Starting phenix.real_space_refine on Thu Mar 5 20:56:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6s_33646/03_2026/7y6s_33646.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6s_33646/03_2026/7y6s_33646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6s_33646/03_2026/7y6s_33646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6s_33646/03_2026/7y6s_33646.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6s_33646/03_2026/7y6s_33646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6s_33646/03_2026/7y6s_33646.cif" } resolution = 3.1 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= 0.040 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 105 5.16 5 C 15744 2.51 5 N 3933 2.21 5 O 5070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24852 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 7766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7766 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 38, 'TRANS': 965} Chain breaks: 9 Chain: "B" Number of atoms: 7766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7766 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 38, 'TRANS': 965} Chain breaks: 9 Chain: "C" Number of atoms: 7766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7766 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 38, 'TRANS': 965} Chain breaks: 9 Chain: "D" 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "d" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.00, per 1000 atoms: 0.24 Number of scatterers: 24852 At special positions: 0 Unit cell: (171.72, 174.9, 154.76, 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 105 16.00 O 5070 8.00 N 3933 7.00 C 15744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " 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=2.03 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 B1122 " - pdb=" SG CYS B1133 " 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 ALPHA1-2 " MAN E 4 " - " MAN E 5 " " MAN Q 4 " - " MAN Q 5 " " MAN c 4 " - " MAN c 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " MAN E 6 " - " MAN E 7 " " BMA Q 3 " - " MAN Q 4 " " MAN Q 6 " - " MAN Q 7 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " ALPHA1-6 " BMA E 3 " - " MAN E 6 " " BMA Q 3 " - " MAN Q 6 " " BMA c 3 " - " MAN c 6 " 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 G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " 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 i 2 " - " BMA i 3 " " 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 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 2 " " NAG O 1 " - " FUC O 3 " " NAG P 1 " - " FUC P 4 " " NAG R 1 " - " FUC R 2 " " NAG a 1 " - " FUC a 3 " " NAG b 1 " - " FUC b 4 " " NAG d 1 " - " FUC d 2 " " NAG m 1 " - " FUC m 3 " NAG-ASN " NAG A1501 " - " ASN A 667 " " NAG A1502 " - " ASN A 787 " " NAG A1503 " - " ASN A1009 " " NAG A1504 " - " ASN A1249 " " NAG B1501 " - " ASN B 667 " " NAG B1502 " - " ASN B 787 " " NAG B1503 " - " ASN B1009 " " NAG B1504 " - " ASN B1249 " " NAG C1501 " - " ASN C 667 " " NAG C1502 " - " ASN C 787 " " NAG C1503 " - " ASN C1009 " " NAG C1504 " - " ASN C1249 " " NAG D 1 " - " ASN A 216 " " NAG E 1 " - " ASN A 264 " " NAG F 1 " - " ASN A 300 " " NAG G 1 " - " ASN A 324 " " NAG H 1 " - " ASN A 344 " " NAG I 1 " - " ASN A 425 " " NAG J 1 " - " ASN A 726 " " NAG K 1 " - " ASN A 688 " " NAG L 1 " - " ASN A 743 " " NAG M 1 " - " ASN A 781 " " NAG N 1 " - " ASN A 873 " " NAG O 1 " - " ASN A1232 " " NAG P 1 " - " ASN B 216 " " NAG Q 1 " - " ASN B 264 " " NAG R 1 " - " ASN B 300 " " NAG S 1 " - " ASN B 324 " " NAG T 1 " - " ASN B 344 " " NAG U 1 " - " ASN B 425 " " NAG V 1 " - " ASN B 726 " " NAG W 1 " - " ASN B 688 " " NAG X 1 " - " ASN B 743 " " NAG Y 1 " - " ASN B 781 " " NAG Z 1 " - " ASN B 873 " " NAG a 1 " - " ASN B1232 " " NAG b 1 " - " ASN C 216 " " NAG c 1 " - " ASN C 264 " " NAG d 1 " - " ASN C 300 " " NAG e 1 " - " ASN C 324 " " NAG f 1 " - " ASN C 344 " " NAG g 1 " - " ASN C 425 " " NAG h 1 " - " ASN C 726 " " NAG i 1 " - " ASN C 688 " " NAG j 1 " - " ASN C 743 " " NAG k 1 " - " ASN C 781 " " NAG l 1 " - " ASN C 873 " " NAG m 1 " - " ASN C1232 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.0 seconds 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5604 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 39 sheets defined 26.0% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 32 through 37 Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.508A pdb=" N CYS A 234 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 removed outlier: 3.621A pdb=" N VAL A 328 " --> pdb=" O ASP A 325 " (cutoff:3.500A) 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: 3.719A pdb=" N GLN A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 822 " --> pdb=" O ARG A 818 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN A 825 " --> pdb=" O GLN A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 852 removed outlier: 4.193A pdb=" N GLU A 834 " --> pdb=" O CYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 861 removed outlier: 3.848A pdb=" N LEU A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 910 through 914 Processing helix chain 'A' and resid 928 through 935 Processing helix chain 'A' and resid 946 through 961 Processing helix chain 'A' and resid 967 through 971 Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.587A pdb=" N ALA A 977 " --> pdb=" O PRO A 973 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1015 removed outlier: 4.146A pdb=" N LEU A 999 " --> pdb=" O ASN A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1055 removed outlier: 4.146A pdb=" N GLN A1045 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY A1046 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A1055 " --> pdb=" O GLN A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1058 No H-bonds generated for 'chain 'A' and resid 1056 through 1058' Processing helix chain 'A' and resid 1066 through 1074 Processing helix chain 'A' and resid 1075 through 1123 removed outlier: 3.707A pdb=" N VAL A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A1086 " --> pdb=" O GLN A1082 " (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 1237 through 1242 Processing helix chain 'A' and resid 1247 through 1253 Processing helix chain 'B' and resid 32 through 38 removed outlier: 3.851A pdb=" N LYS B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 238 removed outlier: 3.953A pdb=" N GLY B 236 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 238 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 329 removed outlier: 3.552A pdb=" N VAL B 328 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 475 Processing helix chain 'B' and resid 807 through 814 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.650A pdb=" N GLN B 821 " --> pdb=" O SER B 817 