Starting phenix.real_space_refine on Wed Sep 17 13:07:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rzl_19608/09_2025/8rzl_19608.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rzl_19608/09_2025/8rzl_19608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rzl_19608/09_2025/8rzl_19608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rzl_19608/09_2025/8rzl_19608.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rzl_19608/09_2025/8rzl_19608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rzl_19608/09_2025/8rzl_19608.map" } resolution = 2.65 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= 0.006 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 45 5.16 5 C 5545 2.51 5 N 1145 2.21 5 O 2160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8895 Number of models: 1 Model: "" Number of chains: 35 Chain: "C" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1393 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 164} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "U" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "b" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.08, per 1000 atoms: 0.23 Number of scatterers: 8895 At special positions: 0 Unit cell: (82.071, 78.755, 214.711, 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 45 16.00 O 2160 8.00 N 1145 7.00 C 5545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=3, symmetry=0 Links applied ?1-3 " NAG F 2 " - " YZT F 3 " " NAG G 2 " - " YZT G 3 " " NAG H 2 " - " YZT H 3 " " NAG I 2 " - " YZT I 3 " " NAG J 2 " - " YZT J 3 " " NAG K 2 " - " YZT K 3 " " NAG L 2 " - " YZT L 3 " " NAG M 2 " - " YZT M 3 " " NAG N 2 " - " YZT N 3 " " NAG O 2 " - " YZT O 3 " " NAG P 2 " - " YZT P 3 " " NAG Q 2 " - " YZT Q 3 " " NAG R 2 " - " YZT R 3 " " NAG S 2 " - " YZT S 3 " " NAG T 2 " - " YZT T 3 " " NAG U 2 " - " YZT U 3 " " NAG V 2 " - " YZT V 3 " " NAG W 2 " - " YZT W 3 " " NAG X 2 " - " YZT X 3 " " NAG Y 2 " - " YZT Y 3 " " NAG Z 2 " - " YZT Z 3 " " NAG a 2 " - " YZT a 3 " " NAG b 2 " - " YZT b 3 " " NAG c 2 " - " YZT c 3 " " NAG d 2 " - " YZT d 3 " ALPHA1-4 " NAG F 2 " - " MAN F 5 " " NAG G 2 " - " MAN G 5 " " NAG H 2 " - " MAN H 5 " " NAG I 2 " - " MAN I 5 " " NAG J 2 " - " MAN J 5 " " NAG K 2 " - " MAN K 5 " " NAG L 2 " - " MAN L 5 " " NAG M 2 " - " MAN M 5 " " NAG N 2 " - " MAN N 5 " " NAG O 2 " - " MAN O 5 " " NAG P 2 " - " MAN P 5 " " NAG Q 2 " - " MAN Q 5 " " NAG R 2 " - " MAN R 5 " " NAG S 2 " - " MAN S 5 " " NAG T 2 " - " MAN T 5 " " NAG U 2 " - " MAN U 5 " " NAG V 2 " - " MAN V 5 " " NAG W 2 " - " MAN W 5 " " NAG X 2 " - " MAN X 5 " " NAG Y 2 " - " MAN Y 5 " " NAG Z 2 " - " MAN Z 5 " " NAG a 2 " - " MAN a 5 " " NAG b 2 " - " MAN b 5 " " NAG c 2 " - " MAN c 5 " " NAG d 2 " - " MAN d 5 " ALPHA1-6 " NAG F 2 " - " MAN F 6 " " NAG G 2 " - " MAN G 6 " " NAG H 2 " - " MAN H 6 " " NAG I 2 " - " MAN I 6 " " NAG J 2 " - " MAN J 6 " " NAG K 2 " - " MAN K 6 " " NAG L 2 " - " MAN L 6 " " NAG M 2 " - " MAN M 6 " " NAG N 2 " - " MAN N 6 " " NAG O 2 " - " MAN O 6 " " NAG P 2 " - " MAN P 6 " " NAG Q 2 " - " MAN Q 6 " " NAG R 2 " - " MAN R 6 " " NAG S 2 " - " MAN S 6 " " NAG T 2 " - " MAN T 6 " " NAG U 2 " - " MAN U 6 " " NAG V 2 " - " MAN V 6 " " NAG W 2 " - " MAN W 6 " " NAG X 2 " - " MAN X 6 " " NAG Y 2 " - " MAN Y 6 " " NAG Z 2 " - " MAN Z 6 " " NAG a 2 " - " MAN a 6 " " NAG b 2 " - " MAN b 6 " " NAG c 2 " - " MAN c 6 " " NAG d 2 " - " MAN d 6 " BETA1-4 " NAG F 1 " - " NAG F 2 " " YZT F 3 " - " BGC F 4 " " NAG G 1 " - " NAG G 2 " " YZT G 3 " - " BGC G 4 " " NAG H 1 " - " NAG H 2 " " YZT H 3 " - " BGC H 4 " " NAG I 1 " - " NAG I 2 " " YZT I 3 " - " BGC I 4 " " NAG J 1 " - " NAG J 2 " " YZT J 3 " - " BGC J 4 " " NAG K 1 " - " NAG K 2 " " YZT K 3 " - " BGC K 4 " " NAG L 1 " - " NAG L 2 " " YZT L 3 " - " BGC L 4 " " NAG M 1 " - " NAG M 2 " " YZT M 3 " - " BGC M 4 " " NAG N 1 " - " NAG N 2 " " YZT N 3 " - " BGC N 4 " " NAG O 1 " - " NAG O 2 " " YZT O 3 " - " BGC O 4 " " NAG P 1 " - " NAG P 2 " " YZT P 3 " - " BGC P 4 " " NAG Q 1 " - " NAG Q 2 " " YZT Q 3 " - " BGC Q 4 " " NAG R 1 " - " NAG R 2 " " YZT R 3 " - " BGC R 4 " " NAG S 1 " - " NAG S 2 " " YZT S 3 " - " BGC S 4 " " NAG T 1 " - " NAG T 2 " " YZT T 3 " - " BGC T 4 " " NAG U 1 " - " NAG U 2 " " YZT U 3 " - " BGC U 4 " " NAG V 1 " - " NAG V 2 " " YZT V 3 " - " BGC V 4 " " NAG W 1 " - " NAG W 2 " " YZT W 3 " - " BGC W 4 " " NAG X 1 " - " NAG X 2 " " YZT X 3 " - " BGC X 4 " " NAG Y 1 " - " NAG Y 2 " " YZT Y 3 " - " BGC Y 4 " " NAG Z 1 " - " NAG Z 2 " " YZT Z 3 " - " BGC Z 4 " " NAG a 1 " - " NAG a 2 " " YZT a 3 " - " BGC a 4 " " NAG b 1 " - " NAG b 2 " " YZT b 3 " - " BGC b 4 " " NAG c 1 " - " NAG c 2 " " YZT c 3 " - " BGC