Starting phenix.real_space_refine on Sun Jul 5 14:21:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y6t_33647/07_2026/7y6t_33647.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6t_33647/07_2026/7y6t_33647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7y6t_33647/07_2026/7y6t_33647.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y6t_33647/07_2026/7y6t_33647.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y6t_33647/07_2026/7y6t_33647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6t_33647/07_2026/7y6t_33647.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6t_33647/07_2026/7y6t_33647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6t_33647/07_2026/7y6t_33647.cif" } resolution = 4.2 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 17678 2.51 5 N 4487 2.21 5 O 5708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27988 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 8648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1124, 8648 Classifications: {'peptide': 1124} Link IDs: {'PTRANS': 45, 'TRANS': 1078} Chain breaks: 3 Chain: "C" Number of atoms: 8440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8440 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 43, 'TRANS': 1054} Chain breaks: 1 Chain: "B" Number of atoms: 9398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1224, 9398 Classifications: {'peptide': 1224} Link IDs: {'PTRANS': 47, 'TRANS': 1176} Chain: "D" 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 chiralities: 5 Chain: "E" 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 chiralities: 3 Chain: "F" 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 chiralities: 3 Chain: "G" 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 chiralities: 3 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 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 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 chiralities: 2 Chain: "K" 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 chiralities: 3 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 chiralities: 2 Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 5 Chain: "P" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 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 chiralities: 3 Chain: "R" 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 chiralities: 2 Chain: "S" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" 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 chiralities: 3 Chain: "U" 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 chiralities: 2 Chain: "V" 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 chiralities: 3 Chain: "W" 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 chiralities: 2 Chain: "X" 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 chiralities: 3 Chain: "Y" 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 chiralities: 2 Chain: "Z" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "b" 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 chiralities: 5 Chain: "c" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" 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 chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" 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 chiralities: 3 Chain: "h" 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 chiralities: 3 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 chiralities: 2 Chain: "j" 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 chiralities: 3 Chain: "k" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.96, per 1000 atoms: 0.21 Number of scatterers: 27988 At special positions: 0 Unit cell: (165.36, 181.26, 165.36, 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 115 16.00 O 5708 8.00 N 4487 7.00 C 17678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.02 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 373 " distance=2.03 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.02 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 700 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 830 " distance=2.03 Simple disulfide: pdb=" SG CYS C 920 " - pdb=" SG CYS C 931 " distance=2.02 Simple disulfide: pdb=" SG CYS C1122 " - pdb=" SG CYS C1133 " distance=2.03 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 599 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 830 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 931 " distance=2.03 Simple disulfide: pdb=" SG CYS B1122 " - pdb=" SG CYS B1133 " distance=2.03 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1226 " 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 D 3 " - " MAN D 4 " " BMA O 3 " - " MAN O 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA O 3 " - " MAN O 5 " " BMA b 3 " - " MAN b 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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 K 2 " - " BMA K 3 " " 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 Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " BETA1-6 " NAG M 1 " - " FUC M 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 4 " " NAG P 1 " - " FUC P 2 " " NAG S 1 " - " FUC S 2 " " NAG Z 1 " - " FUC Z 3 " " NAG a 1 " - " FUC a 4 " " NAG c 1 " - " FUC c 2 " " NAG f 1 " - " FUC f 2 " " NAG k 1 " - " FUC k 4 " NAG-ASN " NAG A1501 " - " ASN A 300 " " NAG A1502 " - " ASN A 425 " " NAG A1503 " - " ASN A 344 " " NAG A1504 " - " ASN A 667 " " NAG A1505 " - " ASN A1009 " " NAG A1506 " - " ASN A 381 " " NAG B1501 " - " ASN B 118 " " NAG B1502 " - " ASN B 514 " " NAG B1503 " - " ASN B 556 " " NAG B1504 " - " ASN B 667 " " NAG B1505 " - " ASN B 743 " " NAG B1506 " - " ASN B 787 " " NAG B1507 " - " ASN B1009 " " NAG C1501 " - " ASN C 118 " " NAG C1502 " - " ASN C 381 " " NAG C1503 " - " ASN C 667 " " NAG C1504 " - " ASN C 787 " " NAG C1505 " - " ASN C1009 " " NAG D 1 " - " ASN A 264 " " NAG E 1 " - " ASN A 324 " " NAG F 1 " - " ASN A 726 " " NAG H 1 " - " ASN A 743 " " NAG I 1 " - " ASN A 781 " " NAG J 1 " - " ASN A 787 " " NAG K 1 " - " ASN A 873 " " NAG L 1 " - " ASN A1232 " " NAG M 1 " - " ASN A 216 " " NAG N 1 " - " ASN C 216 " " NAG O 1 " - " ASN C 264 " " NAG P 1 " - " ASN C 300 " " NAG Q 1 " - " ASN C 324 " " NAG R 1 " - " ASN C 344 " " NAG S 1 " - " ASN C 351 " " NAG T 1 " - " ASN C 425 " " NAG U 1 " - " ASN C 726 " " NAG V 1 " - " ASN C 688 " " NAG W 1 " - " ASN C 743 " " NAG X 1 " - " ASN C 781 " " NAG Y 1 " - " ASN C 873 " " NAG Z 1 " - " ASN C1232 " " NAG a 1 " - " ASN B 216 " " NAG b 1 " - " ASN B 264 " " NAG c 1 " - " ASN B 300 " " NAG d 1 " - " ASN B 324 " " NAG e 1 " - " ASN B 344 " " NAG f 1 " - " ASN B 351 " " NAG g 1 " - " ASN B 425 " " NAG h 1 " - " ASN B 688 " " NAG i 1 " - " ASN B 781 " " NAG j 1 " - " ASN B 873 " " NAG k 1 " - " ASN B1232 " Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.2 seconds 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6388 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 49 sheets defined 25.6% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.894A pdb=" N LEU A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 807 through 814 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.928A pdb=" N LEU A 822 " --> pdb=" O ARG A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 852 Processing helix chain 'A' and resid 855 through 