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 822 " --> pdb=" O ARG B 818 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 825 " --> pdb=" O GLN B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 852 Processing helix chain 'B' and resid 855 through 861 Processing helix chain 'B' and resid 895 through 904 removed outlier: 3.589A pdb=" N LYS B 904 " --> pdb=" O LEU B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 914 Processing helix chain 'B' and resid 928 through 935 Processing helix chain 'B' and resid 946 through 961 Processing helix chain 'B' and resid 967 through 971 Processing helix chain 'B' and resid 973 through 986 removed outlier: 3.509A pdb=" N ALA B 977 " --> pdb=" O PRO B 973 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 985 " --> pdb=" O ARG B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1014 removed outlier: 3.922A pdb=" N LEU B 999 " --> pdb=" O ASN B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1055 removed outlier: 4.135A pdb=" N GLN B1045 " --> pdb=" O VAL B1041 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY B1046 " --> pdb=" O VAL B1042 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B1055 " --> pdb=" O GLN B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1074 Processing helix chain 'B' and resid 1075 through 1122 removed outlier: 3.707A pdb=" N VAL B1081 " --> pdb=" O PRO B1077 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B1085 " --> pdb=" O VAL B1081 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B1086 " --> pdb=" O GLN B1082 " (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 1237 through 1242 removed outlier: 3.553A pdb=" N VAL B1241 " --> pdb=" O GLN B1237 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 325 through 329 removed outlier: 3.665A pdb=" N VAL C 328 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 476 Processing helix chain 'C' and resid 807 through 814 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 825 through 829 removed outlier: 6.739A pdb=" N ALA C 828 " --> pdb=" O GLN C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 852 removed outlier: 3.814A pdb=" N ALA C 836 " --> pdb=" O THR C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 861 removed outlier: 3.882A pdb=" N LEU C 861 " --> pdb=" O GLU C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 910 through 914 Processing helix chain 'C' and resid 928 through 935 Processing helix chain 'C' and resid 946 through 961 Processing helix chain 'C' and resid 967 through 971 Processing helix chain 'C' and resid 973 through 986 removed outlier: 3.653A pdb=" N ALA C 977 " --> pdb=" O PRO C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1015 removed outlier: 4.590A pdb=" N LEU C 999 " --> pdb=" O ASN C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1055 removed outlier: 4.058A pdb=" N GLN C1045 " --> pdb=" O VAL C1041 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY C1046 " --> pdb=" O VAL C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1074 Processing helix chain 'C' and resid 1075 through 1123 removed outlier: 3.670A pdb=" N VAL C1081 " --> pdb=" O PRO C1077 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C1086 " --> pdb=" O GLN C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1218 No H-bonds generated for 'chain 'C' and resid 1216 through 1218' Processing helix chain 'C' and resid 1237 through 1242 removed outlier: 3.505A pdb=" N VAL C1241 " --> pdb=" O GLN C1237 " (cutoff:3.500A) Processing helix chain 'C' and resid 1247 through 1253 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.617A pdb=" N ALA A 74 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 192 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 184 removed outlier: 3.647A pdb=" N VAL A 175 " --> pdb=" O TYR A 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 268 removed outlier: 5.445A pdb=" N LEU B 684 " --> pdb=" O VAL B 697 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 694 " --> pdb=" O THR B 666 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 288 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 270 through 288 current: chain 'A' and resid 397 through 401 removed outlier: 3.870A pdb=" N LEU A 414 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL A 408 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 412 through 415 current: chain 'A' and resid 457 through 463 Processing sheet with id=AA6, first strand: chain 'A' and resid 294 through 298 removed outlier: 6.752A pdb=" N HIS A 338 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL A 422 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 336 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N PHE A 375 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE A 387 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 488 removed outlier: 3.682A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 499 through 502 removed outlier: 5.495A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR A 675 " --> pdb=" O THR C 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB1, first strand: chain 'A' and resid 780 through 798 removed outlier: 6.690A pdb=" N ASN A 781 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A1167 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER A 783 " --> pdb=" O ASP A1165 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP A1165 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE A1163 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASN A 787 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLY A1150 " --> pdb=" O ALA A1146 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ALA A1146 " --> pdb=" O GLY A1150 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A1152 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL A1144 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A1154 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER A1142 " --> pdb=" O LEU A1154 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR A1156 " --> pdb=" O ILE A1140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB3, first strand: chain 'A' and resid 881 through 884 removed outlier: 4.039A pdb=" N ASP A 884 " --> pdb=" O ARG A 889 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG A 889 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1220 through 1223 removed outlier: 4.185A pdb=" N ALA A1179 " --> pdb=" O ILE A1223 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS A1173 " --> pdb=" O LEU A1233 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1187 through 1190 Processing sheet with id=AB6, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.188A pdb=" N TYR B 212 " --> pdb=" O CYS B 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.599A pdb=" N ALA B 74 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 192 