c 4 " " NAG d 1 " - " NAG d 2 " " YZT d 3 " - " BGC d 4 " MAN-THR " MAN A 311 " - " THR A 195 " " MAN B 311 " - " THR B 195 " " MAN C 311 " - " THR C 195 " " MAN D 311 " - " THR D 195 " " MAN E 311 " - " THR E 195 " NAG-ASN " NAG F 1 " - " ASN C 56 " " NAG G 1 " - " ASN C 80 " " NAG H 1 " - " ASN C 83 " " NAG I 1 " - " ASN C 146 " " NAG J 1 " - " ASN C 121 " " NAG K 1 " - " ASN E 56 " " NAG L 1 " - " ASN E 80 " " NAG M 1 " - " ASN E 83 " " NAG N 1 " - " ASN E 146 " " NAG O 1 " - " ASN E 121 " " NAG P 1 " - " ASN A 56 " " NAG Q 1 " - " ASN A 80 " " NAG R 1 " - " ASN A 83 " " NAG S 1 " - " ASN A 146 " " NAG T 1 " - " ASN A 121 " " NAG U 1 " - " ASN B 56 " " NAG V 1 " - " ASN B 80 " " NAG W 1 " - " ASN B 83 " " NAG X 1 " - " ASN B 146 " " NAG Y 1 " - " ASN B 121 " " NAG Z 1 " - " ASN D 56 " " NAG a 1 " - " ASN D 80 " " NAG b 1 " - " ASN D 83 " " NAG c 1 " - " ASN D 146 " " NAG d 1 " - " ASN D 121 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 268.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1690 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 11 sheets defined 4.5% alpha, 54.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'E' and resid 47 through 51 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 145 removed outlier: 6.428A pdb=" N ALA A 122 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A 141 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLN A 120 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY A 159 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU A 95 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TYR A 161 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET A 93 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL A 163 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 91 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN C 37 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASP B 181 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY B 190 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU B 105 " --> pdb=" O GLY B 190 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N SER B 192 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE B 103 " --> pdb=" O SER B 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 45 Processing sheet with id=AA4, first strand: chain 'C' and resid 144 through 145 removed outlier: 6.428A pdb=" N ALA C 122 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL C 141 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN C 120 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY C 159 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU C 95 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N TYR C 161 " --> pdb=" O MET C 93 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET C 93 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL C 163 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN C 91 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASN E 37 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASP D 181 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY D 190 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU D 105 " --> pdb=" O GLY D 190 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N SER D 192 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE D 103 " --> pdb=" O SER D 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.589A pdb=" N PHE C 75 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N THR D 34 " --> pdb=" O PHE C 75 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA C 77 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLY D 36 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL C 79 " --> pdb=" O GLY D 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 154 through 156 removed outlier: 5.638A pdb=" N ILE C 103 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N SER C 192 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU C 105 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY C 190 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ASP C 181 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ASN D 37 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 91 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL B 163 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET B 93 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TYR B 161 " --> pdb=" O MET B 93 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU B 95 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY B 159 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN B 120 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 141 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA B 122 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 42 through 45 removed outlier: 3.514A pdb=" N ASN E 91 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL E 163 " --> pdb=" O ASN E 91 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N MET E 93 " --> pdb=" O TYR E 161 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TYR E 161 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU E 95 " --> pdb=" O GLY E 159 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY E 159 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN E 120 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL E 141 " --> pdb=" O GLN E 120 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA E 122 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 59 through 60 Processing sheet with id=AA9, first strand: chain 'E' and resid 154 through 156 removed outlier: 5.637A pdb=" N ILE E 103 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER E 192 " --> pdb=" O ILE E 103 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU E 105 " --> pdb=" O GLY E 190 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY E 190 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.529A pdb=" N PHE A 75 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N THR B 34 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA A 77 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N GLY B 36 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL A 79 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASN B 37 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASP A 181 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY A 190 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU A 105 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER A 192 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE A 103 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 42 through 45 removed outlier: 3.512A pdb=" N ASN D 91 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL D 163 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET D 93 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N TYR D 161 " --> pdb=" O MET D 93 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU D 95 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY D 159 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN D 120 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL D 141 " --> pdb=" O GLN D 120 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA D 122 " --> pdb=" O LEU D 139 " (cutoff:3.500A) 284 hydrogen bonds defined for protein. 732 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: 1.32 Time building geometry restraints manager: 2.02 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: 1416 1.34 - 1.46: 3025 1.46 - 1.58: 4589 1.58 - 1.70: 0 1.70 - 1.81: 65 Bond restraints: 9095 Sorted by residual: bond pdb=" CA SER A 58 " pdb=" CB SER A 58 " ideal model delta sigma weight residual 1.529 1.449 0.080 1.74e-02 3.30e+03 2.10e+01 bond pdb=" CA SER D 58 " pdb=" CB SER D 58 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.74e-02 3.30e+03 2.08e+01 bond pdb=" CA SER B 58 " pdb=" CB SER B 58 " ideal model delta sigma weight residual 1.529 1.451 0.079 1.74e-02 3.30e+03 2.04e+01 bond pdb=" CA SER E 58 " pdb=" CB SER E 58 " ideal model delta sigma weight residual 1.529 1.451 0.078 1.74e-02 3.30e+03 2.02e+01 bond pdb=" CA SER C 58 " pdb=" CB SER C 58 " ideal model delta sigma weight residual 1.529 1.451 0.078 1.74e-02 3.30e+03 2.01e+01 ... (remaining 9090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 10941 2.32 - 4.64: 1449 4.64 - 6.96: 115 6.96 - 9.27: 5 9.27 - 11.59: 20 Bond angle restraints: 12530 Sorted by residual: angle pdb=" C ASN A 57 " pdb=" N SER A 58 " pdb=" CA SER A 58 " ideal model delta sigma weight residual 120.72 109.13 11.59 1.67e+00 3.59e-01 4.82e+01 angle pdb=" C ASN D 57 " pdb=" N SER D 58 " pdb=" CA SER D 58 " ideal model delta sigma weight residual 120.72 109.14 11.58 1.67e+00 3.59e-01 4.81e+01 angle pdb=" C ASN E 57 " pdb=" N SER E 58 " pdb=" CA SER E 58 " ideal model delta sigma weight residual 120.72 109.14 11.58 1.67e+00 3.59e-01 4.81e+01 angle pdb=" C ASN C 57 " pdb=" N SER C 58 " pdb=" CA SER C 58 " ideal model delta sigma weight residual 120.72 109.19 11.53 1.67e+00 3.59e-01 4.77e+01 angle pdb=" C ASN B 57 " pdb=" N SER B 58 " pdb=" CA SER B 58 " ideal model delta sigma weight residual 120.72 109.19 11.53 1.67e+00 3.59e-01 4.77e+01 ... (remaining 12525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.52: 7034 23.52 - 47.05: 221 47.05 - 70.57: 45 70.57 - 94.09: 25 94.09 - 117.61: 45 Dihedral angle restraints: 7370 sinusoidal: 4685 harmonic: 