Starting phenix.real_space_refine on Mon May 12 07:26:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rzl_19608/05_2025/8rzl_19608.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rzl_19608/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rzl_19608/05_2025/8rzl_19608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rzl_19608/05_2025/8rzl_19608.map" model { file = "/net/cci-nas-00/data/ceres_data/8rzl_19608/05_2025/8rzl_19608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rzl_19608/05_2025/8rzl_19608.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.20, per 1000 atoms: 0.70 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: 7.90 Conformation dependent library (CDL) restraints added in 898.9 milliseconds 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: 1.08 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: 2.53 Time building geometry restraints manager: 6.00 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: 0.00 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.990 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.830 ------------------------------------------------------------------------------- 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 : 1.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 PHE 0.012 0.003 PHE A 191 TYR 0.052 0.009 TYR A 89 Details of bonding type rmsd 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) 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) hydrogen bonds : bond 0.16061 ( 272) hydrogen bonds : angle 8.70755 ( 732) glycosidic custom : bond 0.01727 ( 25) glycosidic custom : angle 4.90689 ( 75) covalent geometry : bond 0.01210 ( 9095) covalent geometry : angle 1.57136 (12530) Misc. bond : bond 0.09630 ( 3) *********************** 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 : 0.838 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: 1.1988 time to fit residues: 111.7492 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 : 0.838 ------------------------------------------------------------------------------- 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 75 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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** D 129 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.073634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.046513 restraints weight = 22905.508| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 4.07 r_work: 0.2555 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9253 Z= 0.181 Angle : 0.855 8.398 12990 Z= 0.362 Chirality : 0.047 0.205 1870 Planarity : 0.005 0.032 1330 Dihedral : 11.880 112.632 4134 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.67 % Allowed : 10.38 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.28), residues: 905 helix: None (None), residues: 0 sheet: 0.61 (0.25), residues: 405 loop : 1.28 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE B 189 TYR 0.018 0.002 TYR B 89 Details of bonding type rmsd link_MAN-THR : bond 0.00044 ( 5) link_MAN-THR : angle 0.79366 ( 10) link_NAG-ASN : bond 0.00416 ( 25) link_NAG-ASN : angle 2.77385 ( 75) link_ALPHA1-4 : bond 0.00676 ( 25) link_ALPHA1-4 : angle 2.34951 ( 75) link_ALPHA1-6 : bond 0.00543 ( 25) link_ALPHA1-6 : angle 1.58542 ( 75) link_BETA1-4 : bond 0.00309 ( 50) link_BETA1-4 : angle 1.86481 ( 150) hydrogen bonds : bond 0.03992 ( 272) hydrogen bonds : angle 6.71092 ( 732) glycosidic custom : bond 0.00251 ( 25) glycosidic custom : angle 2.22403 ( 75) covalent geometry : bond 0.00415 ( 9095) covalent geometry : angle 0.76954 (12530) Misc. bond : bond 0.00106 ( 3) *********************** 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 55 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.989 Fit side-chains REVERT: A 99 LYS cc_start: 0.7386 (ptpt) cc_final: 0.6967 (ptmm) outliers start: 13 outliers final: 6 residues processed: 52 average time/residue: 1.2563 time to fit residues: 70.5384 Evaluate side-chains 48 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 24 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.045236 restraints weight = 23212.396| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 4.04 r_work: 0.2521 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9253 Z= 0.214 Angle : 0.760 5.426 12990 Z= 0.325 Chirality : 0.044 0.185 1870 Planarity : 0.005 0.036 1330 Dihedral : 9.698 112.352 4125 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.41 % Allowed : 11.