862 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.752A pdb=" N VAL A 913 " --> pdb=" O LEU A 910 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 914 " --> pdb=" O GLY A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 910 through 914' Processing helix chain 'A' and resid 916 through 923 removed outlier: 3.928A pdb=" N CYS A 920 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 937 Processing helix chain 'A' and resid 946 through 963 Processing helix chain 'A' and resid 967 through 971 removed outlier: 3.813A pdb=" N ALA A 971 " --> pdb=" O ALA A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 986 Processing helix chain 'A' and resid 992 through 1016 removed outlier: 3.795A pdb=" N LEU A 999 " --> pdb=" O ASN A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1022 removed outlier: 3.548A pdb=" N SER A1021 " --> pdb=" O LYS A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1056 removed outlier: 4.031A pdb=" N GLN A1045 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY A1046 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1074 removed outlier: 4.113A pdb=" N ILE A1070 " --> pdb=" O SER A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1122 removed outlier: 3.931A pdb=" N ARG A1085 " --> pdb=" O VAL A1081 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A1086 " --> pdb=" O GLN A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1197 removed outlier: 4.400A pdb=" N HIS A1197 " --> pdb=" O LEU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'A' and resid 1236 through 1242 removed outlier: 3.786A pdb=" N ASP A1240 " --> pdb=" O ASP A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1254 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 115 through 118 removed outlier: 3.689A pdb=" N ASN C 118 " --> pdb=" O GLY C 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 115 through 118' Processing helix chain 'C' and resid 231 through 238 removed outlier: 3.994A pdb=" N ILE C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.925A pdb=" N ALA C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 689 through 692 Processing helix chain 'C' and resid 807 through 813 Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.923A pdb=" N GLN C 825 " --> pdb=" O GLN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 852 Processing helix chain 'C' and resid 855 through 862 Processing helix chain 'C' and resid 885 through 888 removed outlier: 3.634A pdb=" N GLY C 888 " --> pdb=" O PRO C 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 885 through 888' Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 910 through 914 removed outlier: 3.852A pdb=" N VAL C 913 " --> pdb=" O LEU C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 923 removed outlier: 3.732A pdb=" N GLY C 923 " --> pdb=" O ARG C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 936 Processing helix chain 'C' and resid 946 through 963 Processing helix chain 'C' and resid 967 through 971 removed outlier: 3.660A pdb=" N ALA C 970 " --> pdb=" O THR C 967 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA C 971 " --> pdb=" O ALA C 968 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 967 through 971' Processing helix chain 'C' and resid 973 through 986 removed outlier: 3.638A pdb=" N ALA C 977 " --> pdb=" O PRO C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1016 removed outlier: 4.146A pdb=" N LEU C 999 " --> pdb=" O ASN C 995 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C1016 " --> pdb=" O SER C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1055 removed outlier: 4.069A pdb=" N GLN C1045 " --> pdb=" O VAL C1041 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY C1046 " --> pdb=" O VAL C1042 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C1055 " --> pdb=" O GLN C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1058 No H-bonds generated for 'chain 'C' and resid 1056 through 1058' Processing helix chain 'C' and resid 1066 through 1074 Processing helix chain 'C' and resid 1075 through 1122 removed outlier: 3.675A pdb=" N LEU C1086 " --> pdb=" O GLN C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1193 through 1197 removed outlier: 3.962A pdb=" N HIS C1197 " --> pdb=" O LEU C1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 1236 through 1242 removed outlier: 3.853A pdb=" N ASP C1240 " --> pdb=" O ASP C1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 1247 through 1254 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 115 through 118 Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 232 through 238 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 466 through 475 Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.168A pdb=" N GLY B 526 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 527 " --> pdb=" O HIS B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 523 through 527' Processing helix chain 'B' and resid 575 through 580 removed outlier: 4.214A pdb=" N ASN B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 814 Processing helix chain 'B' and resid 816 through 827 removed outlier: 4.141A pdb=" N LEU B 822 " --> pdb=" O ARG B 818 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN B 825 " --> pdb=" O GLN B 821 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 827 " --> pdb=" O LEU B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 852 removed outlier: 4.005A pdb=" N LYS B 831 " --> pdb=" O THR B 827 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE B 833 " --> pdb=" O ALA B 829 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 834 " --> pdb=" O CYS B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 863 removed outlier: 3.974A pdb=" N THR B 863 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 918 through 922 Processing helix chain 'B' and resid 928 through 936 Processing helix chain 'B' and resid 946 through 962 Processing helix chain 'B' and resid 973 through 986 Processing helix chain 'B' and resid 992 through 1016 removed outlier: 3.589A pdb=" N GLN B 996 " --> pdb=" O LEU B 992 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B1016 " --> pdb=" O SER B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1054 removed outlier: 4.223A pdb=" N GLN B1045 " --> pdb=" O VAL B1041 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY B1046 " --> pdb=" O VAL B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1074 Processing helix chain 'B' and resid 1075 through 1123 Processing helix chain 'B' and resid 1193 through 1197 removed outlier: 3.856A pdb=" N HIS B1197 " --> pdb=" O LEU B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1216 through 1218 No H-bonds generated for 'chain 'B' and resid 1216 through 1218' Processing helix chain 'B' and resid 1236 through 1242 removed outlier: 3.598A pdb=" N ASP B1240 " --> pdb=" O ASP B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1247 through 1253 removed outlier: 3.668A pdb=" N ASP B1253 " --> pdb=" O ASN B1249 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 184 Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 150 removed outlier: 3.659A pdb=" N ASN A 147 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE A 125 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 285 removed outlier: 7.352A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N CYS