3936) link_ALPHA1-3 : bond 0.00912 ( 2) link_ALPHA1-3 : angle 1.72340 ( 6) link_ALPHA1-6 : bond 0.00572 ( 2) link_ALPHA1-6 : angle 1.40058 ( 6) link_BETA1-4 : bond 0.00447 ( 17) link_BETA1-4 : angle 1.44279 ( 51) link_NAG-ASN : bond 0.00579 ( 55) link_NAG-ASN : angle 3.61621 ( 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 202 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6626 (ppp) cc_final: 0.6092 (ppp) REVERT: A 196 ASN cc_start: 0.8143 (t0) cc_final: 0.7515 (m-40) REVERT: A 238 PHE cc_start: 0.8515 (p90) cc_final: 0.7871 (p90) REVERT: A 240 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.7174 (t) REVERT: A 392 PHE cc_start: 0.7760 (m-80) cc_final: 0.7440 (m-10) REVERT: A 517 LEU cc_start: 0.6606 (mm) cc_final: 0.6335 (mm) REVERT: A 855 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.6971 (p90) REVERT: B 119 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7706 (mp) REVERT: B 133 PHE cc_start: 0.7077 (m-80) cc_final: 0.6773 (m-80) REVERT: B 365 TYR cc_start: 0.7725 (m-10) cc_final: 0.7296 (m-10) REVERT: B 563 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7373 (mt0) REVERT: C 125 ASN cc_start: 0.7974 (p0) cc_final: 0.7751 (t0) REVERT: C 207 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.8142 (p90) REVERT: C 338 PHE cc_start: 0.8738 (m-80) cc_final: 0.8525 (m-80) REVERT: C 351 TYR cc_start: 0.6242 (p90) cc_final: 0.5841 (p90) REVERT: E 562 LYS cc_start: 0.3022 (mtpt) cc_final: 0.2564 (tttt) REVERT: E 579 MET cc_start: 0.3365 (mtt) cc_final: 0.3066 (mmm) REVERT: D 249 MET cc_start: 0.1368 (mmt) cc_final: 0.0883 (mmt) REVERT: D 332 MET cc_start: 0.4519 (ppp) cc_final: 0.4226 (ptp) REVERT: D 516 TYR cc_start: 0.7425 (t80) cc_final: 0.6914 (m-80) outliers start: 37 outliers final: 21 residues processed: 195 average time/residue: 0.1967 time to fit residues: 65.8890 Evaluate side-chains 183 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 302 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 119 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1017 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 167 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 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: 3.9990 chunk 397 optimal weight: 50.0000 chunk 8 optimal weight: 9.9990 chunk 307 optimal weight: 30.0000 chunk 253 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 901 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.153926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.097151 restraints weight = 85198.372| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 4.37 r_work: 0.2885 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35172 Z= 0.187 Angle : 0.631 16.873 47984 Z= 0.308 Chirality : 0.047 0.829 5513 Planarity : 0.004 0.046 6052 Dihedral : 6.104 59.970 6071 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.98 % Allowed : 13.53 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.13), residues: 4139 helix: 1.69 (0.14), residues: 1400 sheet: 0.48 (0.20), residues: 698 loop : -1.14 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 983 TYR 0.026 0.001 TYR B1067 PHE 0.019 0.001 PHE C 133 TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00454 (35052) covalent geometry : angle 0.59060 (47668) SS BOND : bond 0.00389 ( 44) SS BOND : angle 1.74515 ( 88) hydrogen bonds : bond 0.05416 ( 1407) hydrogen bonds : angle 4.62059 ( 3936) link_ALPHA1-3 : bond 0.00999 ( 2) link_ALPHA1-3 : angle 1.83516 ( 6) link_ALPHA1-6 : bond 0.00742 ( 2) link_ALPHA1-6 : angle 1.46687 ( 6) link_BETA1-4 : bond 0.00463 ( 17) link_BETA1-4 : angle 1.49545 ( 51) link_NAG-ASN : bond 0.00576 ( 55) link_NAG-ASN : angle 3.51471 ( 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 195 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6634 (ppp) cc_final: 0.6118 (ppp) REVERT: A 196 ASN cc_start: 0.8104 (t0) cc_final: 0.7489 (m-40) REVERT: A 238 PHE cc_start: 0.8532 (p90) cc_final: 0.7886 (p90) REVERT: A 240 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7160 (t) REVERT: A 392 PHE cc_start: 0.7717 (m-80) cc_final: 0.7373 (m-10) REVERT: A 517 LEU cc_start: 0.6575 (mm) cc_final: 0.6290 (mm) REVERT: A 855 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7003 (p90) REVERT: B 119 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7695 (mp) REVERT: B 133 PHE cc_start: 0.7073 (m-80) cc_final: 0.6810 (m-80) REVERT: B 365 TYR cc_start: 0.7690 (m-10) cc_final: 0.7325 (m-10) REVERT: B 563 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7355 (mt0) REVERT: C 177 MET cc_start: 0.6711 (pmm) cc_final: 0.6025 (pmm) REVERT: C 351 TYR cc_start: 0.6224 (p90) cc_final: 0.5853 (p90) REVERT: E 562 LYS cc_start: 0.2977 (mtpt) cc_final: 0.2497 (tttt) REVERT: E 579 MET cc_start: 0.2845 (mtt) cc_final: 0.2472 (mmm) REVERT: D 249 MET cc_start: 0.1135 (mmt) cc_final: 0.0697 (mmt) REVERT: D 332 MET cc_start: 0.4371 (ppp) cc_final: 0.4003 (ptp) REVERT: D 516 TYR cc_start: 0.7365 (t80) cc_final: 0.6723 (m-80) outliers start: 36 outliers final: 26 residues processed: 188 average time/residue: 0.1796 time to fit residues: 58.7272 Evaluate side-chains 183 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 207 HIS 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 B residue 576 VAL Chi-restraints excluded: chain B residue 1017 GLU 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 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 E residue 55 THR Chi-restraints excluded: chain E residue 123 MET 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 462 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 336 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 chunk 238 optimal weight: 0.0670 chunk 37 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 372 optimal weight: 40.0000 chunk 267 optimal weight: 2.