2685 Sorted by residual: dihedral pdb=" CA VAL A 60 " pdb=" C VAL A 60 " pdb=" N PRO A 61 " pdb=" CA PRO A 61 " ideal model delta harmonic sigma weight residual 180.00 -152.84 -27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA VAL D 60 " pdb=" C VAL D 60 " pdb=" N PRO D 61 " pdb=" CA PRO D 61 " ideal model delta harmonic sigma weight residual -180.00 -153.36 -26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA VAL E 60 " pdb=" C VAL E 60 " pdb=" N PRO E 61 " pdb=" CA PRO E 61 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 7367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1302 0.095 - 0.191: 473 0.191 - 0.286: 65 0.286 - 0.381: 16 0.381 - 0.477: 14 Chirality restraints: 1870 Sorted by residual: chirality pdb=" C1 MAN R 6 " pdb=" O6 NAG R 2 " pdb=" C2 MAN R 6 " pdb=" O5 MAN R 6 " both_signs ideal model delta sigma weight residual False 2.40 2.00 0.40 2.00e-02 2.50e+03 3.96e+02 chirality pdb=" C1 MAN b 6 " pdb=" O6 NAG b 2 " pdb=" C2 MAN b 6 " pdb=" O5 MAN b 6 " both_signs ideal model delta sigma weight residual False 2.40 2.01 0.39 2.00e-02 2.50e+03 3.87e+02 chirality pdb=" C1 MAN H 6 " pdb=" O6 NAG H 2 " pdb=" C2 MAN H 6 " pdb=" O5 MAN H 6 " both_signs ideal model delta sigma weight residual False 2.40 2.01 0.39 2.00e-02 2.50e+03 3.84e+02 ... (remaining 1867 not shown) Planarity restraints: 1355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.107 2.00e-02 2.50e+03 8.79e-02 9.65e+01 pdb=" C7 NAG R 1 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.082 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.138 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 1 " -0.099 2.00e-02 2.50e+03 8.13e-02 8.26e+01 pdb=" C7 NAG b 1 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG b 1 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NAG b 1 " 0.128 2.00e-02 2.50e+03 pdb=" O7 NAG b 1 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " -0.099 2.00e-02 2.50e+03 8.10e-02 8.20e+01 pdb=" C7 NAG W 1 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " 0.128 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.018 2.00e-02 2.50e+03 ... (remaining 1352 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 2880 2.86 - 3.37: 7553 3.37 - 3.88: 15070 3.88 - 4.39: 16990 4.39 - 4.90: 28287 Nonbonded interactions: 70780 Sorted by model distance: nonbonded pdb=" N ASN B 57 " pdb=" N SER B 58 " model vdw 2.347 2.560 nonbonded pdb=" N ASN C 57 " pdb=" N SER C 58 " model vdw 2.348 2.560 nonbonded pdb=" N ASN E 57 " pdb=" N SER E 58 " model vdw 2.348 2.560 nonbonded pdb=" N ASN D 57 " pdb=" N SER D 58 " model vdw 2.348 2.560 nonbonded pdb=" N ASN A 57 " pdb=" N SER A 58 " model vdw 2.349 2.560 ... (remaining 70775 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 1.110 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.190 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 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 : 0.012 0.098 9253 Z= 0.710 Angle : 1.709 11.592 12990 Z= 0.862 Chirality : 0.102 0.477 1870 Planarity : 0.009 0.088 1330 Dihedral : 15.365 117.611 5680 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.21 % Allowed : 4.49 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.27), residues: 905 helix: None (None), residues: 0 sheet: 1.22 (0.25), residues: 380 loop : 0.28 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.052 0.009 TYR A 89 PHE 0.012 0.003 PHE A 191 Details of bonding type rmsd covalent geometry : bond 0.01210 ( 9095) covalent geometry : angle 1.57136 (12530) hydrogen bonds : bond 0.16061 ( 272) hydrogen bonds : angle 8.70755 ( 732) glycosidic custom : bond 0.01727 ( 25) glycosidic custom : angle 4.90689 ( 75) Misc. bond : bond 0.09630 ( 3) link_ALPHA1-4 : bond 0.00524 ( 25) link_ALPHA1-4 : angle 2.27560 ( 75) link_ALPHA1-6 : bond 0.01267 ( 25) link_ALPHA1-6 : angle 2.92815 ( 75) link_BETA1-4 : bond 0.02035 ( 50) link_BETA1-4 : angle 4.38926 ( 150) link_MAN-THR : bond 0.01122 ( 5) link_MAN-THR : angle 2.31562 ( 10) link_NAG-ASN : bond 0.01056 ( 25) link_NAG-ASN : angle 4.05326 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 87 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8449 (m-40) outliers start: 25 outliers final: 11 residues processed: 87 average time/residue: 0.5956 time to fit residues: 55.3412 Evaluate side-chains 52 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 195 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.0070 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 0.0040 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 GLN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN D 78 