A 283 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER A 443 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 398 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 285 removed outlier: 7.352A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N CYS A 283 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER A 443 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASP A 448 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TYR A 463 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 450 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE A 461 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU A 452 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 298 removed outlier: 6.622A pdb=" N CYS A 373 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 488 removed outlier: 4.321A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL A 709 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 502 removed outlier: 4.305A pdb=" N VAL A 694 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AB1, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB2, first strand: chain 'A' and resid 780 through 798 removed outlier: 5.816A pdb=" N PHE A 788 " --> pdb=" O PRO A1160 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET A 790 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A1158 " --> pdb=" O MET A 790 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 792 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR A1156 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 794 " --> pdb=" O LEU A1154 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A1154 " --> pdb=" O THR A 794 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR A 796 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A1152 " --> pdb=" O TYR A 796 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN A 798 " --> pdb=" O GLY A1150 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY A1150 " --> pdb=" O GLN A 798 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A1141 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU A1158 " --> pdb=" O HIS A1139 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N HIS A1139 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB4, first strand: chain 'A' and resid 881 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1220 through 1223 removed outlier: 4.198A pdb=" N ALA A1179 " --> pdb=" O ILE A1223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1187 through 1190 Processing sheet with id=AB7, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.138A pdb=" N TYR C 212 " --> pdb=" O CYS C 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 181 through 184 Processing sheet with id=AB9, first strand: chain 'C' and resid 147 through 150 removed outlier: 3.567A pdb=" N ASN C 147 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE C 125 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 147 through 150 removed outlier: 3.567A pdb=" N ASN C 147 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE C 125 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 271 through 288 removed outlier: 5.349A pdb=" N LYS C 272 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL C 453 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL C 274 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE C 451 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN C 276 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA C 449 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL C 447 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER C 443 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU C 284 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE C 441 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA C 286 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP C 439 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 406 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU C 414 " --> pdb=" O VAL C 406 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL C 408 " --> pdb=" O GLY C 412 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLY C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 271 through 288 removed outlier: 5.349A pdb=" N LYS C 272 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL C 453 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL C 274 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE C 451 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN C 276 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA C 449 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL C 447 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER C 443 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU C 284 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE C 441 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA C 286 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP C 439 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN C 454 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ILE C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 293 through 297 removed outlier: 5.248A pdb=" N ILE C 335 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 483 through 488 removed outlier: 9.202A pdb=" N SER C 703 " --> pdb=" O SER C 718 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N SER C 718 " --> pdb=" O SER C 703 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN C 705 " --> pdb=" O VAL C 716 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL C 716 " --> pdb=" O GLN C 705 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA C 707 " --> pdb=" O VAL C 714 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 499 through 502 removed outlier: 4.257A pdb=" N VAL C 694 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU C 684 " --> pdb=" O VAL C 697 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 749 through 751 Processing sheet with id=AC8, first strand: chain 'C' and resid 781 through 786 Processing sheet with id=AC9, first strand: chain 'C' and resid 789 through 798 removed outlier: 6.750A pdb=" N GLY C1150 " --> pdb=" O ALA C1146 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ALA C1146 " --> pdb=" O GLY C1150 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C1152 " --> pdb=" O VAL C1144 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL C1144 " --> pdb=" O LEU C1152 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU C1154 " --> pdb=" O SER C1142 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER C1142 " --> pdb=" O LEU C1154 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR C1156 " --> pdb=" O ILE C1140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AD2, first strand: chain 'C' and resid 879 through 883 Processing sheet with id=AD3, first strand: chain 'C' and resid 1220 through 1223 removed outlier: 3.951A pdb=" N ALA C1179 " --> pdb=" O ILE C1223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.959A pdb=" N TYR B 212 " --> pdb=" O CYS B 230 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AD6, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AD7, first strand: chain 'B' and resid 271 through 288 removed outlier: 5.128A pdb=" N LYS B 272 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL B 453 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL B 274 