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 901 GLN C 207 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.154322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.096134 restraints weight = 84679.113| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 5.12 r_work: 0.2865 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35172 Z= 0.164 Angle : 0.609 16.991 47984 Z= 0.298 Chirality : 0.047 0.931 5513 Planarity : 0.004 0.046 6052 Dihedral : 5.950 59.726 6071 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.84 % Allowed : 13.80 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.13), residues: 4139 helix: 1.75 (0.14), residues: 1400 sheet: 0.51 (0.20), residues: 700 loop : -1.11 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 983 TYR 0.022 0.001 TYR B1067 PHE 0.021 0.001 PHE D 555 TRP 0.009 0.001 TRP C 436 HIS 0.011 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00393 (35052) covalent geometry : angle 0.56912 (47668) SS BOND : bond 0.00387 ( 44) SS BOND : angle 1.67046 ( 88) hydrogen bonds : bond 0.05118 ( 1407) hydrogen bonds : angle 4.56953 ( 3936) link_ALPHA1-3 : bond 0.01060 ( 2) link_ALPHA1-3 : angle 1.83293 ( 6) link_ALPHA1-6 : bond 0.00708 ( 2) link_ALPHA1-6 : angle 1.41536 ( 6) link_BETA1-4 : bond 0.00450 ( 17) link_BETA1-4 : angle 1.44503 ( 51) link_NAG-ASN : bond 0.00642 ( 55) link_NAG-ASN : angle 3.46695 ( 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 190 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7714 (t0) cc_final: 0.7478 (t70) REVERT: A 177 MET cc_start: 0.6636 (ppp) cc_final: 0.6099 (ppp) REVERT: A 196 ASN cc_start: 0.8185 (t0) cc_final: 0.7546 (m-40) REVERT: A 238 PHE cc_start: 0.8502 (p90) cc_final: 0.7870 (p90) REVERT: A 240 THR cc_start: 0.7476 (OUTLIER) cc_final: 0.7161 (t) REVERT: A 392 PHE cc_start: 0.7769 (m-80) cc_final: 0.7444 (m-10) REVERT: A 517 LEU cc_start: 0.6660 (mm) cc_final: 0.6387 (mm) REVERT: A 855 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.6899 (p90) REVERT: B 119 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7576 (mp) REVERT: B 133 PHE cc_start: 0.7031 (m-80) cc_final: 0.6765 (m-80) REVERT: B 365 TYR cc_start: 0.7834 (m-10) cc_final: 0.7465 (m-10) REVERT: B 563 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7309 (mt0) REVERT: C 351 TYR cc_start: 0.6161 (p90) cc_final: 0.5803 (p90) REVERT: E 227 GLU cc_start: 0.4439 (mt-10) cc_final: 0.4220 (tm-30) REVERT: E 562 LYS cc_start: 0.2908 (mtpt) cc_final: 0.2374 (tttt) REVERT: E 579 MET cc_start: 0.3344 (mtt) cc_final: 0.2947 (mmm) REVERT: D 249 MET cc_start: 0.1355 (mmt) cc_final: 0.0927 (mmt) REVERT: D 332 MET cc_start: 0.4570 (ppp) cc_final: 0.4335 (ptp) REVERT: D 516 TYR cc_start: 0.7380 (t80) cc_final: 0.6780 (m-80) outliers start: 31 outliers final: 24 residues processed: 185 average time/residue: 0.1828 time to fit residues: 58.7939 Evaluate side-chains 183 residues out of total 3681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 441 LEU 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 119 ILE Chi-restraints excluded: chain B residue 207 HIS 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 B residue 576 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1017 GLU 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 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 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 462 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 359 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 268 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 302 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 226 optimal weight: 0.9990 chunk 199 optimal weight: 0.7980 chunk 385 optimal weight: 20.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 580 GLN B 755 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.155169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.097701 restraints weight = 85395.821| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 5.50 r_work: 0.2876 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 35172 Z= 0.111 Angle : 0.571 16.151 47984 Z= 0.278 Chirality : 0.045 0.768 5513 Planarity : 0.004 0.047 6052 Dihedral : 5.628 58.247 6071 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.62 % Allowed : 14.13 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.13), residues: 4139 helix: 1.82 (0.14), residues: 1401 sheet: 0.74 (0.20), residues: 694 loop : -1.02 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 983 TYR 0.017 0.001 TYR C1067 PHE 0.022 0.001 PHE D 555 TRP 0.009 0.001 TRP A 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00248 (35052) covalent geometry : angle 0.53301 (47668) SS BOND : bond 0.00366 ( 44) SS BOND : angle 1.41644 ( 88) hydrogen bonds : bond 0.04291 ( 1407) hydrogen bonds : angle 4.43144 ( 3936) link_ALPHA1-3 : bond 0.00875 ( 2) link_ALPHA1-3 : angle 1.67362 ( 6) link_ALPHA1-6 : bond 0.00674 ( 2) link_ALPHA1-6 : angle 1.35540 ( 6) link_BETA1-4 : bond 0.00454 ( 17) link_BETA1-4 : angle 1.36380 ( 51) link_NAG-ASN : bond 0.00609 ( 55) link_NAG-ASN : angle 3.31556 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11828.83 seconds wall clock time: 201 minutes 48.50 seconds (12108.50 seconds total)