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B 123 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN B 151 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE B 125 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AB9, first strand: chain 'B' and resid 267 through 268 removed outlier: 5.502A pdb=" N LEU C 684 " --> pdb=" O VAL C 697 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 271 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 271 through 288 current: chain 'B' and resid 397 through 401 removed outlier: 3.898A pdb=" N LEU B 414 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL B 408 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLY B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 412 through 415 current: chain 'B' and resid 457 through 463 Processing sheet with id=AC2, first strand: chain 'B' and resid 293 through 298 removed outlier: 3.715A pdb=" N GLN B 295 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS B 338 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 422 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 336 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN B 344 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N CYS B 373 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 483 through 488 removed outlier: 3.786A pdb=" N GLY B 715 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 709 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE B 713 " --> pdb=" O VAL B 709 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AC5, first strand: chain 'B' and resid 780 through 798 removed outlier: 6.621A pdb=" N ASN B 781 " --> pdb=" O ILE B1167 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B1167 " --> pdb=" O ASN B 781 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER B 783 " --> pdb=" O ASP B1165 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP B1165 " --> pdb=" O SER B 783 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE B1163 " --> pdb=" O PRO B 785 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN B 787 " --> pdb=" O SER B1161 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY B1150 " --> pdb=" O ALA B1146 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA B1146 " --> pdb=" O GLY B1150 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B1152 " --> pdb=" O VAL B1144 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B1144 " --> pdb=" O LEU B1152 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B1154 " --> pdb=" O SER B1142 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER B1142 " --> pdb=" O LEU B1154 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR B1156 " --> pdb=" O ILE B1140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AC7, first strand: chain 'B' and resid 881 through 883 Processing sheet with id=AC8, first strand: chain 'B' and resid 1220 through 1223 removed outlier: 3.729A pdb=" N ALA B1179 " --> pdb=" O ILE B1223 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYS B1173 " --> pdb=" O LEU B1233 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1187 through 1190 Processing sheet with id=AD1, first strand: chain 'C' and resid 46 through 51 removed outlier: 4.338A pdb=" N TYR C 212 " --> pdb=" O CYS C 230 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 73 through 74 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 73 through 74 current: chain 'C' and resid 106 through 110 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 148 through 152 current: chain 'C' and resid 172 through 175 Processing sheet with id=AD3, first strand: chain 'C' and resid 271 through 288 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 271 through 288 current: chain 'C' and resid 397 through 401 removed outlier: 3.723A pdb=" N LEU C 414 " --> pdb=" O VAL C 406 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL C 408 " --> pdb=" O GLY C 412 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLY C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 411 through 415 current: chain 'C' and resid 457 through 463 Processing sheet with id=AD4, first strand: chain 'C' and resid 296 through 298 removed outlier: 7.112A pdb=" N HIS C 338 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL C 422 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 336 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 483 through 488 removed outlier: 3.748A pdb=" N GLY C 715 " --> pdb=" O ALA C 707 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 749 through 751 Processing sheet with id=AD7, first strand: chain 'C' and resid 780 through 786 Processing sheet with id=AD8, first strand: chain 'C' and resid 789 through 798 removed outlier: 7.101A pdb=" N GLY C1150 " --> pdb=" O ALA C1146 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA C1146 " --> pdb=" O GLY C1150 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU C1152 " --> pdb=" O VAL C1144 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL C1144 " --> pdb=" O LEU C1152 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU C1154 " --> pdb=" O SER C1142 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER C1142 " --> pdb=" O LEU C1154 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR C1156 " --> pdb=" O ILE C1140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AE1, first strand: chain 'C' and resid 881 through 882 Processing sheet with id=AE2, first strand: chain 'C' and resid 1220 through 1223 removed outlier: 3.659A pdb=" N ALA C1179 " --> pdb=" O ILE C1223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1187 through 1190 877 hydrogen bonds defined for protein. 2355 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: 5.35 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7719 1.34 - 1.46: 6440 1.46 - 1.58: 11047 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 25341 Sorted by residual: bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.42e+00 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.22e+00 bond pdb=" C1 NAG B1501 " pdb=" O5 NAG B1501 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" CA SER B 506 " pdb=" CB SER B 506 " ideal model delta sigma weight residual 1.535 1.492 0.043 1.71e-02 3.42e+03 6.36e+00 ... (remaining 25336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 33121 1.71 - 3.42: 1066 3.42 - 5.12: 205 5.12 - 6.83: 80 6.83 - 8.54: 7 Bond angle restraints: 34479 Sorted by residual: angle pdb=" C PHE C 725 " pdb=" N ASN C 726 " pdb=" CA ASN C 726 " ideal model delta sigma weight residual 122.53 129.95 -7.42 1.92e+00 2.71e-01 1.49e+01 angle pdb=" N ASN C 726 " pdb=" CA ASN C 726 " pdb=" CB ASN C 726 " ideal model delta sigma weight residual 110.42 105.22 5.20 1.53e+00 4.27e-01 1.16e+01 angle pdb=" C ASP C 434 " pdb=" N VAL C 435 " pdb=" CA VAL C 435 " ideal model delta sigma weight residual 121.97 127.01 -5.04 