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.074669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.047453 restraints weight = 23019.463| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 4.12 r_work: 0.2583 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9253 Z= 0.142 Angle : 0.842 8.210 12990 Z= 0.358 Chirality : 0.047 0.215 1870 Planarity : 0.005 0.032 1330 Dihedral : 12.057 111.131 4134 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.67 % Allowed : 9.74 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.28), residues: 905 helix: None (None), residues: 0 sheet: 0.94 (0.26), residues: 375 loop : 1.13 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR B 89 PHE 0.011 0.001 PHE B 189 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9095) covalent geometry : angle 0.75468 (12530) hydrogen bonds : bond 0.03950 ( 272) hydrogen bonds : angle 6.82323 ( 732) glycosidic custom : bond 0.00297 ( 25) glycosidic custom : angle 2.20318 ( 75) Misc. bond : bond 0.00302 ( 3) link_ALPHA1-4 : bond 0.00837 ( 25) link_ALPHA1-4 : angle 2.39340 ( 75) link_ALPHA1-6 : bond 0.00689 ( 25) link_ALPHA1-6 : angle 1.51740 ( 75) link_BETA1-4 : bond 0.00300 ( 50) link_BETA1-4 : angle 1.84555 ( 150) link_MAN-THR : bond 0.00055 ( 5) link_MAN-THR : angle 0.95204 ( 10) link_NAG-ASN : bond 0.00394 ( 25) link_NAG-ASN : angle 2.82266 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.316 Fit side-chains REVERT: E 99 LYS cc_start: 0.8604 (ptmm) cc_final: 0.8378 (ptmm) outliers start: 13 outliers final: 6 residues processed: 53 average time/residue: 0.6094 time to fit residues: 34.6203 Evaluate side-chains 47 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 36 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.071958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.044861 restraints weight = 23167.038| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 4.04 r_work: 0.2511 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9253 Z= 0.249 Angle : 0.788 6.083 12990 Z= 0.337 Chirality : 0.044 0.179 1870 Planarity : 0.005 0.036 1330 Dihedral : 9.809 113.902 4125 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.67 % Allowed : 11.92 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.27), residues: 905 helix: None (None), residues: 0 sheet: 0.68 (0.26), residues: 340 loop : 1.16 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR B 89 PHE 0.009 0.001 PHE E 189 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 9095) covalent geometry : angle 0.70998 (12530) hydrogen bonds : bond 0.03850 ( 272) hydrogen bonds : angle 6.10723 ( 732) glycosidic custom : bond 0.00233 ( 25) glycosidic custom : angle 1.84882 ( 75) Misc. bond : bond 0.00155 ( 3) link_ALPHA1-4 : bond 0.00628 ( 25) link_ALPHA1-4 : angle 2.14785 ( 75) link_ALPHA1-6 : bond 0.00355 ( 25) link_ALPHA1-6 : angle 1.66087 ( 75) link_BETA1-4 : bond 0.00219 ( 50) link_BETA1-4 : angle 1.77302 ( 150) link_MAN-THR : bond 0.00013 ( 5) link_MAN-THR : angle 0.29255 ( 10) link_NAG-ASN : bond 0.00502 ( 25) link_NAG-ASN : angle 2.52230 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: C 93 MET cc_start: 0.9088 (tpp) cc_final: 0.8881 (tpt) REVERT: E 181 ASP cc_start: 0.9045 (t0) cc_final: 0.8779 (t0) REVERT: A 99 LYS cc_start: 0.7576 (ptpt) cc_final: 0.7210 (ptmm) outliers start: 13 outliers final: 7 residues processed: 55 average time/residue: 0.6500 time to fit residues: 38.1649 Evaluate side-chains 49 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 37 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** 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 = 0.3416 r_free = 0.3416 target = 0.073273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.046606 restraints weight = 23380.360| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 4.02 r_work: 0.2563 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9253 Z= 0.126 Angle : 0.691 5.083 12990 Z= 0.294 Chirality : 0.044 0.222 1870 Planarity : 0.004 0.034 1330 Dihedral : 9.253 107.195 4125 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.67 % Allowed : 11.67 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.28), residues: 905 helix: None (None), residues: 0 sheet: 0.48 (0.26), residues: 340 loop : 1.49 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR C 89 PHE 0.009 0.001 PHE A 189 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9095) covalent geometry : angle 0.61775 (12530) hydrogen bonds : bond 0.03010 ( 272) hydrogen bonds : angle 5.88503 ( 732) glycosidic custom : bond 0.00196 ( 25) glycosidic custom : angle 1.61950 ( 75) Misc. bond : bond 0.00051 ( 3) link_ALPHA1-4 : bond 0.00773 ( 25) link_ALPHA1-4 : angle 2.06808 ( 75) link_ALPHA1-6 : bond 0.00505 ( 25) link_ALPHA1-6 : angle 1.46435 ( 75) link_BETA1-4 : bond 0.00197 ( 50) link_BETA1-4 : angle 1.53396 ( 150) link_MAN-THR : bond 0.00072 ( 5) link_MAN-THR : angle 0.14116 ( 10) link_NAG-ASN : bond 0.00203 ( 25) link_NAG-ASN : angle 2.25953 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.302 Fit side-chains REVERT: C 37 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8269 (p0) REVERT: E 181 ASP cc_start: 0.9083 (t0) cc_final: 0.8840 (t0) REVERT: A 99 LYS cc_start: 0.7645 (ptpt) cc_final: 0.7336 (ptmm) REVERT: B 32 GLN cc_start: 0.8838 (tt0) cc_final: 0.8512 (tp40) outliers start: 13 outliers final: 9 residues processed: 56 average time/residue: 0.5742 time to fit residues: 34.4741 Evaluate side-chains 52 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 19 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 1 optimal weight: 0.4980 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 chunk 49 optimal weight: 8.9990 chunk 61 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** D 87 ASN ** 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 = 0.3419 r_free = 0.3419 target = 0.073488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.046624 restraints weight = 23094.005| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 4.03 r_work: 0.2583 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9253 Z= 0.108 Angle : 0.677 5.790 12990 Z= 0.288 Chirality : 0.044 0.210 1870 Planarity : 0.004 0.031 1330 Dihedral : 9.053 106.689 4125 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.79 % Allowed : 11.54 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.28), residues: 905 helix: None (None), residues: 0 sheet: 0.03 (0.25), residues: 370 loop : 1.82 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR B 89 PHE 0.008 0.001 PHE E 189 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9095) covalent geometry : angle 0.60832 (12530) hydrogen bonds : bond 0.02850 ( 272) hydrogen bonds : angle 5.70294 ( 732) glycosidic custom : bond 0.00142 ( 25) glycosidic custom : angle 1.58963 ( 75) Misc. bond : bond 0.00069 ( 3) link_ALPHA1-4 : bond 0.00744 ( 25) link_ALPHA1-4 : angle 2.05128 ( 75) link_ALPHA1-6 : bond 0.00500 ( 25) link_ALPHA1-6 : angle 1.46996 ( 75) link_BETA1-4 : bond 0.00199 ( 50) link_BETA1-4 : angle 1.45749 ( 150) link_MAN-THR : bond 0.00027 ( 5) link_MAN-THR : angle 0.08345 ( 10) link_NAG-ASN : bond 0.00176 ( 25) link_NAG-ASN : angle 2.11450 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: E 181 ASP cc_start: 0.9103 (t0) cc_final: 0.8831 (t0) REVERT: A 99 LYS cc_start: 0.7662 (ptpt) cc_final: 0.7309 (ptmm) REVERT: B 32 GLN cc_start: 0.8858 (tt0) cc_final: 0.8540 (tp40) outliers start: 14 outliers final: 10 residues processed: 57 average time/residue: 0.5742 time to fit residues: 35.2179 Evaluate side-chains 52 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 69 optimal weight: 0.0170 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** 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 = 0.3425 r_free = 0.3425 target = 0.073624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.046898 restraints weight = 23113.299| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 4.02 r_work: 0.2585 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9253 Z= 0.117 Angle : 0.665 5.651 12990 Z= 0.281 Chirality : 0.043 0.209 1870 Planarity : 0.004 0.030 1330 Dihedral : 8.864 106.673 4125 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.79 % Allowed : 11.41 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.29), residues: 905 helix: None (None), residues: 0 sheet: -0.01 (0.25), residues: 370 loop : 1.86 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR B 89 PHE 0.008 0.001 PHE A 189 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9095) covalent geometry : angle 0.59789 (12530) hydrogen bonds : bond 0.02812 ( 272) hydrogen bonds : angle 5.48321 ( 732) glycosidic custom : bond 0.00112 ( 25) glycosidic custom : angle 1.58620 ( 75) Misc. bond : bond 0.00056 ( 3) link_ALPHA1-4 : bond 0.00710 ( 25) link_ALPHA1-4 : angle 2.02606 ( 75) link_ALPHA1-6 : bond 0.00485 ( 25) link_ALPHA1-6 : angle 1.47124 ( 75) link_BETA1-4 : bond 0.00181 ( 50) link_BETA1-4 : angle 1.42215 ( 150) link_MAN-THR : bond 0.00014 ( 5) link_MAN-THR : angle 0.12494 ( 10) link_NAG-ASN : bond 0.00147 ( 25) link_NAG-ASN : angle 2.01169 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: C 67 GLN cc_start: 0.9108 (mt0) cc_final: 0.8885 (mm-40) REVERT: E 181 ASP cc_start: 0.9114 (t0) cc_final: 0.8812 (t0) REVERT: A 99 LYS cc_start: 0.7710 (ptpt) cc_final: 0.7375 (ptmm) REVERT: B 32 GLN cc_start: 0.8846 (tt0) cc_final: 0.8525 (mm-40) REVERT: D 99 LYS cc_start: 0.8978 (ptpp) cc_final: 0.8703 (ptmm) outliers start: 14 outliers final: 11 residues processed: 54 average time/residue: 0.6413 time to fit residues: 37.0151 Evaluate side-chains 54 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 7 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 71 optimal weight: 0.0770 chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.071859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.045040 restraints weight = 23387.480| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 4.02 r_work: 0.2522 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9253 Z= 0.220 Angle : 0.722 6.945 12990 Z= 0.306 Chirality : 0.043 0.184 1870 Planarity : 0.004 0.029 1330 Dihedral : 9.029 110.079 4125 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.44 % Allowed : 10.90 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.28), residues: 905 helix: None (None), residues: 0 sheet: -0.01 (0.25), residues: 370 loop : 1.73 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR C 89 PHE 0.010 0.001 PHE B 92 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 9095) covalent geometry : angle 0.65315 (12530) hydrogen bonds : bond 0.03243 ( 272) hydrogen bonds : angle 5.63371 ( 732) glycosidic custom : bond 0.00139 ( 25) glycosidic custom : angle 1.69597 ( 75) Misc. bond : bond 0.00139 ( 3) link_ALPHA1-4 : bond 0.00565 ( 25) link_ALPHA1-4 : angle 2.08198 ( 75) link_ALPHA1-6 : bond 0.00322 ( 25) link_ALPHA1-6 : angle 1.59790 ( 75) link_BETA1-4 : bond 0.00175 ( 50) link_BETA1-4 : angle 1.54277 ( 150) link_MAN-THR : bond 0.00058 ( 5) link_MAN-THR : angle 0.47023 ( 10) link_NAG-ASN : bond 0.00351 ( 25) link_NAG-ASN : angle 2.14075 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: E 53 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8690 (mtpp) REVERT: E 181 ASP cc_start: 0.9146 (t0) cc_final: 0.8836 (t0) REVERT: A 99 LYS cc_start: 0.7735 (ptpt) cc_final: 0.7380 (ptmm) REVERT: B 32 GLN cc_start: 0.8874 (tt0) cc_final: 0.8490 (tp40) outliers start: 19 outliers final: 11 residues processed: 59 average time/residue: 0.5816 time to fit residues: 36.9195 Evaluate side-chains 55 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.071436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.044569 restraints weight = 23428.450| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 4.00 r_work: 0.2505 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9253 Z= 0.235 Angle : 0.734 6.742 12990 Z= 0.311 Chirality : 0.043 0.196 1870 Planarity : 0.004 0.032 1330 Dihedral : 9.104 108.994 4125 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.31 % Allowed : 11.03 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.29), residues: 905 helix: None (None), residues: 0 sheet: -0.13 (0.25), residues: 370 loop : 1.60 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR C 89 PHE 0.009 0.001 PHE B 92 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 9095) covalent geometry : angle 0.66599 (12530) hydrogen bonds : bond 0.03231 ( 272) hydrogen bonds : angle 5.67600 ( 732) glycosidic custom : bond 0.00152 ( 25) glycosidic custom : angle 1.67852 ( 75) Misc. bond : bond 0.00116 ( 3) link_ALPHA1-4 : bond 0.00568 ( 25) link_ALPHA1-4 : angle 2.08552 ( 75) link_ALPHA1-6 : bond 0.00351 ( 25) link_ALPHA1-6 : angle 1.56995 ( 75) link_BETA1-4 : bond 0.00178 ( 50) link_BETA1-4 : angle 1.57749 ( 150) link_MAN-THR : bond 0.00108 ( 5) link_MAN-THR : angle 0.51703 ( 10) link_NAG-ASN : bond 0.00363 ( 25) link_NAG-ASN : angle 2.15654 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: E 53 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8641 (mtpp) REVERT: E 181 ASP cc_start: 0.9126 (t0) cc_final: 0.8770 (t0) REVERT: A 99 LYS cc_start: 0.7971 (ptpt) cc_final: 0.7645 (ptmm) REVERT: D 99 LYS cc_start: 0.9013 (ptpp) cc_final: 0.8700 (ptmm) outliers start: 18 outliers final: 13 residues processed: 57 average time/residue: 0.5479 time to fit residues: 33.7173 Evaluate side-chains 56 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 30 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.071994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.045329 restraints weight = 23234.149| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.98 r_work: 0.2529 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9253 Z= 0.160 Angle : 0.700 6.941 12990 Z= 0.297 Chirality : 0.043 0.196 1870 Planarity : 0.004 0.030 1330 Dihedral : 8.888 106.140 4125 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.67 % Allowed : 11.54 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.29), residues: 905 helix: None (None), residues: 0 sheet: -0.18 (0.25), residues: 370 loop : 1.62 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR B 89 PHE 0.007 0.001 PHE D 75 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9095) covalent geometry : angle 0.63337 (12530) hydrogen bonds : bond 0.02982 ( 272) hydrogen bonds : angle 5.58942 ( 732) glycosidic custom : bond 0.00138 ( 25) glycosidic custom : angle 1.57273 ( 75) Misc. bond : bond 0.00099 ( 3) link_ALPHA1-4 : bond 0.00655 ( 25) link_ALPHA1-4 : angle 2.07004 ( 75) link_ALPHA1-6 : bond 0.00422 ( 25) link_ALPHA1-6 : angle 1.50417 ( 75) link_BETA1-4 : bond 0.00139 ( 50) link_BETA1-4 : angle 1.49053 ( 150) link_MAN-THR : bond 0.00073 ( 5) link_MAN-THR : angle 0.28160 ( 10) link_NAG-ASN : bond 0.00222 ( 25) link_NAG-ASN : angle 2.06692 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: E 53 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8656 (mtpp) REVERT: E 181 ASP cc_start: 0.9104 (t0) cc_final: 0.8758 (t0) REVERT: A 99 LYS cc_start: 0.7952 (ptpt) cc_final: 0.7614 (ptmm) REVERT: B 32 GLN cc_start: 0.8869 (tt0) cc_final: 0.8456 (tp40) REVERT: D 99 LYS cc_start: 0.8983 (ptpp) cc_final: 0.8676 (ptmm) outliers start: 13 outliers final: 12 residues processed: 55 average time/residue: 0.5882 time to fit residues: 34.8110 Evaluate side-chains 55 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 74 optimal weight: 0.3980 chunk 71 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.045288 restraints weight = 23195.038| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.91 r_work: 0.2522 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9253 Z= 0.193 Angle : 0.712 7.367 12990 Z= 0.301 Chirality : 0.043 0.197 1870 Planarity : 0.004 0.031 1330 Dihedral : 8.880 106.375 4125 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.79 % Allowed : 11.54 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.29), residues: 905 helix: None (None), residues: 0 sheet: -0.19 (0.25), residues: 370 loop : 1.62 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR C 89 PHE 0.008 0.001 PHE B 92 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 9095) covalent geometry : angle 0.64595 (12530) hydrogen bonds : bond 0.03039 ( 272) hydrogen bonds : angle 5.60788 ( 732) glycosidic custom : bond 0.00146 ( 25) glycosidic custom : angle 1.59527 ( 75) Misc. bond : bond 0.00131 ( 3) link_ALPHA1-4 : bond 0.00594 ( 25) link_ALPHA1-4 : angle 2.07942 ( 75) link_ALPHA1-6 : bond 0.00377 ( 25) link_ALPHA1-6 : angle 1.54757 ( 75) link_BETA1-4 : bond 0.00147 ( 50) link_BETA1-4 : angle 1.51059 ( 150) link_MAN-THR : bond 0.00070 ( 5) link_MAN-THR : angle 0.47857 ( 10) link_NAG-ASN : bond 0.00300 ( 25) link_NAG-ASN : angle 2.07553 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: E 53 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8638 (mtpp) REVERT: E 181 ASP cc_start: 0.9091 (t0) cc_final: 0.8769 (t0) REVERT: A 99 LYS cc_start: 0.7946 (ptpt) cc_final: 0.7616 (ptmm) REVERT: D 99 LYS cc_start: 0.8987 (ptpp) cc_final: 0.8676 (ptmm) outliers start: 14 outliers final: 13 residues processed: 55 average time/residue: 0.5725 time to fit residues: 33.9715 Evaluate side-chains 56 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 48 optimal weight: 0.4980 chunk 79 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.046182 restraints weight = 23063.470| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 3.98 r_work: 0.2555 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9253 Z= 0.117 Angle : 0.670 6.338 12990 Z= 0.285 Chirality : 0.043 0.201 1870 Planarity : 0.004 0.030 1330 Dihedral : 8.611 102.725 4125 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.28 % Allowed : 11.92 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.29), residues: 905 helix: None (None), residues: 0 sheet: 0.10 (0.27), residues: 340 loop : 1.52 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR C 89 PHE 0.007 0.001 PHE E 189 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9095) covalent geometry : angle 0.60678 (12530) hydrogen bonds : bond 0.02733 ( 272) hydrogen bonds : angle 5.45381 ( 732) glycosidic custom : bond 0.00123 ( 25) glycosidic custom : angle 1.48836 ( 75) Misc. bond : bond 0.00084 ( 3) link_ALPHA1-4 : bond 0.00716 ( 25) link_ALPHA1-4 : angle 2.02222 ( 75) link_ALPHA1-6 : bond 0.00509 ( 25) link_ALPHA1-6 : angle 1.43691 ( 75) link_BETA1-4 : bond 0.00175 ( 50) link_BETA1-4 : angle 1.40752 ( 150) link_MAN-THR : bond 0.00042 ( 5) link_MAN-THR : angle 0.16175 ( 10) link_NAG-ASN : bond 0.00138 ( 25) link_NAG-ASN : angle 1.97953 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3118.99 seconds wall clock time: 54 minutes 12.15 seconds (3252.15 seconds total)