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 451 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASN B 276 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 449 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 447 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER B 443 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU B 284 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 441 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA B 286 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TRP B 439 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 414 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 408 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 271 through 288 removed outlier: 5.128A pdb=" N LYS B 272 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL B 453 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL B 274 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 451 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASN B 276 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 449 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 447 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER B 443 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU B 284 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 441 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA B 286 " --> pdb=" O TRP B 439 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TRP B 439 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLN B 454 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 294 through 298 removed outlier: 5.476A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN B 344 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR B 371 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 390 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N CYS B 373 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 483 through 488 removed outlier: 4.376A pdb=" N GLY B 715 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 709 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE B 713 " --> pdb=" O VAL B 709 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 510 through 513 removed outlier: 6.441A pdb=" N TYR B 619 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL B 590 " --> pdb=" O TYR B 619 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN B 621 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE B 588 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR B 623 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY B 625 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER B 584 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 510 through 513 Processing sheet with id=AE4, first strand: chain 'B' and resid 528 through 535 removed outlier: 6.383A pdb=" N SER B 520 " --> pdb=" O ILE B 530 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER B 532 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N SER B 518 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR B 534 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR B 516 " --> pdb=" O THR B 534 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 565 through 568 removed outlier: 3.848A pdb=" N VAL B 613 " --> pdb=" O GLY B 605 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 649 through 654 removed outlier: 4.028A pdb=" N VAL B 694 " --> pdb=" O THR B 666 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU B 684 " --> pdb=" O VAL B 697 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AE8, first strand: chain 'B' and resid 780 through 786 removed outlier: 4.036A pdb=" N GLY B 780 " --> pdb=" O ALA B1168 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 789 through 798 removed outlier: 6.533A pdb=" N LEU B1158 " --> pdb=" O HIS B1139 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N HIS B1139 " --> pdb=" O LEU B1158 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AF2, first strand: chain 'B' and resid 881 through 883 Processing sheet with id=AF3, first strand: chain 'B' and resid 1220 through 1223 removed outlier: 3.614A pdb=" N ALA B1179 " --> pdb=" O ILE B1223 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N CYS B1173 " --> pdb=" O LEU B1233 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1187 through 1191 removed outlier: 4.430A pdb=" N SER B1206 " --> pdb=" O GLU B1211 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLU B1211 " --> pdb=" O SER B1206 " (cutoff:3.500A) 1085 hydrogen bonds defined for protein. 2943 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: 6.00 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6282 1.33 - 1.45: 7689 1.45 - 1.58: 14459 1.58 - 1.70: 1 1.70 - 1.83: 145 Bond restraints: 28576 Sorted by residual: bond pdb=" C1 BMA j 3 " pdb=" C2 BMA j 3 " ideal model delta sigma weight residual 1.519 1.595 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C1 BMA j 3 " pdb=" O5 BMA j 3 " ideal model delta sigma weight residual 1.410 1.474 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 NAG k 1 " pdb=" O5 NAG k 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.96e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.347 0.059 2.00e-02 2.50e+03 8.63e+00 bond pdb=" C1 NAG a 1 " pdb=" O5 NAG a 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.47e+00 ... (remaining 28571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 37453 2.31 - 4.62: 1280 4.62 - 6.92: 178 6.92 - 9.23: 22 9.23 - 11.54: 3 Bond angle restraints: 38936 Sorted by residual: angle pdb=" N GLN C 127 " pdb=" CA GLN C 127 " pdb=" C GLN C 127 " ideal model delta sigma weight residual 110.80 99.26 11.54 2.13e+00 2.20e-01 2.93e+01 angle pdb=" C GLY C1008 " pdb=" N ASN C1009 " pdb=" CA ASN C1009 " ideal model delta sigma weight residual 122.38 113.99 8.39 1.81e+00 3.05e-01 2.15e+01 angle pdb=" N GLY A 294 " pdb=" CA GLY A 294 " pdb=" C GLY A 294 " ideal model delta sigma weight residual 113.18 103.12 10.06 2.37e+00 1.78e-01 1.80e+01 angle pdb=" N GLN B 127 " pdb=" CA GLN B 127 " pdb=" C GLN B 127 " ideal model delta sigma weight residual 110.80 102.05 8.75 2.13e+00 2.20e-01 1.69e+01 angle pdb=" C TRP A 439 " pdb=" N THR A 440 " pdb=" CA THR A 440 " ideal model delta sigma weight residual 122.29 115.56 6.73 1.65e+00 3.67e-01 1.66e+01 ... (remaining 38931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14588 17.94 - 35.89: 1154 35.89 - 53.83: 173 53.83 - 71.78: 40 71.78 - 89.72: 25 Dihedral angle restraints: 15980 sinusoidal: 5993 harmonic: 9987 Sorted by residual: dihedral pdb=" CB CYS C 920 " pdb=" SG CYS C 920 " pdb=" SG CYS C 931 " pdb=" CB CYS C 931 " ideal model delta sinusoidal sigma weight residual 93.00 168.65 -75.65 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" CB CYS B 920 " pdb=" SG CYS B 920 " pdb=" SG CYS B 931 " pdb=" CB CYS B 931 " ideal model delta sinusoidal sigma weight residual -86.00 -152.82 66.82 1 1.00e+01 1.00e-02 5.82e+01 dihedral pdb=" CB CYS A 920 " pdb=" SG CYS A 920 " pdb=" SG CYS A 931 " pdb=" CB CYS A 931 " ideal model delta sinusoidal sigma weight residual 93.00 158.85 -65.85 1 1.00e+01 1.00e-02 5.67e+01 ... (remaining 15977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 4746 0.163 - 0.326: 56 0.326 - 0.489: 10 0.489 - 0.652: 6 0.652 - 0.815: 3 Chirality restraints: 4821 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 