1.80e+00 3.09e-01 7.83e+00 angle pdb=" C ILE B 424 " pdb=" N ASN B 425 " pdb=" CA ASN B 425 " ideal model delta sigma weight residual 123.23 127.61 -4.38 1.57e+00 4.06e-01 7.77e+00 angle pdb=" CA SER B 506 " pdb=" C SER B 506 " pdb=" O SER B 506 " ideal model delta sigma weight residual 121.58 118.36 3.22 1.16e+00 7.43e-01 7.70e+00 ... (remaining 34474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.46: 15215 24.46 - 48.92: 774 48.92 - 73.39: 202 73.39 - 97.85: 156 97.85 - 122.31: 81 Dihedral angle restraints: 16428 sinusoidal: 7698 harmonic: 8730 Sorted by residual: 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 -86.00 -163.17 77.17 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS A 808 " pdb=" SG CYS A 808 " pdb=" SG CYS A 830 " pdb=" CB CYS A 830 " ideal model delta sinusoidal sigma weight residual -86.00 -128.21 42.21 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CA ILE B 424 " pdb=" C ILE B 424 " pdb=" N ASN B 425 " pdb=" CA ASN B 425 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 16425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 4299 0.188 - 0.377: 33 0.377 - 0.565: 2 0.565 - 0.753: 2 0.753 - 0.942: 2 Chirality restraints: 4338 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN B 726 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" C1 NAG k 1 " pdb=" ND2 ASN C 781 " pdb=" C2 NAG k 1 " pdb=" O5 NAG k 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 726 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 4335 not shown) Planarity restraints: 4305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 425 " -0.034 2.00e-02 2.50e+03 3.32e-02 1.37e+01 pdb=" CG ASN B 425 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN B 425 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 425 " 0.034 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 726 " 0.033 2.00e-02 2.50e+03 3.10e-02 1.20e+01 pdb=" CG ASN C 726 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN C 726 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 726 " -0.037 2.00e-02 2.50e+03 pdb=" C1 NAG h 1 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 425 " 0.002 2.00e-02 2.50e+03 2.90e-02 1.05e+01 pdb=" CG ASN A 425 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 425 " -0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN A 425 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.032 2.00e-02 2.50e+03 ... (remaining 4302 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 820 2.70 - 3.25: 25244 3.25 - 3.80: 39013 3.80 - 4.35: 50719 4.35 - 4.90: 84513 Nonbonded interactions: 200309 Sorted by model distance: nonbonded pdb=" OD1 ASP B 265 " pdb=" OH TYR C 675 " model vdw 2.147 3.040 nonbonded pdb=" ND2 ASN C 240 " pdb=" O PHE C 438 " model vdw 2.163 3.120 nonbonded pdb=" O PRO C 498 " pdb=" OG1 THR C 650 " model vdw 2.172 3.040 nonbonded pdb=" O PRO A 498 " pdb=" OG1 THR A 650 " model vdw 2.180 3.040 nonbonded pdb=" OG1 THR A1234 " pdb=" OD1 ASP A1236 " model vdw 2.181 3.040 ... (remaining 200304 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'P' selection = chain 'b' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'c' } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'j' and resid 1) selection = (chain 'l' and resid 1) } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.480 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 25473 Z= 0.224 Angle : 0.836 18.020 34863 Z= 0.361 Chirality : 0.059 0.942 4338 Planarity : 0.004 0.053 4257 Dihedral : 19.821 122.311 10788 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.53 % Rotamer: Outliers : 0.31 % Allowed : 0.54 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 2952 helix: 0.67 (0.20), residues: 672 sheet: -1.01 (0.20), residues: 588 loop : -0.60 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 924 TYR 0.034 0.001 TYR B 403 PHE 0.021 0.001 PHE C 725 TRP 0.019 0.001 TRP A 65 HIS 0.003 0.001 HIS C1139 Details of bonding type rmsd covalent geometry : bond 0.00457 (25341) covalent geometry : angle 0.75566 (34479) SS BOND : bond 0.00195 ( 12) SS BOND : angle 1.27112 ( 24) hydrogen bonds : bond 0.18481 ( 877) hydrogen bonds : angle 6.90678 ( 2355) link_ALPHA1-2 : bond 0.00735 ( 3) link_ALPHA1-2 : angle 1.90557 ( 9) link_ALPHA1-3 : bond 0.00839 ( 6) link_ALPHA1-3 : angle 2.43075 ( 18) link_ALPHA1-6 : bond 0.00452 ( 3) link_ALPHA1-6 : angle 2.52246 ( 9) link_BETA1-4 : bond 0.00652 ( 51) link_BETA1-4 : angle 2.05334 ( 153) link_BETA1-6 : bond 0.00612 ( 9) link_BETA1-6 : angle 1.74901 ( 27) link_NAG-ASN : bond 0.00968 ( 48) link_NAG-ASN : angle 5.07122 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.861 Fit side-chains REVERT: A 158 MET cc_start: 0.8700 (pmm) cc_final: 0.8480 (pmm) REVERT: A 435 VAL cc_start: 0.8529 (m) cc_final: 0.8275 (p) REVERT: A 492 LEU cc_start: 0.8917 (mm) cc_final: 0.8614 (tp) REVERT: A 952 MET cc_start: 0.9167 (mtp) cc_final: 0.8858 (mtm) REVERT: A 1107 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8658 (mt-10) REVERT: A 1136 ASP cc_start: 0.8597 (m-30) cc_final: 0.8197 (m-30) REVERT: A 1209 MET cc_start: 0.9370 (mtt) cc_final: 0.9127 (mtp) REVERT: B 214 MET cc_start: 0.8368 (mtp) cc_final: 0.7889 (tmm) REVERT: B 435 VAL cc_start: 0.8521 (m) cc_final: 0.8312 (p) REVERT: B 814 ASN cc_start: 0.9571 (t0) cc_final: 0.9333 (t0) REVERT: B 1244 ASP cc_start: 0.9152 (t70) cc_final: 0.8705 (t0) REVERT: C 1209 MET cc_start: 0.9270 (mtt) cc_final: 0.9047 (mtp) outliers start: 8 outliers final: 3 residues processed: 63 average time/residue: 0.1680 time to fit residues: 17.9809 Evaluate side-chains 49 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 639 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 322 ASN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.045732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.035260 restraints weight = 153252.610| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 4.62 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 25473 Z= 0.274 Angle : 0.814 16.748 34863 Z= 0.365 Chirality : 0.052 0.699 4338 Planarity : 0.004 0.065 4257 Dihedral : 16.665 113.826 5659 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.23 % Allowed : 5.78 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.15), residues: 2952 helix: 1.07 (0.19), residues: 702 sheet: -0.92 (0.20), residues: 564 loop : -0.60 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1235 TYR 0.018 0.001 TYR B 403 PHE 0.015 0.001 PHE A 347 TRP 0.015 0.001 TRP A 65 HIS 0.005 0.001 HIS B 951 Details of bonding type rmsd covalent geometry : bond 0.00600 (25341) covalent geometry : angle 0.73747 (34479) SS BOND : bond 0.00301 ( 12) SS BOND : angle 1.04111 ( 24) hydrogen bonds : bond 0.04915 ( 877) hydrogen bonds : angle 5.39921 ( 2355) link_ALPHA1-2 : bond 0.00757 ( 3) link_ALPHA1-2 : angle 2.97120 ( 9) link_ALPHA1-3 : bond 