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.27), residues: 905 helix: None (None), residues: 0 sheet: 0.71 (0.26), residues: 340 loop : 1.21 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE B 92 TYR 0.013 0.001 TYR D 63 Details of bonding type rmsd link_MAN-THR : bond 0.00017 ( 5) link_MAN-THR : angle 0.26221 ( 10) link_NAG-ASN : bond 0.00464 ( 25) link_NAG-ASN : angle 2.46100 ( 75) link_ALPHA1-4 : bond 0.00665 ( 25) link_ALPHA1-4 : angle 2.13866 ( 75) link_ALPHA1-6 : bond 0.00378 ( 25) link_ALPHA1-6 : angle 1.57211 ( 75) link_BETA1-4 : bond 0.00177 ( 50) link_BETA1-4 : angle 1.72267 ( 150) hydrogen bonds : bond 0.03760 ( 272) hydrogen bonds : angle 6.04765 ( 732) glycosidic custom : bond 0.00240 ( 25) glycosidic custom : angle 1.78871 ( 75) covalent geometry : bond 0.00490 ( 9095) covalent geometry : angle 0.68190 (12530) Misc. bond : bond 0.00160 ( 3) *********************** 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 55 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.858 Fit side-chains REVERT: C 93 MET cc_start: 0.8988 (tpp) cc_final: 0.8787 (tpt) REVERT: A 99 LYS cc_start: 0.7582 (ptpt) cc_final: 0.7292 (ptmm) outliers start: 11 outliers final: 5 residues processed: 55 average time/residue: 1.2498 time to fit residues: 73.8216 Evaluate side-chains 47 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 51 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 87 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 37 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN E 120 GLN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.071582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.044634 restraints weight = 23188.931| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 4.00 r_work: 0.2507 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9253 Z= 0.240 Angle : 0.751 5.436 12990 Z= 0.320 Chirality : 0.044 0.196 1870 Planarity : 0.004 0.035 1330 Dihedral : 9.500 112.803 4125 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.18 % Allowed : 10.77 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.28), residues: 905 helix: None (None), residues: 0 sheet: 0.40 (0.26), residues: 340 loop : 1.42 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE B 92 TYR 0.012 0.001 TYR C 89 Details of bonding type rmsd link_MAN-THR : bond 0.00070 ( 5) link_MAN-THR : angle 0.34012 ( 10) link_NAG-ASN : bond 0.00444 ( 25) link_NAG-ASN : angle 2.41197 ( 75) link_ALPHA1-4 : bond 0.00594 ( 25) link_ALPHA1-4 : angle 2.10724 ( 75) link_ALPHA1-6 : bond 0.00311 ( 25) link_ALPHA1-6 : angle 1.66617 ( 75) link_BETA1-4 : bond 0.00181 ( 50) link_BETA1-4 : angle 1.64508 ( 150) hydrogen bonds : bond 0.03511 ( 272) hydrogen bonds : angle 5.97399 ( 732) glycosidic custom : bond 0.00182 ( 25) glycosidic custom : angle 1.76226 ( 75) covalent geometry : bond 0.00553 ( 9095) covalent geometry : angle 0.67508 (12530) Misc. bond : bond 0.00102 ( 3) *********************** 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 61 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: C 37 ASN cc_start: 0.9330 (OUTLIER) cc_final: 0.8388 (p0) REVERT: E 53 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8618 (mtpp) REVERT: A 99 LYS cc_start: 0.7646 (ptpt) cc_final: 0.7339 (ptmm) REVERT: D 99 LYS cc_start: 0.8994 (ptmm) cc_final: 0.8787 (ptpp) outliers start: 17 outliers final: 9 residues processed: 58 average time/residue: 1.0910 time to fit residues: 68.6565 Evaluate side-chains 53 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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 163 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 42 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 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 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** D 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.071491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.044592 restraints weight = 23255.504| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 4.01 r_work: 0.2503 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9253 Z= 0.241 Angle : 0.752 7.426 12990 Z= 0.319 Chirality : 0.044 0.190 1870 Planarity : 0.004 0.034 1330 Dihedral : 9.412 111.770 4125 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.31 % Allowed : 10.