743 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 425 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 787 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 4818 not shown) Planarity restraints: 4926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 324 " 0.002 2.00e-02 2.50e+03 5.57e-02 3.88e+01 pdb=" CG ASN A 324 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN A 324 " -0.068 2.00e-02 2.50e+03 pdb=" ND2 ASN A 324 " 0.054 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 322 " 0.019 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C ASN A 322 " -0.068 2.00e-02 2.50e+03 pdb=" O ASN A 322 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE A 323 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 216 " 0.003 2.00e-02 2.50e+03 3.36e-02 1.41e+01 pdb=" CG ASN B 216 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B 216 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN B 216 " 0.041 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " -0.037 2.00e-02 2.50e+03 ... (remaining 4923 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 904 2.61 - 3.19: 31351 3.19 - 3.76: 50032 3.76 - 4.33: 69243 4.33 - 4.90: 103134 Nonbonded interactions: 254664 Sorted by model distance: nonbonded pdb=" NE2 GLN B1116 " pdb=" OD1 ASN B1120 " model vdw 2.044 3.120 nonbonded pdb=" O PRO B 498 " pdb=" OG1 THR B 650 " model vdw 2.054 3.040 nonbonded pdb=" O PRO A 498 " pdb=" OG1 THR A 650 " model vdw 2.056 3.040 nonbonded pdb=" OG1 THR B1234 " pdb=" OD1 ASP B1236 " model vdw 2.072 3.040 nonbonded pdb=" NE2 GLN A 59 " pdb=" OH TYR A 213 " model vdw 2.076 3.120 ... (remaining 254659 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 31 through 509 or resid 636 through 1505)) selection = (chain 'B' and (resid 31 through 509 or resid 636 through 1505)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'O' selection = chain 'b' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'F' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } ncs_group { reference = (chain 'H' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'i' and resid 1) } ncs_group { reference = chain 'N' selection = chain 'a' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 25.280 Find NCS groups from input model: 1.170 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: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 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 : 0.008 0.076 28721 Z= 0.405 Angle : 1.076 19.785 39340 Z= 0.520 Chirality : 0.064 0.815 4821 Planarity : 0.005 0.056 4875 Dihedral : 13.613 89.719 9499 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 40.25 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.18 % Favored : 90.38 % Rotamer: Outliers : 0.41 % Allowed : 1.87 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.14), residues: 3432 helix: 0.33 (0.18), residues: 745 sheet: -1.33 (0.19), residues: 713 loop : -1.73 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1085 TYR 0.025 0.003 TYR C 676 PHE 0.031 0.003 PHE A 360 TRP 0.023 0.004 TRP C 259 HIS 0.012 0.002 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00782 / 0.40 (28576) covalent geometry : angle 0.97442 / 0.50 (38936) SS BOND : bond 0.00375 / 0.23 ( 31) SS BOND : angle 1.76816 / 1.16 ( 62) hydrogen bonds : bond 0.14968 / 10.36 ( 1071) hydrogen bonds : angle 8.52823 / 5.86 ( 2943) link_ALPHA1-3 : bond 0.00698 / 0.34 ( 3) link_ALPHA1-3 : angle 3.22451 / 2.05 ( 9) link_ALPHA1-6 : bond 0.00509 / 0.27 ( 3) link_ALPHA1-6 : angle 2.08448 / 1.39 ( 9) link_BETA1-4 : bond 0.00946 / 0.72 ( 48) link_BETA1-4 : angle 3.76851 / 2.94 ( 144) link_BETA1-6 : bond 0.00679 / 0.38 ( 9) link_BETA1-6 : angle 2.33457 / 1.53 ( 27) link_NAG-ASN : bond 0.00902 / 0.58 ( 51) link_NAG-ASN : angle 6.28263 / 4.65 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 939 MET cc_start: 0.7191 (mmp) cc_final: 0.6868 (mmp) REVERT: B 961 MET cc_start: 0.9446 (ptt) cc_final: 0.9231 (ptp) outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 0.1474 time to fit residues: 15.6070 Evaluate side-chains 41 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 GLN C 70 GLN C 170 ASN C 187 ASN C 705 GLN C1116 GLN C1120 ASN C1149 GLN B 170 ASN B 258 ASN B 445 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN B 621 GLN B 849 ASN B 988 GLN B1051 GLN B1116 GLN B1120 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.028297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.020948 restraints weight = 484310.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.021591 restraints weight = 312499.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.022059 restraints weight = 232156.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.022402 restraints weight = 187616.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.022644 restraints weight = 160393.130| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28721 Z= 0.157 Angle : 0.833 19.033 39340 Z= 0.393 Chirality : 0.053 0.500 4821 Planarity : 0.005 0.065 4875 Dihedral : 5.835 25.466 3709 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.93 % Favored : 91.72 % Rotamer: Outliers : 0.27 % Allowed : 7.49 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 3432 helix: 0.75 (0.19), residues: 748 sheet: -1.33 (0.20), residues: 682 loop : -1.73 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1207 TYR 0.037 0.002 TYR B 751 PHE 0.027 0.002 PHE B1014 TRP 0.009 0.002 TRP A 189 HIS 0.007 0.001 HIS B 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (28576) covalent geometry : angle 0.75782 / 0.38 (38936) SS BOND : bond 0.00261 / 0.17 ( 31) SS BOND : angle 1.45459 / 1.03 ( 62) hydrogen bonds : bond 0.04864 / 3.32 ( 1071) hydrogen bonds : angle 7.05987 / 4.93 ( 2943) link_ALPHA1-3 : bond 0.00399 / 0.21 ( 3) link_ALPHA1-3 : angle 1.76009 / 1.10 ( 9) link_ALPHA1-6 : bond 0.00463 / 0.24 ( 3) link_ALPHA1-6 : angle 1.67201 / 1.02 ( 9) link_BETA1-4 : bond 0.00981 / 0.75 ( 48) link_BETA1-4 : angle 2.81528 / 2.38 ( 144) link_BETA1-6 : bond 0.00445 / 0.23 ( 9) link_BETA1-6 : angle 1.60014 / 1.03 ( 27) link_NAG-ASN : bond 0.00805 / 0.50 ( 51) link_NAG-ASN : angle 4.82310 / 3.67 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.9624 (tmm) cc_final: 0.9414 (tmm) REVERT: A 1014 PHE cc_start: 0.9477 (m-80) cc_final: 0.9219 (m-80) REVERT: B 939 MET cc_start: 0.7721 (mmp) cc_final: 0.7514 (mmm) REVERT: B 1014 PHE cc_start: 0.8920 (m-80) cc_final: 0.8705 (m-80) REVERT: B 1051 GLN cc_start: 0.9839 (OUTLIER) cc_final: 0.9599 (tp-100) outliers start: 8 outliers final: 4 residues processed: 54 average time/residue: 0.1650 time to fit residues: 16.3085 Evaluate side-chains 45 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 199 optimal weight: 9.9990 chunk 251 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 226 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 328 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 ASN A 258 ASN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 GLN B1116 GLN B1120 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.027322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.020200 restraints weight = 498569.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.020822 restraints weight = 320534.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.021274 restraints weight = 237569.