0.01372 ( 6) link_ALPHA1-3 : angle 3.30705 ( 18) link_ALPHA1-6 : bond 0.00358 ( 3) link_ALPHA1-6 : angle 2.55819 ( 9) link_BETA1-4 : bond 0.00634 ( 51) link_BETA1-4 : angle 2.27426 ( 153) link_BETA1-6 : bond 0.00732 ( 9) link_BETA1-6 : angle 1.87068 ( 27) link_NAG-ASN : bond 0.00720 ( 48) link_NAG-ASN : angle 4.65330 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.851 Fit side-chains REVERT: A 158 MET cc_start: 0.8663 (pmm) cc_final: 0.8411 (pmm) REVERT: A 322 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8111 (t0) REVERT: A 435 VAL cc_start: 0.8541 (m) cc_final: 0.8205 (p) REVERT: A 492 LEU cc_start: 0.8867 (mm) cc_final: 0.8623 (tp) REVERT: A 952 MET cc_start: 0.8810 (mtp) cc_final: 0.8556 (mtm) REVERT: A 1107 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8446 (mt-10) REVERT: B 214 MET cc_start: 0.8176 (mtp) cc_final: 0.7642 (tmm) REVERT: B 435 VAL cc_start: 0.8492 (m) cc_final: 0.8273 (p) REVERT: B 814 ASN cc_start: 0.9457 (t0) cc_final: 0.9127 (t0) REVERT: B 952 MET cc_start: 0.8904 (tpp) cc_final: 0.8567 (tpp) REVERT: B 1244 ASP cc_start: 0.9144 (t70) cc_final: 0.8608 (t0) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.1373 time to fit residues: 13.1063 Evaluate side-chains 46 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 214 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 264 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 192 optimal weight: 7.9990 chunk 273 optimal weight: 4.9990 chunk 263 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.046111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.035621 restraints weight = 152814.474| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 4.64 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25473 Z= 0.178 Angle : 0.741 16.231 34863 Z= 0.325 Chirality : 0.050 0.678 4338 Planarity : 0.004 0.068 4257 Dihedral : 14.331 109.490 5658 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.81 % Allowed : 8.02 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 2952 helix: 1.40 (0.20), residues: 693 sheet: -0.86 (0.20), residues: 570 loop : -0.56 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1235 TYR 0.011 0.001 TYR B 675 PHE 0.012 0.001 PHE A 347 TRP 0.014 0.001 TRP A 65 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00379 (25341) covalent geometry : angle 0.66570 (34479) SS BOND : bond 0.00189 ( 12) SS BOND : angle 0.75976 ( 24) hydrogen bonds : bond 0.04450 ( 877) hydrogen bonds : angle 5.06257 ( 2355) link_ALPHA1-2 : bond 0.01303 ( 3) link_ALPHA1-2 : angle 2.75687 ( 9) link_ALPHA1-3 : bond 0.01569 ( 6) link_ALPHA1-3 : angle 2.93959 ( 18) link_ALPHA1-6 : bond 0.00323 ( 3) link_ALPHA1-6 : angle 2.17302 ( 9) link_BETA1-4 : bond 0.00590 ( 51) link_BETA1-4 : angle 2.14425 ( 153) link_BETA1-6 : bond 0.00816 ( 9) link_BETA1-6 : angle 2.13206 ( 27) link_NAG-ASN : bond 0.00703 ( 48) link_NAG-ASN : angle 4.39436 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.8676 (pmm) cc_final: 0.8437 (pmm) REVERT: A 214 MET cc_start: 0.8265 (tpp) cc_final: 0.7602 (tmm) REVERT: A 231 THR cc_start: 0.7824 (OUTLIER) cc_final: 0.7585 (m) REVERT: A 435 VAL cc_start: 0.8427 (m) cc_final: 0.8092 (p) REVERT: A 492 LEU cc_start: 0.8869 (mm) cc_final: 0.8634 (tp) REVERT: A 952 MET cc_start: 0.8796 (mtp) cc_final: 0.8565 (mtm) REVERT: A 1107 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8390 (mt-10) REVERT: A 1209 MET cc_start: 0.8638 (mtp) cc_final: 0.8391 (mtp) REVERT: B 158 MET cc_start: 0.6276 (ppp) cc_final: 0.6005 (ppp) REVERT: B 214 MET cc_start: 0.8133 (mtp) cc_final: 0.7810 (tmm) REVERT: B 814 ASN cc_start: 0.9409 (t0) cc_final: 0.9044 (t0) REVERT: B 952 MET cc_start: 0.8952 (tpp) cc_final: 0.8538 (tpp) REVERT: B 1244 ASP cc_start: 0.9142 (t70) cc_final: 0.8585 (t0) outliers start: 21 outliers final: 15 residues processed: 60 average time/residue: 0.1394 time to fit residues: 15.7884 Evaluate side-chains 56 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 280 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN C 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.045779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.035136 restraints weight = 154663.300| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 4.68 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 25473 Z= 0.216 Angle : 0.741 15.833 34863 Z= 0.326 Chirality : 0.049 0.633 4338 Planarity : 0.004 0.066 4257 Dihedral : 12.752 107.329 5658 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.58 % Allowed : 9.79 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.16), residues: 2952 helix: 1.49 (0.20), residues: 702 sheet: -0.83 (0.21), residues: 561 loop : -0.52 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1207 TYR 0.013 0.001 TYR B 403 PHE 0.013 0.001 PHE A 347 TRP 0.010 0.001 TRP A 65 HIS 0.003 0.001 HIS B 951 Details of bonding type rmsd covalent geometry : bond 0.00468 (25341) covalent geometry : angle 0.66673 (34479) SS BOND : bond 0.00204 ( 12) SS BOND : angle 0.77569 ( 24) hydrogen bonds : bond 0.04158 ( 877) hydrogen bonds : angle 4.95310 ( 2355) link_ALPHA1-2 : bond 0.01022 ( 3) link_ALPHA1-2 : angle 2.97513 ( 9) link_ALPHA1-3 : bond 0.01511 ( 6) link_ALPHA1-3 : angle 2.98879 ( 18) link_ALPHA1-6 : bond 0.00241 ( 3) link_ALPHA1-6 : angle 2.19152 ( 9) link_BETA1-4 : bond 0.00554 ( 51) link_BETA1-4 : angle 2.09478 ( 153) link_BETA1-6 : bond 0.00795 ( 9) link_BETA1-6 : angle 2.53591 ( 27) link_NAG-ASN : bond 0.00655 ( 48) link_NAG-ASN : angle 4.31358 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 41 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8686 (pmm) cc_final: 0.8434 (pmm) REVERT: A 214 MET cc_start: 0.8279 (tpp) cc_final: 0.7707 (tmm) REVERT: A 231 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7583 (m) REVERT: A 435 VAL cc_start: 0.8449 (m) cc_final: 0.8113 (p) REVERT: A 492 LEU cc_start: 0.8898 (mm) cc_final: 0.8654 (tp) REVERT: A 952 MET cc_start: 0.8828 (mtp) cc_final: 0.8596 (mtm) REVERT: A 1107 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8410 (mt-10) REVERT: A 1209 MET cc_start: 0.8652 (mtp) cc_final: 0.8436 (mtp) REVERT: B 46 VAL cc_start: 0.7779 (OUTLIER) cc_final: 0.7559 (p) REVERT: B 158 MET cc_start: 0.6392 (ppp) cc_final: 0.5873 (ppp) REVERT: B 214 MET cc_start: 0.8170 (mtp) cc_final: 0.7804 (tmm) REVERT: B 639 THR cc_start: 0.7613 (OUTLIER) cc_final: 0.7402 (p) REVERT: B 814 ASN cc_start: 0.9367 (t0) cc_final: 0.8985 (t0) REVERT: B 952 MET cc_start: 0.8968 (tpp) cc_final: 0.8486 (tpp) REVERT: B 1244 ASP cc_start: 0.9187 (t70) cc_final: 0.8617 (t0) outliers start: 41 outliers final: 26 residues processed: 77 average time/residue: 0.1398 time to fit residues: 19.5340 Evaluate side-chains 68 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 39 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 184 