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.28), residues: 905 helix: None (None), residues: 0 sheet: -0.14 (0.25), residues: 370 loop : 1.62 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE B 92 TYR 0.013 0.001 TYR C 89 Details of bonding type rmsd link_MAN-THR : bond 0.00100 ( 5) link_MAN-THR : angle 0.39851 ( 10) link_NAG-ASN : bond 0.00439 ( 25) link_NAG-ASN : angle 2.36317 ( 75) link_ALPHA1-4 : bond 0.00593 ( 25) link_ALPHA1-4 : angle 2.11228 ( 75) link_ALPHA1-6 : bond 0.00313 ( 25) link_ALPHA1-6 : angle 1.64586 ( 75) link_BETA1-4 : bond 0.00185 ( 50) link_BETA1-4 : angle 1.66393 ( 150) hydrogen bonds : bond 0.03404 ( 272) hydrogen bonds : angle 5.94765 ( 732) glycosidic custom : bond 0.00168 ( 25) glycosidic custom : angle 1.72289 ( 75) covalent geometry : bond 0.00557 ( 9095) covalent geometry : angle 0.67785 (12530) Misc. bond : bond 0.00141 ( 3) *********************** 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 60 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 99 LYS cc_start: 0.7654 (ptpt) cc_final: 0.7324 (ptmm) outliers start: 18 outliers final: 12 residues processed: 59 average time/residue: 1.0700 time to fit residues: 68.5142 Evaluate side-chains 53 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 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 163 VAL Chi-restraints excluded: chain D residue 184 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 86 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.072832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.045877 restraints weight = 23117.585| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 4.04 r_work: 0.2555 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2561 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= 0.122 Angle : 0.687 5.684 12990 Z= 0.291 Chirality : 0.043 0.213 1870 Planarity : 0.004 0.032 1330 Dihedral : 9.008 106.344 4125 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.18 % Allowed : 10.26 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.28), residues: 905 helix: None (None), residues: 0 sheet: 0.19 (0.26), residues: 340 loop : 1.54 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE A 189 TYR 0.012 0.001 TYR B 89 Details of bonding type rmsd link_MAN-THR : bond 0.00060 ( 5) link_MAN-THR : angle 0.15479 ( 10) link_NAG-ASN : bond 0.00170 ( 25) link_NAG-ASN : angle 2.16863 ( 75) link_ALPHA1-4 : bond 0.00720 ( 25) link_ALPHA1-4 : angle 2.05696 ( 75) link_ALPHA1-6 : bond 0.00472 ( 25) link_ALPHA1-6 : angle 1.47582 ( 75) link_BETA1-4 : bond 0.00155 ( 50) link_BETA1-4 : angle 1.48678 ( 150) hydrogen bonds : bond 0.02896 ( 272) hydrogen bonds : angle 5.69080 ( 732) glycosidic custom : bond 0.00148 ( 25) glycosidic custom : angle 1.58164 ( 75) covalent geometry : bond 0.00274 ( 9095) covalent geometry : angle 0.61753 (12530) Misc. bond : bond 0.00047 ( 3) *********************** 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 60 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: E 53 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8649 (mtpp) REVERT: A 99 LYS cc_start: 0.7717 (ptpt) cc_final: 0.7386 (ptmm) REVERT: B 32 GLN cc_start: 0.8858 (tt0) cc_final: 0.8463 (tp40) REVERT: D 99 LYS cc_start: 0.8965 (ptpp) cc_final: 0.8701 (ptmm) outliers start: 17 outliers final: 12 residues processed: 56 average time/residue: 1.0999 time to fit residues: 66.7331 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 : 0.904 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 8 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.071115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.044519 restraints weight = 23460.461| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 3.95 r_work: 0.2494 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9253 Z= 0.279 Angle : 0.759 6.390 12990 Z= 0.321 Chirality : 0.044 0.180 1870 Planarity : 0.004 0.032 1330 Dihedral : 9.241 111.016 4125 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.18 % Allowed : 10.38 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 905 helix: None (None), residues: 0 sheet: -0.20 (0.25), residues: 370 loop : 1.65 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE C 92 TYR 0.013 0.001 TYR C 89 Details of bonding type rmsd link_MAN-THR : bond 0.00068 ( 5) link_MAN-THR : angle 0.59116 ( 10) link_NAG-ASN : bond 0.00482 ( 25) link_NAG-ASN : angle 2.28928 ( 75) link_ALPHA1-4 : bond 0.00532 ( 25) link_ALPHA1-4 : angle 2.12571 ( 75) link_ALPHA1-6 : bond 0.00281 ( 25) link_ALPHA1-6 : angle 1.67166 ( 75) link_BETA1-4 : bond 0.00229 ( 50) link_BETA1-4 : angle 1.64753 ( 150) hydrogen bonds : bond 0.03394 ( 272) hydrogen bonds : angle 5.78473 ( 732) glycosidic custom : bond 0.00178 ( 25) glycosidic custom : angle 1.75383 ( 75) covalent geometry : bond 0.00648 ( 9095) covalent geometry : angle 0.68575 (12530) Misc. bond : bond 0.00174 ( 3) *********************** 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 59 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: E 53 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8662 (mtpp) REVERT: A 99 LYS cc_start: 0.7721 (ptpt) cc_final: 0.7377 (ptmm) REVERT: D 99 LYS cc_start: 0.9004 (ptpp) cc_final: 0.8764 (ptmm) outliers start: 17 outliers final: 14 residues processed: 56 average time/residue: 1.0865 time to fit residues: 65.9807 Evaluate side-chains 56 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 73 optimal weight: 0.0980 chunk 36 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.045166 restraints weight = 23628.836| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 3.94 r_work: 0.2516 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9253 Z= 0.186 Angle : 0.715 6.811 12990 Z= 0.303 Chirality : 0.043 0.200 1870 Planarity : 0.004 0.032 1330 Dihedral : 9.076 107.853 4125 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.05 % Allowed : 10.13 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.29), residues: 905 helix: None (None), residues: 0 sheet: -0.24 (0.25), residues: 370 loop : 1.65 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE C 75 TYR 0.014 0.001 TYR C 89 Details of bonding type rmsd link_MAN-THR : bond 0.00085 ( 5) link_MAN-THR : angle 0.34896 ( 10) link_NAG-ASN : bond 0.00275 ( 25) link_NAG-ASN : angle 2.17894 ( 75) link_ALPHA1-4 : bond 0.00628 ( 25) link_ALPHA1-4 : angle 2.07444 ( 75) link_ALPHA1-6 : bond 0.00393 ( 25) link_ALPHA1-6 : angle 1.53949 ( 75) link_BETA1-4 : bond 0.00143 ( 50) link_BETA1-4 : angle 1.54915 ( 150) hydrogen bonds : bond 0.03068 ( 272) hydrogen bonds : angle 5.71677 ( 732) glycosidic custom : bond 0.00147 ( 25) glycosidic custom : angle 1.61536 ( 75) covalent geometry : bond 0.00431 ( 9095) covalent geometry : angle 0.64570 (12530) Misc. bond : bond 0.00089 ( 3) *********************** 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 58 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: E 53 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8658 (mtpp) REVERT: A 99 LYS cc_start: 0.7758 (ptpt) cc_final: 0.7427 (ptmm) REVERT: B 127 MET cc_start: 0.9335 (mtp) cc_final: 0.9096 (mtm) REVERT: D 99 LYS cc_start: 0.8974 (ptpp) cc_final: 0.8746 (ptmm) outliers start: 16 outliers final: 14 residues processed: 55 average time/residue: 1.0969 time to fit residues: 65.6515 Evaluate side-chains 56 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.0000 chunk 30 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 overall best weight: 0.7990 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.046200 restraints weight = 23184.071| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.97 r_work: 0.2558 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9253 Z= 0.117 Angle : 0.677 6.773 12990 Z= 0.286 Chirality : 0.043 0.209 1870 Planarity : 0.004 0.032 1330 Dihedral : 8.738 104.062 4125 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.92 % Allowed : 10.13 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.29), residues: 905 helix: None (None), residues: 0 sheet: 0.10 (0.27), residues: 340 loop : 1.54 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE B 92 TYR 0.011 0.001 TYR C 89 Details of bonding type rmsd link_MAN-THR : bond 0.00058 ( 5) link_MAN-THR : angle 0.09465 ( 10) link_NAG-ASN : bond 0.00134 ( 25) link_NAG-ASN : angle 2.04316 ( 75) link_ALPHA1-4 : bond 0.00732 ( 25) link_ALPHA1-4 : angle 2.03700 ( 75) link_ALPHA1-6 : bond 0.00494 ( 25) link_ALPHA1-6 : angle 1.45313 ( 75) link_BETA1-4 : bond 0.00169 ( 50) link_BETA1-4 : angle 1.42644 ( 150) hydrogen bonds : bond 0.02714 ( 272) hydrogen bonds : angle 5.52154 ( 732) glycosidic custom : bond 0.00131 ( 25) glycosidic custom : angle 1.52281 ( 