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.021597 restraints weight = 191577.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.021840 restraints weight = 164415.415| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28721 Z= 0.183 Angle : 0.808 19.214 39340 Z= 0.381 Chirality : 0.050 0.467 4821 Planarity : 0.004 0.073 4875 Dihedral : 5.765 26.419 3709 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.07 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3432 helix: 0.73 (0.18), residues: 754 sheet: -1.36 (0.19), residues: 697 loop : -1.73 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 86 TYR 0.029 0.002 TYR B 676 PHE 0.019 0.002 PHE B 91 TRP 0.013 0.002 TRP A 259 HIS 0.007 0.001 HIS C 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (28576) covalent geometry : angle 0.73214 / 0.36 (38936) SS BOND : bond 0.00239 / 0.14 ( 31) SS BOND : angle 1.48772 / 1.04 ( 62) hydrogen bonds : bond 0.04626 / 3.19 ( 1071) hydrogen bonds : angle 6.87862 / 4.81 ( 2943) link_ALPHA1-3 : bond 0.00303 / 0.16 ( 3) link_ALPHA1-3 : angle 1.79452 / 1.15 ( 9) link_ALPHA1-6 : bond 0.00368 / 0.19 ( 3) link_ALPHA1-6 : angle 1.64172 / 1.06 ( 9) link_BETA1-4 : bond 0.00958 / 0.75 ( 48) link_BETA1-4 : angle 2.77387 / 2.36 ( 144) link_BETA1-6 : bond 0.00387 / 0.22 ( 9) link_BETA1-6 : angle 1.54254 / 1.00 ( 27) link_NAG-ASN : bond 0.00840 / 0.59 ( 51) link_NAG-ASN : angle 4.72978 / 3.54 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.9458 (m-80) cc_final: 0.9240 (m-80) REVERT: B 1014 PHE cc_start: 0.8685 (m-80) cc_final: 0.8484 (m-80) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1704 time to fit residues: 15.2427 Evaluate side-chains 39 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 211 optimal weight: 9.9990 chunk 295 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 213 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 248 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 342 optimal weight: 2.9990 chunk 332 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 933 GLN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.025171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.017929 restraints weight = 494670.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.018515 restraints weight = 329247.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.018947 restraints weight = 247746.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.019269 restraints weight = 201230.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.019505 restraints weight = 172515.487| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28721 Z= 0.228 Angle : 0.822 19.036 39340 Z= 0.391 Chirality : 0.050 0.466 4821 Planarity : 0.004 0.073 4875 Dihedral : 5.817 26.348 3709 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.80 % Favored : 90.88 % Rotamer: Outliers : 0.03 % Allowed : 4.92 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.14), residues: 3432 helix: 0.56 (0.18), residues: 761 sheet: -1.38 (0.20), residues: 693 loop : -1.76 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 86 TYR 0.021 0.002 TYR C 676 PHE 0.022 0.002 PHE C1014 TRP 0.017 0.002 TRP C 259 HIS 0.007 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.23 (28576) covalent geometry : angle 0.75023 / 0.38 (38936) SS BOND : bond 0.00297 / 0.15 ( 31) SS BOND : angle 1.50069 / 1.07 ( 62) hydrogen bonds : bond 0.04648 / 3.23 ( 1071) hydrogen bonds : angle 6.91622 / 4.84 ( 2943) link_ALPHA1-3 : bond 0.00256 / 0.13 ( 3) link_ALPHA1-3 : angle 1.94645 / 1.25 ( 9) link_ALPHA1-6 : bond 0.00270 / 0.14 ( 3) link_ALPHA1-6 : angle 1.68496 / 1.07 ( 9) link_BETA1-4 : bond 0.00883 / 0.70 ( 48) link_BETA1-4 : angle 2.67827 / 2.30 ( 144) link_BETA1-6 : bond 0.00349 / 0.20 ( 9) link_BETA1-6 : angle 1.61127 / 1.06 ( 27) link_NAG-ASN : bond 0.00728 / 0.48 ( 51) link_NAG-ASN : angle 4.66843 / 3.54 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.9471 (m-80) cc_final: 0.9258 (m-80) REVERT: C 1014 PHE cc_start: 0.9705 (m-80) cc_final: 0.9482 (m-80) REVERT: B 939 MET cc_start: 0.6812 (mmp) cc_final: 0.6448 (mmp) outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.1518 time to fit residues: 13.3687 Evaluate side-chains 40 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 9 optimal weight: 20.0000 chunk 332 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 330 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1149 GLN B 170 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.025374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.018078 restraints weight = 497584.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.018683 restraints weight = 328631.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.019129 restraints weight = 246361.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.019459 restraints weight = 199627.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.019708 restraints weight = 170920.668| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28721 Z= 0.186 Angle : 0.794 18.721 39340 Z= 0.375 Chirality : 0.050 0.467 4821 Planarity : 0.004 0.073 4875 Dihedral : 5.752 26.304 3709 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.51 % Favored : 91.17 % Rotamer: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.14), residues: 3432 helix: 0.76 (0.18), residues: 753 sheet: -1.39 (0.19), residues: 705 loop : -1.76 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1208 TYR 0.019 0.001 TYR C 676 PHE 0.024 0.002 PHE C1014 TRP 0.013 0.002 TRP C 259 HIS 0.006 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (28576) covalent geometry : angle 0.72101 / 0.36 (38936) SS BOND : bond 0.00214 / 0.12 ( 31) SS BOND : angle 1.34454 / 0.91 ( 62) hydrogen bonds : bond 0.04319 / 2.99 ( 1071) hydrogen bonds : angle 6.73060 / 4.71 ( 2943) link_ALPHA1-3 : bond 0.00334 / 0.18 ( 3) link_ALPHA1-3 : angle 1.80204 / 1.16 ( 9) link_ALPHA1-6 : bond 0.00314 / 0.16 ( 3) link_ALPHA1-6 : angle 1.58600 / 1.04 ( 9) link_BETA1-4 : bond 0.00913 / 0.71 ( 48) link_BETA1-4 : angle 2.64932 / 2.29 ( 144) link_BETA1-6 : bond 0.00422 / 0.24 ( 9) link_BETA1-6 : angle 1.56161 / 1.02 ( 27) link_NAG-ASN : bond 0.00712 / 0.47 ( 51) link_NAG-ASN : angle 4.64027 / 3.51 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.9463 (m-80) cc_final: 0.9243 (m-80) REVERT: C 1014 PHE cc_start: 0.9694 (m-80) cc_final: 0.9476 (m-80) REVERT: B 939 MET cc_start: 0.6661 (mmp) cc_final: 0.6388 (mmp) outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.1593 time to fit residues: 13.7876 Evaluate side-chains 39 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 248 optimal weight: 7.9990 chunk 252 optimal weight: 10.0000 chunk 283 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 238 optimal weight: 9.9990 chunk 140 optimal weight: 0.3980 chunk 339 optimal weight: 5.9990 chunk 232 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 GLN ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN B 459 GLN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** B 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.025319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.018121 restraints weight = 496478.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.018704 restraints weight = 330443.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.019139 restraints weight = 249471.