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 276 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 988 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.045872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.035146 restraints weight = 155301.235| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 4.77 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 25473 Z= 0.330 Angle : 0.805 15.550 34863 Z= 0.360 Chirality : 0.050 0.631 4338 Planarity : 0.004 0.067 4257 Dihedral : 12.464 106.597 5658 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.04 % Allowed : 10.91 % Favored : 87.05 % 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: -0.32 (0.15), residues: 2952 helix: 1.42 (0.20), residues: 693 sheet: -0.93 (0.20), residues: 573 loop : -0.61 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 994 TYR 0.015 0.001 TYR A 66 PHE 0.014 0.001 PHE A 411 TRP 0.010 0.002 TRP A 168 HIS 0.006 0.001 HIS B 951 Details of bonding type rmsd covalent geometry : bond 0.00719 (25341) covalent geometry : angle 0.73634 (34479) SS BOND : bond 0.00883 ( 12) SS BOND : angle 1.19918 ( 24) hydrogen bonds : bond 0.04414 ( 877) hydrogen bonds : angle 5.06084 ( 2355) link_ALPHA1-2 : bond 0.01074 ( 3) link_ALPHA1-2 : angle 3.20325 ( 9) link_ALPHA1-3 : bond 0.01480 ( 6) link_ALPHA1-3 : angle 3.06088 ( 18) link_ALPHA1-6 : bond 0.00283 ( 3) link_ALPHA1-6 : angle 1.77295 ( 9) link_BETA1-4 : bond 0.00569 ( 51) link_BETA1-4 : angle 2.06667 ( 153) link_BETA1-6 : bond 0.00746 ( 9) link_BETA1-6 : angle 2.08958 ( 27) link_NAG-ASN : bond 0.00710 ( 48) link_NAG-ASN : angle 4.40493 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 38 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8737 (pmm) cc_final: 0.8442 (pmm) REVERT: A 214 MET cc_start: 0.8274 (tpp) cc_final: 0.7704 (tmm) REVERT: A 231 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7455 (m) REVERT: A 435 VAL cc_start: 0.8519 (m) cc_final: 0.8145 (p) REVERT: A 492 LEU cc_start: 0.8913 (mm) cc_final: 0.8646 (tp) REVERT: A 952 MET cc_start: 0.8903 (mtp) cc_final: 0.8637 (mtm) REVERT: A 1107 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8485 (mt-10) REVERT: A 1209 MET cc_start: 0.8733 (mtp) cc_final: 0.8519 (mtp) REVERT: B 46 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7592 (p) REVERT: B 158 MET cc_start: 0.6569 (ppp) cc_final: 0.6068 (ppp) REVERT: B 214 MET cc_start: 0.8237 (mtp) cc_final: 0.7907 (tmm) REVERT: B 952 MET cc_start: 0.9077 (tpp) cc_final: 0.8585 (tpp) REVERT: B 1244 ASP cc_start: 0.9169 (t70) cc_final: 0.8557 (t0) REVERT: C 427 THR cc_start: 0.9537 (OUTLIER) cc_final: 0.9246 (p) REVERT: C 1107 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8667 (tm-30) outliers start: 53 outliers final: 34 residues processed: 87 average time/residue: 0.1364 time to fit residues: 22.2772 Evaluate side-chains 75 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 38 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1181 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 57 optimal weight: 0.9990 chunk 223 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 0.0020 chunk 195 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.047140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036513 restraints weight = 150658.477| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 4.77 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25473 Z= 0.117 Angle : 0.704 15.203 34863 Z= 0.307 Chirality : 0.049 0.632 4338 Planarity : 0.003 0.063 4257 Dihedral : 11.860 106.265 5657 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.73 % Allowed : 11.33 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.16), residues: 2952 helix: 1.73 (0.20), residues: 693 sheet: -0.80 (0.21), residues: 573 loop : -0.50 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 320 TYR 0.012 0.001 TYR B 675 PHE 0.011 0.001 PHE A 347 TRP 0.013 0.001 TRP A 65 HIS 0.002 0.000 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00239 (25341) covalent geometry : angle 0.63111 (34479) SS BOND : bond 0.00436 ( 12) SS BOND : angle 0.98370 ( 24) hydrogen bonds : bond 0.03802 ( 877) hydrogen bonds : angle 4.66192 ( 2355) link_ALPHA1-2 : bond 0.01426 ( 3) link_ALPHA1-2 : angle 2.83938 ( 9) link_ALPHA1-3 : bond 0.01783 ( 6) link_ALPHA1-3 : angle 2.89049 ( 18) link_ALPHA1-6 : bond 0.00228 ( 3) link_ALPHA1-6 : angle 1.77503 ( 9) link_BETA1-4 : bond 0.00606 ( 51) link_BETA1-4 : angle 1.98125 ( 153) link_BETA1-6 : bond 0.00800 ( 9) link_BETA1-6 : angle 1.99448 ( 27) link_NAG-ASN : bond 0.00723 ( 48) link_NAG-ASN : angle 4.21151 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 43 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8673 (pmm) cc_final: 0.8419 (pmm) REVERT: A 214 MET cc_start: 0.8297 (tpp) cc_final: 0.7688 (tmm) REVERT: A 231 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7511 (m) REVERT: A 435 VAL cc_start: 0.8450 (m) cc_final: 0.8112 (p) REVERT: A 492 LEU cc_start: 0.8914 (mm) cc_final: 0.8661 (tp) REVERT: A 814 ASN cc_start: 0.9382 (t0) cc_final: 0.9067 (t0) REVERT: A 952 MET cc_start: 0.8840 (mtp) cc_final: 0.8583 (mtm) REVERT: A 1107 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8351 (mt-10) REVERT: A 1144 VAL cc_start: 0.9635 (OUTLIER) cc_final: 0.9417 (p) REVERT: A 1209 MET cc_start: 0.8732 (mtp) cc_final: 0.8516 (mtp) REVERT: B 46 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7562 (p) REVERT: B 158 MET cc_start: 0.6359 (ppp) cc_final: 0.5983 (ppp) REVERT: B 214 MET cc_start: 0.8162 (mtp) cc_final: 0.7774 (tmm) REVERT: B 814 ASN cc_start: 0.9404 (t0) cc_final: 0.8981 (t0) REVERT: B 952 MET cc_start: 0.9074 (tpp) cc_final: 0.8538 (tpp) REVERT: B 1244 ASP cc_start: 0.9111 (t70) cc_final: 0.8521 (t0) REVERT: C 158 MET cc_start: 0.8427 (pmm) cc_final: 0.8149 (pmm) REVERT: C 427 THR cc_start: 0.9493 (OUTLIER) cc_final: 0.9220 (p) REVERT: C 1107 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8598 (tm-30) outliers start: 45 outliers final: 31 residues processed: 85 average time/residue: 0.1302 time to fit residues: 20.8405 Evaluate side-chains 75 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 40 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 292 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.047005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.036366 restraints weight = 151127.230| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 4.78 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25473 Z= 0.127 Angle : 0.694 14.842 34863 Z= 0.302 Chirality : 0.048 0.581 4338 Planarity : 0.003 0.061 4257 Dihedral : 11.517 105.291 5657 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.77 % Allowed : 11.48 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.16), residues: 2952 helix: 1.82 (0.20), residues: 693 sheet: -0.69 (0.21), residues: 567 loop : -0.48 