75) covalent geometry : bond 0.00268 ( 9095) covalent geometry : angle 0.61176 (12530) Misc. bond : bond 0.00074 ( 3) *********************** 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 58 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: E 53 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8704 (mtpp) REVERT: A 99 LYS cc_start: 0.7980 (ptpt) cc_final: 0.7667 (ptmm) REVERT: B 32 GLN cc_start: 0.8872 (tt0) cc_final: 0.8491 (tp40) REVERT: B 127 MET cc_start: 0.9317 (mtp) cc_final: 0.9043 (mtm) outliers start: 15 outliers final: 12 residues processed: 55 average time/residue: 1.1727 time to fit residues: 69.6296 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 : 0.894 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.071196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.044423 restraints weight = 23372.547| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 3.98 r_work: 0.2502 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9253 Z= 0.258 Angle : 0.743 7.063 12990 Z= 0.314 Chirality : 0.043 0.186 1870 Planarity : 0.004 0.031 1330 Dihedral : 8.957 107.355 4125 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.05 % Allowed : 10.26 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.29), residues: 905 helix: None (None), residues: 0 sheet: -0.27 (0.25), residues: 370 loop : 1.62 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE B 92 TYR 0.014 0.001 TYR C 89 Details of bonding type rmsd link_MAN-THR : bond 0.00116 ( 5) link_MAN-THR : angle 0.65063 ( 10) link_NAG-ASN : bond 0.00414 ( 25) link_NAG-ASN : angle 2.17995 ( 75) link_ALPHA1-4 : bond 0.00536 ( 25) link_ALPHA1-4 : angle 2.11115 ( 75) link_ALPHA1-6 : bond 0.00299 ( 25) link_ALPHA1-6 : angle 1.61749 ( 75) link_BETA1-4 : bond 0.00212 ( 50) link_BETA1-4 : angle 1.58004 ( 150) hydrogen bonds : bond 0.03228 ( 272) hydrogen bonds : angle 5.70411 ( 732) glycosidic custom : bond 0.00161 ( 25) glycosidic custom : angle 1.68114 ( 75) covalent geometry : bond 0.00597 ( 9095) covalent geometry : angle 0.67437 (12530) Misc. bond : bond 0.00132 ( 3) ********************** 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 57 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: E 53 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8665 (mtpp) REVERT: A 99 LYS cc_start: 0.7973 (ptpt) cc_final: 0.7634 (ptmm) REVERT: B 127 MET cc_start: 0.9370 (mtp) cc_final: 0.9142 (mtm) REVERT: D 99 LYS cc_start: 0.9019 (ptpp) cc_final: 0.8703 (ptmm) outliers start: 16 outliers final: 15 residues processed: 55 average time/residue: 1.0855 time to fit residues: 64.8743 Evaluate side-chains 57 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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 184 THR 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 54 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 78 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.072282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.045933 restraints weight = 23171.214| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.92 r_work: 0.2546 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9253 Z= 0.121 Angle : 0.680 6.102 12990 Z= 0.289 Chirality : 0.043 0.204 1870 Planarity : 0.004 0.031 1330 Dihedral : 8.730 104.047 4125 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.18 % Allowed : 10.13 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.29), residues: 905 helix: None (None), residues: 0 sheet: 0.05 (0.27), residues: 340 loop : 1.49 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE B 75 TYR 0.011 0.001 TYR C 89 Details of bonding type rmsd link_MAN-THR : bond 0.00040 ( 5) link_MAN-THR : angle 0.15272 ( 10) link_NAG-ASN : bond 0.00133 ( 25) link_NAG-ASN : angle 2.06544 ( 75) link_ALPHA1-4 : bond 0.00707 ( 25) link_ALPHA1-4 : angle 2.02411 ( 75) link_ALPHA1-6 : bond 0.00490 ( 25) link_ALPHA1-6 : angle 1.45410 ( 75) link_BETA1-4 : bond 0.00165 ( 50) link_BETA1-4 : angle 1.42504 ( 150) hydrogen bonds : bond 0.02801 ( 272) hydrogen bonds : angle 5.62926 ( 732) glycosidic custom : bond 0.00135 ( 25) glycosidic custom : angle 1.49729 ( 75) covalent geometry : bond 0.00280 ( 9095) covalent geometry : angle 0.61518 (12530) Misc. bond : bond 0.00073 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5786.57 seconds wall clock time: 100 minutes 47.78 seconds (6047.78 seconds total)