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.019460 restraints weight = 203070.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.019691 restraints weight = 174183.392| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28721 Z= 0.178 Angle : 0.786 18.744 39340 Z= 0.372 Chirality : 0.050 0.456 4821 Planarity : 0.004 0.074 4875 Dihedral : 5.698 28.289 3709 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.39 % Favored : 91.32 % Rotamer: Outliers : 0.07 % Allowed : 2.54 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.14), residues: 3432 helix: 0.86 (0.18), residues: 746 sheet: -1.34 (0.20), residues: 673 loop : -1.75 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 34 TYR 0.019 0.001 TYR C 676 PHE 0.035 0.002 PHE C 360 TRP 0.014 0.002 TRP C 259 HIS 0.005 0.001 HIS C 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (28576) covalent geometry : angle 0.71787 / 0.36 (38936) SS BOND : bond 0.00326 / 0.20 ( 31) SS BOND : angle 1.68969 / 1.08 ( 62) hydrogen bonds : bond 0.04264 / 2.95 ( 1071) hydrogen bonds : angle 6.64923 / 4.66 ( 2943) link_ALPHA1-3 : bond 0.00352 / 0.18 ( 3) link_ALPHA1-3 : angle 1.76179 / 1.14 ( 9) link_ALPHA1-6 : bond 0.00313 / 0.16 ( 3) link_ALPHA1-6 : angle 1.55459 / 1.02 ( 9) link_BETA1-4 : bond 0.00920 / 0.72 ( 48) link_BETA1-4 : angle 2.56601 / 2.24 ( 144) link_BETA1-6 : bond 0.00375 / 0.21 ( 9) link_BETA1-6 : angle 1.52577 / 1.01 ( 27) link_NAG-ASN : bond 0.00848 / 0.62 ( 51) link_NAG-ASN : angle 4.44450 / 3.39 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.9459 (m-80) cc_final: 0.9244 (m-80) REVERT: C 448 ASP cc_start: 0.9560 (m-30) cc_final: 0.9200 (p0) REVERT: C 1014 PHE cc_start: 0.9711 (m-80) cc_final: 0.9473 (m-80) REVERT: B 204 MET cc_start: 0.7733 (mpp) cc_final: 0.7528 (mmt) REVERT: B 939 MET cc_start: 0.6601 (mmp) cc_final: 0.6391 (mmp) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.1459 time to fit residues: 12.7978 Evaluate side-chains 40 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 326 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 329 optimal weight: 0.9980 chunk 295 optimal weight: 20.0000 chunk 221 optimal weight: 10.0000 chunk 284 optimal weight: 0.9990 chunk 331 optimal weight: 7.9990 chunk 306 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN C 170 ASN ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 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 = 0.3090 r_free = 0.3090 target = 0.025083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.017903 restraints weight = 504910.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.018490 restraints weight = 334338.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.018923 restraints weight = 250931.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.019243 restraints weight = 203930.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.019474 restraints weight = 174800.359| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28721 Z= 0.227 Angle : 0.821 18.689 39340 Z= 0.392 Chirality : 0.050 0.463 4821 Planarity : 0.004 0.073 4875 Dihedral : 5.813 27.305 3709 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.92 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.14), residues: 3432 helix: 0.80 (0.18), residues: 746 sheet: -1.40 (0.20), residues: 671 loop : -1.80 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 172 TYR 0.023 0.002 TYR B 66 PHE 0.035 0.002 PHE C 360 TRP 0.027 0.003 TRP C 259 HIS 0.008 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.23 (28576) covalent geometry : angle 0.74991 / 0.38 (38936) SS BOND : bond 0.00276 / 0.16 ( 31) SS BOND : angle 1.65150 / 1.03 ( 62) hydrogen bonds : bond 0.04398 / 3.06 ( 1071) hydrogen bonds : angle 6.74407 / 4.72 ( 2943) link_ALPHA1-3 : bond 0.00410 / 0.21 ( 3) link_ALPHA1-3 : angle 1.94057 / 1.17 ( 9) link_ALPHA1-6 : bond 0.00242 / 0.12 ( 3) link_ALPHA1-6 : angle 1.72303 / 1.11 ( 9) link_BETA1-4 : bond 0.00895 / 0.70 ( 48) link_BETA1-4 : angle 2.60072 / 2.26 ( 144) link_BETA1-6 : bond 0.00344 / 0.19 ( 9) link_BETA1-6 : angle 1.58994 / 1.05 ( 27) link_NAG-ASN : bond 0.00756 / 0.52 ( 51) link_NAG-ASN : angle 4.66912 / 3.53 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.9467 (m-80) cc_final: 0.9263 (m-80) REVERT: C 1014 PHE cc_start: 0.9728 (m-80) cc_final: 0.9496 (m-80) REVERT: B 204 MET cc_start: 0.7600 (mpp) cc_final: 0.7350 (mmt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1563 time to fit residues: 13.4310 Evaluate side-chains 38 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 191 optimal weight: 9.9990 chunk 301 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 279 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 155 optimal weight: 0.3980 chunk 319 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 849 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.025289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.018032 restraints weight = 502384.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.018636 restraints weight = 330018.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.019080 restraints weight = 247230.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.019407 restraints weight = 200462.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.019642 restraints weight = 171514.589| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28721 Z= 0.181 Angle : 0.794 18.302 39340 Z= 0.376 Chirality : 0.050 0.467 4821 Planarity : 0.004 0.073 4875 Dihedral : 5.737 25.409 3709 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.51 % Favored : 91.17 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3432 helix: 0.85 (0.18), residues: 754 sheet: -1.36 (0.20), residues: 669 loop : -1.78 (0.14), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 172 TYR 0.019 0.001 TYR C 676 PHE 0.031 0.002 PHE C 360 TRP 0.014 0.002 TRP C 259 HIS 0.005 0.001 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (28576) covalent geometry : angle 0.72335 / 0.36 (38936) SS BOND : bond 0.00208 / 0.12 ( 31) SS BOND : angle 1.66803 / 1.04 ( 62) hydrogen bonds : bond 0.04171 / 2.89 ( 1071) hydrogen bonds : angle 6.62661 / 4.64 ( 2943) link_ALPHA1-3 : bond 0.00421 / 0.22 ( 3) link_ALPHA1-3 : angle 1.76842 / 1.16 ( 9) link_ALPHA1-6 : bond 0.00270 / 0.14 ( 3) link_ALPHA1-6 : angle 1.54769 / 1.02 ( 9) link_BETA1-4 : bond 0.00877 / 0.69 ( 48) link_BETA1-4 : angle 2.53383 / 2.23 ( 144) link_BETA1-6 : bond 0.00394 / 0.21 ( 9) link_BETA1-6 : angle 1.53785 / 1.03 ( 27) link_NAG-ASN : bond 0.00727 / 0.49 ( 51) link_NAG-ASN : angle 4.57622 / 3.46 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 1014 PHE cc_start: 0.9460 (m-80) cc_final: 0.9253 (m-80) REVERT: C 448 ASP cc_start: 0.9567 (m-30) cc_final: 0.9219 (p0) REVERT: C 1014 PHE cc_start: 0.9730 (m-80) cc_final: 0.9493 (m-80) REVERT: B 204 MET cc_start: 0.7823 (mpp) cc_final: 0.7579 (mmt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1607 time to fit residues: 13.6908 Evaluate side-chains 39 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 57 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 333 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 814 ASN C1051 GLN C1055 GLN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 922 ASN ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN B 995 ASN ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.025222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.018692 restraints weight = 486158.