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 33 TYR 0.011 0.001 TYR B 675 PHE 0.023 0.001 PHE A 32 TRP 0.010 0.001 TRP A 65 HIS 0.002 0.000 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00268 (25341) covalent geometry : angle 0.62141 (34479) SS BOND : bond 0.00114 ( 12) SS BOND : angle 0.82692 ( 24) hydrogen bonds : bond 0.03666 ( 877) hydrogen bonds : angle 4.59305 ( 2355) link_ALPHA1-2 : bond 0.01433 ( 3) link_ALPHA1-2 : angle 3.07372 ( 9) link_ALPHA1-3 : bond 0.01699 ( 6) link_ALPHA1-3 : angle 2.92965 ( 18) link_ALPHA1-6 : bond 0.00210 ( 3) link_ALPHA1-6 : angle 1.68616 ( 9) link_BETA1-4 : bond 0.00596 ( 51) link_BETA1-4 : angle 1.96603 ( 153) link_BETA1-6 : bond 0.00790 ( 9) link_BETA1-6 : angle 2.00489 ( 27) link_NAG-ASN : bond 0.00686 ( 48) link_NAG-ASN : angle 4.15843 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 41 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8672 (pmm) cc_final: 0.8412 (pmm) REVERT: A 214 MET cc_start: 0.8287 (tpp) cc_final: 0.7694 (tmm) REVERT: A 231 THR cc_start: 0.7645 (OUTLIER) cc_final: 0.7434 (m) REVERT: A 435 VAL cc_start: 0.8445 (m) cc_final: 0.8111 (p) REVERT: A 492 LEU cc_start: 0.8919 (mm) cc_final: 0.8677 (tp) REVERT: A 814 ASN cc_start: 0.9385 (t0) cc_final: 0.9063 (t0) REVERT: A 952 MET cc_start: 0.8837 (mtp) cc_final: 0.8589 (mtm) REVERT: A 1107 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8313 (mt-10) REVERT: A 1209 MET cc_start: 0.8711 (mtp) cc_final: 0.8495 (mtp) REVERT: B 46 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7552 (p) REVERT: B 214 MET cc_start: 0.8133 (mtp) cc_final: 0.7755 (tmm) REVERT: B 814 ASN cc_start: 0.9378 (t0) cc_final: 0.8949 (t0) REVERT: B 952 MET cc_start: 0.9079 (tpp) cc_final: 0.8610 (tpp) REVERT: B 1244 ASP cc_start: 0.9110 (t70) cc_final: 0.8526 (t0) REVERT: C 158 MET cc_start: 0.8356 (pmm) cc_final: 0.8027 (ppp) REVERT: C 427 THR cc_start: 0.9459 (OUTLIER) cc_final: 0.9157 (p) REVERT: C 1107 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8552 (tm-30) outliers start: 46 outliers final: 33 residues processed: 83 average time/residue: 0.1437 time to fit residues: 21.2701 Evaluate side-chains 76 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 40 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 22 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 274 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 261 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A1126 GLN ** 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 = 0.3309 r_free = 0.3309 target = 0.046815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.036142 restraints weight = 152162.504| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 4.79 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25473 Z= 0.166 Angle : 0.700 14.594 34863 Z= 0.305 Chirality : 0.048 0.566 4338 Planarity : 0.003 0.060 4257 Dihedral : 11.280 104.803 5657 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.77 % Allowed : 11.75 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 2952 helix: 1.84 (0.20), residues: 693 sheet: -0.68 (0.21), residues: 567 loop : -0.46 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1207 TYR 0.010 0.001 TYR B 675 PHE 0.010 0.001 PHE A 347 TRP 0.008 0.001 TRP A 65 HIS 0.002 0.001 HIS B 951 Details of bonding type rmsd covalent geometry : bond 0.00359 (25341) covalent geometry : angle 0.62894 (34479) SS BOND : bond 0.00129 ( 12) SS BOND : angle 0.78724 ( 24) hydrogen bonds : bond 0.03689 ( 877) hydrogen bonds : angle 4.57036 ( 2355) link_ALPHA1-2 : bond 0.01453 ( 3) link_ALPHA1-2 : angle 3.18157 ( 9) link_ALPHA1-3 : bond 0.01653 ( 6) link_ALPHA1-3 : angle 2.94442 ( 18) link_ALPHA1-6 : bond 0.00190 ( 3) link_ALPHA1-6 : angle 1.64973 ( 9) link_BETA1-4 : bond 0.00584 ( 51) link_BETA1-4 : angle 1.95421 ( 153) link_BETA1-6 : bond 0.00757 ( 9) link_BETA1-6 : angle 2.00787 ( 27) link_NAG-ASN : bond 0.00654 ( 48) link_NAG-ASN : angle 4.13937 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 40 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8671 (pmm) cc_final: 0.8377 (pmm) REVERT: A 214 MET cc_start: 0.8343 (tpp) cc_final: 0.7723 (tmm) REVERT: A 231 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7460 (m) REVERT: A 435 VAL cc_start: 0.8457 (m) cc_final: 0.8117 (p) REVERT: A 492 LEU cc_start: 0.8946 (mm) cc_final: 0.8700 (tp) REVERT: A 814 ASN cc_start: 0.9382 (t0) cc_final: 0.9048 (t0) REVERT: A 1107 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8302 (mt-10) REVERT: B 46 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7555 (p) REVERT: B 158 MET cc_start: 0.6371 (ppp) cc_final: 0.6012 (ppp) REVERT: B 214 MET cc_start: 0.8137 (mtp) cc_final: 0.7737 (tmm) REVERT: B 343 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9074 (p) REVERT: B 814 ASN cc_start: 0.9379 (t0) cc_final: 0.8945 (t0) REVERT: B 952 MET cc_start: 0.9085 (tpp) cc_final: 0.8618 (tpp) REVERT: B 1244 ASP cc_start: 0.9115 (t70) cc_final: 0.8528 (t0) REVERT: C 158 MET cc_start: 0.8342 (pmm) cc_final: 0.8134 (pmm) REVERT: C 427 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.9118 (p) REVERT: C 1107 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8549 (tm-30) outliers start: 46 outliers final: 35 residues processed: 83 average time/residue: 0.1386 time to fit residues: 21.0031 Evaluate side-chains 79 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 40 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 229 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 276 optimal weight: 10.0000 chunk 208 optimal weight: 0.0050 chunk 7 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 280 optimal weight: 0.9990 chunk 190 optimal weight: 0.7980 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 979 GLN A 996 GLN ** A1126 GLN ** 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 = 0.3312 r_free = 0.3312 target = 0.046879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.036256 restraints weight = 152029.811| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 4.75 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25473 Z= 0.156 Angle : 0.695 14.296 34863 Z= 0.302 Chirality : 0.048 0.560 4338 Planarity : 0.003 0.059 4257 Dihedral : 10.986 104.598 5657 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.73 % Allowed : 11.83 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 2952 helix: 1.90 (0.20), residues: 693 sheet: -0.66 (0.21), residues: 567 loop : -0.44 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1207 TYR 0.011 0.001 TYR B 675 PHE 0.019 0.001 PHE A 788 TRP 0.009 0.001 TRP A 65 HIS 0.002 0.000 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00336 (25341) covalent geometry : angle 0.62428 (34479) SS BOND : bond 0.00137 ( 12) SS BOND : angle 0.74440 ( 24) hydrogen bonds : bond 0.03642 ( 877) hydrogen bonds : angle 4.51372 ( 2355) link_ALPHA1-2 : bond 0.01561 ( 3) link_ALPHA1-2 : angle 3.14161 ( 9) link_ALPHA1-3 : bond 0.01678 ( 6) link_ALPHA1-3 : angle 2.89880 ( 18) link_ALPHA1-6 : bond 0.00222 ( 3) link_ALPHA1-6 : angle 1.62396 ( 9) link_BETA1-4 : bond 0.00584 ( 51) link_BETA1-4 : angle 1.94139 ( 153) link_BETA1-6 : bond 0.00745 ( 9) link_BETA1-6 : angle 2.00719 ( 27) link_NAG-ASN : bond 0.00658 ( 48) link_NAG-ASN : angle 4.10085 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 42 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8668 (pmm) cc_final: 0.8376 (pmm) REVERT: A 214 MET cc_start: 0.8342 (tpp) cc_final: 0.7741 (tmm) REVERT: A 231 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7455 (m) REVERT: A 435 VAL cc_start: 0.8454 (m) cc_final: 0.8115 (p) REVERT: A 492 LEU cc_start: 0.8958 (mm) cc_final: 0.8711 (tp) REVERT: A 814 ASN cc_start: 0.9381 (t0) cc_final: 0.9038 (t0) REVERT: A 1107 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8293 (mt-10) REVERT: B 46 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7544 (p) REVERT: B 158 MET cc_start: 0.6339 (ppp) cc_final: 0.5897 (ppp) REVERT: B 214 MET cc_start: 0.8139 (mtp) cc_final: 0.7748 (tmm) REVERT: B 343 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9077 (p) REVERT: B 814 ASN cc_start: 0.9382 (t0) cc_final: 0.8934 (t0) REVERT: B 952 MET cc_start: 0.9101 (tpp) cc_final: 0.8629 (tpp) REVERT: B 1244 ASP cc_start: 0.9112 (t70) cc_final: 0.8521 (t0) REVERT: C 427 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9115 (p) REVERT: C 1107 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8511 (tm-30) outliers start: 45 outliers final: 37 residues processed: 85 average time/residue: 0.1398 time to fit residues: 21.7388 Evaluate side-chains 81 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 40 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 997 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 882 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 90 optimal weight: 1.9990 chunk 294 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 252 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 283 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.046986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.036354 restraints weight = 151765.279| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 4.78 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25473 Z= 0.136 Angle : 0.690 14.093 34863 Z= 0.299 Chirality : 0.048 0.553 4338 Planarity : 0.003 0.059 4257 Dihedral : 10.796 104.672 5657 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.81 % Allowed : 12.02 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.16), residues: 2952 helix: 2.17 (0.20), residues: 669 sheet: -0.63 (0.21), residues: 567 loop : -0.39 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 994 TYR 0.011 0.001 TYR B 675 PHE 0.010 0.001 PHE A 788 TRP 0.009 0.001 TRP A 65 HIS 0.002 0.000 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00291 (25341) covalent geometry : angle 0.62044 (34479) SS BOND : bond 0.00113 ( 12) SS BOND : angle 0.71593 ( 24) hydrogen bonds : bond 0.03564 ( 877) hydrogen bonds : angle 4.47930 ( 2355) link_ALPHA1-2 : bond 0.01680 ( 3) link_ALPHA1-2 : angle 2.96872 ( 9) link_ALPHA1-3 : bond 0.01712 ( 6) link_ALPHA1-3 : angle 2.89021 ( 18) link_ALPHA1-6 : bond 0.00265 ( 3) link_ALPHA1-6 : angle 1.59646 ( 9) link_BETA1-4 : bond 0.00587 ( 51) link_BETA1-4 : angle 1.93319 ( 153) link_BETA1-6 : bond 0.00752 ( 9) link_BETA1-6 : angle 2.00779 ( 27) link_NAG-ASN : bond 0.00670 ( 48) link_NAG-ASN : angle 4.07840 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 41 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8671 (pmm) cc_final: 0.8384 (pmm) REVERT: A 214 MET cc_start: 0.8339 (tpp) cc_final: 0.7733 (tmm) REVERT: A 231 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7444 (m) REVERT: A 435 VAL cc_start: 0.8450 (m) cc_final: 0.8153 (p) REVERT: A 492 LEU cc_start: 0.8949 (mm) cc_final: 0.8712 (tp) REVERT: A 814 ASN cc_start: 0.9377 (t0) cc_final: 0.9030 (t0) REVERT: B 158 MET cc_start: 0.6462 (ppp) cc_final: 0.5988 (ppp) REVERT: B 214 MET cc_start: 0.8128 (mtp) cc_final: 0.7731 (tmm) REVERT: B 343 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9078 (p) REVERT: B 814 ASN cc_start: 0.9373 (t0) cc_final: 0.8921 (t0) REVERT: B 952 MET cc_start: 0.9101 (tpp) cc_final: 0.8621 (tpp) REVERT: B 1244 ASP cc_start: 0.9113 (t70) cc_final: 0.8523 (t0) REVERT: C 427 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.9124 (p) REVERT: C 875 THR cc_start: 0.9638 (OUTLIER) cc_final: 0.9368 (p) outliers start: 47 outliers final: 34 residues processed: 84 average time/residue: 0.1416 time to fit residues: 21.2559 Evaluate side-chains 79 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 41 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 172 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 875 THR Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 123 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 295 optimal weight: 5.9990 chunk 188 optimal weight: 0.6980 chunk 194 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 290 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** A1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN C 996 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.047302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.036681 restraints weight = 150541.102| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.79 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25473 Z= 0.113 Angle : 0.684 13.703 34863 Z= 0.298 Chirality : 0.048 0.537 4338 Planarity : 0.003 0.059 4257 Dihedral : 10.470 104.408 5657 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.54 % Allowed : 12.29 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.16), residues: 2952 helix: 1.97 (0.20), residues: 693 sheet: -0.57 (0.21), residues: 588 loop : -0.43 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 994 TYR 0.012 0.001 TYR B 675 PHE 0.010 0.001 PHE A 788 TRP 0.010 0.001 TRP A 65 HIS 0.002 0.000 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00236 (25341) covalent geometry : angle 0.61591 (34479) SS BOND : bond 0.00095 ( 12) SS BOND : angle 0.66673 ( 24) hydrogen bonds : bond 0.03448 ( 877) hydrogen bonds : angle 4.36665 ( 2355) link_ALPHA1-2 : bond 0.01781 ( 3) link_ALPHA1-2 : angle 2.70833 ( 9) link_ALPHA1-3 : bond 0.01768 ( 6) link_ALPHA1-3 : angle 2.85985 ( 18) link_ALPHA1-6 : bond 0.00379 ( 3) link_ALPHA1-6 : angle 1.58148 ( 9) link_BETA1-4 : bond 0.00604 ( 51) link_BETA1-4 : angle 1.92258 ( 153) link_BETA1-6 : bond 0.00713 ( 9) link_BETA1-6 : angle 1.98594 ( 27) link_NAG-ASN : bond 0.00707 ( 48) link_NAG-ASN : angle 4.01472 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4168.09 seconds wall clock time: 73 minutes 13.90 seconds (4393.90 seconds total)