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.019155 restraints weight = 352461.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.019491 restraints weight = 281234.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.019729 restraints weight = 238380.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.019917 restraints weight = 211790.810| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28721 Z= 0.179 Angle : 0.794 18.081 39340 Z= 0.377 Chirality : 0.050 0.465 4821 Planarity : 0.004 0.074 4875 Dihedral : 5.685 27.160 3709 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.45 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.14), residues: 3432 helix: 0.87 (0.18), residues: 750 sheet: -1.36 (0.20), residues: 665 loop : -1.76 (0.14), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 146 TYR 0.031 0.002 TYR A 212 PHE 0.034 0.002 PHE C 128 TRP 0.015 0.002 TRP C 259 HIS 0.005 0.001 HIS B 951 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (28576) covalent geometry : angle 0.72695 / 0.36 (38936) SS BOND : bond 0.00258 / 0.14 ( 31) SS BOND : angle 1.66518 / 1.13 ( 62) hydrogen bonds : bond 0.04134 / 2.87 ( 1071) hydrogen bonds : angle 6.59594 / 4.61 ( 2943) link_ALPHA1-3 : bond 0.00399 / 0.21 ( 3) link_ALPHA1-3 : angle 1.72104 / 1.13 ( 9) link_ALPHA1-6 : bond 0.00277 / 0.14 ( 3) link_ALPHA1-6 : angle 1.54525 / 1.02 ( 9) link_BETA1-4 : bond 0.00863 / 0.68 ( 48) link_BETA1-4 : angle 2.50013 / 2.21 ( 144) link_BETA1-6 : bond 0.00378 / 0.21 ( 9) link_BETA1-6 : angle 1.51551 / 1.01 ( 27) link_NAG-ASN : bond 0.00708 / 0.48 ( 51) link_NAG-ASN : angle 4.47966 / 3.41 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 265 ASP cc_start: 0.9568 (p0) cc_final: 0.9267 (m-30) REVERT: A 952 MET cc_start: 0.9183 (mmp) cc_final: 0.8788 (mmm) REVERT: A 1014 PHE cc_start: 0.9450 (m-80) cc_final: 0.9170 (m-80) REVERT: A 1209 MET cc_start: 0.9828 (ppp) cc_final: 0.9564 (ppp) REVERT: C 265 ASP cc_start: 0.9531 (p0) cc_final: 0.9300 (p0) REVERT: C 448 ASP cc_start: 0.9714 (m-30) cc_final: 0.9112 (p0) REVERT: C 790 MET cc_start: 0.6907 (ptt) cc_final: 0.6315 (ptt) REVERT: C 1014 PHE cc_start: 0.9479 (m-80) cc_final: 0.9217 (m-80) REVERT: C 1202 TYR cc_start: 0.9387 (m-80) cc_final: 0.8913 (m-80) REVERT: C 1209 MET cc_start: 0.9584 (tpt) cc_final: 0.9349 (tpt) REVERT: B 265 ASP cc_start: 0.9299 (p0) cc_final: 0.8940 (p0) REVERT: B 826 TYR cc_start: 0.8769 (m-80) cc_final: 0.8368 (m-80) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1702 time to fit residues: 14.9431 Evaluate side-chains 42 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 280 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 933 GLN C 996 GLN B 114 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.024750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.017712 restraints weight = 512735.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.018293 restraints weight = 340730.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.018717 restraints weight = 255871.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.019034 restraints weight = 207740.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.019258 restraints weight = 177824.812| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28721 Z= 0.276 Angle : 0.869 18.368 39340 Z= 0.419 Chirality : 0.050 0.462 4821 Planarity : 0.004 0.074 4875 Dihedral : 5.963 28.414 3709 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 24.66 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.53 % Favored : 90.18 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.14), residues: 3432 helix: 0.53 (0.18), residues: 745 sheet: -1.39 (0.20), residues: 649 loop : -1.87 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 86 TYR 0.034 0.002 TYR A 212 PHE 0.027 0.002 PHE C 360 TRP 0.023 0.003 TRP C 259 HIS 0.010 0.002 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.28 (28576) covalent geometry : angle 0.80606 / 0.41 (38936) SS BOND : bond 0.00322 / 0.18 ( 31) SS BOND : angle 1.76476 / 1.23 ( 62) hydrogen bonds : bond 0.04665 / 3.26 ( 1071) hydrogen bonds : angle 6.90592 / 4.83 ( 2943) link_ALPHA1-3 : bond 0.00446 / 0.23 ( 3) link_ALPHA1-3 : angle 2.05617 / 1.37 ( 9) link_ALPHA1-6 : bond 0.00189 / 0.10 ( 3) link_ALPHA1-6 : angle 1.68521 / 1.09 ( 9) link_BETA1-4 : bond 0.00855 / 0.68 ( 48) link_BETA1-4 : angle 2.55365 / 2.24 ( 144) link_BETA1-6 : bond 0.00348 / 0.20 ( 9) link_BETA1-6 : angle 1.71956 / 1.15 ( 27) link_NAG-ASN : bond 0.00756 / 0.51 ( 51) link_NAG-ASN : angle 4.52557 / 3.43 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: C 1014 PHE cc_start: 0.9748 (m-80) cc_final: 0.9493 (m-80) REVERT: B 826 TYR cc_start: 0.8335 (m-80) cc_final: 0.7644 (m-80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1755 time to fit residues: 14.7115 Evaluate side-chains 38 residues out of total 2949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 224 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 334 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 222 optimal weight: 30.0000 chunk 163 optimal weight: 0.9990 chunk 13 optimal weight: 50.0000 chunk 173 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 922 ASN ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 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 = 0.3092 r_free = 0.3092 target = 0.025132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.017896 restraints weight = 490209.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.018480 restraints weight = 327540.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.018913 restraints weight = 247190.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.019235 restraints weight = 201125.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.019469 restraints weight = 172433.271| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28721 Z= 0.197 Angle : 0.807 17.784 39340 Z= 0.384 Chirality : 0.050 0.473 4821 Planarity : 0.004 0.073 4875 Dihedral : 5.815 28.768 3709 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.86 % Favored : 90.85 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.14), residues: 3432 helix: 0.74 (0.18), residues: 751 sheet: -1.36 (0.20), residues: 654 loop : -1.83 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 34 TYR 0.025 0.002 TYR A 212 PHE 0.025 0.002 PHE C 360 TRP 0.015 0.002 TRP C 259 HIS 0.009 0.001 HIS C 951 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 (28576) covalent geometry : angle 0.74166 / 0.37 (38936) SS BOND : bond 0.00257 / 0.14 ( 31) SS BOND : angle 1.61091 / 1.12 ( 62) hydrogen bonds : bond 0.04232 / 2.95 ( 1071) hydrogen bonds : angle 6.71075 / 4.69 ( 2943) link_ALPHA1-3 : bond 0.00445 / 0.23 ( 3) link_ALPHA1-3 : angle 1.78755 / 1.18 ( 9) link_ALPHA1-6 : bond 0.00234 / 0.12 ( 3) link_ALPHA1-6 : angle 1.57612 / 1.05 ( 9) link_BETA1-4 : bond 0.00866 / 0.69 ( 48) link_BETA1-4 : angle 2.49324 / 2.22 ( 144) link_BETA1-6 : bond 0.00394 / 0.22 ( 9) link_BETA1-6 : angle 1.62429 / 1.09 ( 27) link_NAG-ASN : bond 0.00696 / 0.47 ( 51) link_NAG-ASN : angle 4.45306 / 3.38 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4468.43 seconds wall clock time: 79 minutes 19.72 seconds (4759.72 seconds total)