Starting phenix.real_space_refine on Tue Aug 4 12:25:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21nt_67850/08_2026/21nt_67850.cif Found real_map, /net/cci-nas-00/data/ceres_data/21nt_67850/08_2026/21nt_67850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21nt_67850/08_2026/21nt_67850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21nt_67850/08_2026/21nt_67850.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21nt_67850/08_2026/21nt_67850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21nt_67850/08_2026/21nt_67850.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.051 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: 3 Type Number sf(0) Gaussians C 1404 2.51 5 N 108 2.21 5 O 1053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2565 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 126 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 126 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 126 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "H" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "I" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "J" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "L" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "M" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "N" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "O" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "P" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "Q" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "R" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "T" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "U" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "V" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "W" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "X" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "Y" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "Z" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "a" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "b" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "c" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "d" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 81 Unusual residues: {'AHR': 1, 'MAN': 2, 'NAG': 1, 'XYP': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 0.58, per 1000 atoms: 0.23 Number of scatterers: 2565 At special positions: 0 Unit cell: (45.0139, 45.0139, 109.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1053 8.00 N 108 7.00 C 1404 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=0, symmetry=0 Links applied ALPHA1-4 " XYP D 5 " - " MAN D 6 " " XYP E 5 " - " MAN E 6 " " XYP F 5 " - " MAN F 6 " " XYP G 5 " - " MAN G 6 " " XYP H 5 " - " MAN H 6 " " XYP I 5 " - " MAN I 6 " " XYP J 5 " - " MAN J 6 " " XYP K 5 " - " MAN K 6 " " XYP L 5 " - " MAN L 6 " " XYP M 5 " - " MAN M 6 " " XYP N 5 " - " MAN N 6 " " XYP O 5 " - " MAN O 6 " " XYP P 5 " - " MAN P 6 " " XYP Q 5 " - " MAN Q 6 " " XYP R 5 " - " MAN R 6 " " XYP S 5 " - " MAN S 6 " " XYP T 5 " - " MAN T 6 " " XYP U 5 " - " MAN U 6 " " XYP V 5 " - " MAN V 6 " " XYP W 5 " - " MAN W 6 " " XYP X 5 " - " MAN X 6 " " XYP Y 5 " - " MAN Y 6 " " XYP Z 5 " - " MAN Z 6 " " XYP a 5 " - " MAN a 6 " " XYP b 5 " - " MAN b 6 " " XYP c 5 " - " MAN c 6 " " XYP d 5 " - " MAN d 6 " BETA1-2 " MAN D 1 " - " NAG D 2 " " XYP D 3 " - " XYP D 4 " " MAN E 1 " - " NAG E 2 " " XYP E 3 " - " XYP E 4 " " MAN F 1 " - " NAG F 2 " " XYP F 3 " - " XYP F 4 " " MAN G 1 " - " NAG G 2 " " XYP G 3 " - " XYP G 4 " " MAN H 1 " - " NAG H 2 " " XYP H 3 " - " XYP H 4 " " MAN I 1 " - " NAG I 2 " " XYP I 3 " - " XYP I 4 " " MAN J 1 " - " NAG J 2 " " XYP J 3 " - " XYP J 4 " " MAN K 1 " - " NAG K 2 " " XYP K 3 " - " XYP K 4 " " MAN L 1 " - " NAG L 2 " " XYP L 3 " - " XYP L 4 " " MAN M 1 " - " NAG M 2 " " XYP M 3 " - " XYP M 4 " " MAN N 1 " - " NAG N 2 " " XYP N 3 " - " XYP N 4 " " MAN O 1 " - " NAG O 2 " " XYP O 3 " - " XYP O 4 " " MAN P 1 " - " NAG P 2 " " XYP P 3 " - " XYP P 4 " " MAN Q 1 " - " NAG Q 2 " " XYP Q 3 " - " XYP Q 4 " " MAN R 1 " - " NAG R 2 " " XYP R 3 " - " XYP R 4 " " MAN S 1 " - " NAG S 2 " " XYP S 3 " - " XYP S 4 " " MAN T 1 " - " NAG T 2 " " XYP T 3 " - " XYP T 4 " " MAN U 1 " - " NAG U 2 " " XYP U 3 " - " XYP U 4 " " MAN V 1 " - " NAG V 2 " " XYP V 3 " - " XYP V 4 " " MAN W 1 " - " NAG W 2 " " XYP W 3 " - " XYP W 4 " " MAN X 1 " - " NAG X 2 " " XYP X 3 " - " XYP X 4 " " MAN Y 1 " - " NAG Y 2 " " XYP Y 3 " - " XYP Y 4 " " MAN Z 1 " - " NAG Z 2 " " XYP Z 3 " - " XYP Z 4 " " MAN a 1 " - " NAG a 2 " " XYP a 3 " - " XYP a 4 " " MAN b 1 " - " NAG b 2 " " XYP b 3 " - " XYP b 4 " " MAN c 1 " - " NAG c 2 " " XYP c 3 " - " XYP c 4 " " MAN d 1 " - " NAG d 2 " " XYP d 3 " - " XYP d 4 " BETA1-3 " MAN D 1 " - " AHR D 8 " ~> Even though AHR is an alpha isomer, a beta linkage is required... " NAG D 2 " - " XYP D 3 " " MAN D 6 " - " XYP D 7 " " MAN E 1 " - " AHR E 8 " " NAG E 2 " - " XYP E 3 " " MAN E 6 " - " XYP E 7 " " MAN F 1 " - " AHR F 8 " " NAG F 2 " - " XYP F 3 " " MAN F 6 " - " XYP F 7 " " MAN G 1 " - " AHR G 8 " " NAG G 2 " - " XYP G 3 " " MAN G 6 " - " XYP G 7 " " MAN H 1 " - " AHR H 8 " " NAG H 2 " - " XYP H 3 " " MAN H 6 " - " XYP H 7 " " MAN I 1 " - " AHR I 8 " " NAG I 2 " - " XYP I 3 " " MAN I 6 " - " XYP I 7 " " MAN J 1 " - " AHR J 8 " " NAG J 2 " - " XYP J 3 " " MAN J 6 " - " XYP J 7 " " MAN K 1 " - " AHR K 8 " " NAG K 2 " - " XYP K 3 " " MAN K 6 " - " XYP K 7 " " MAN L 1 " - " AHR L 8 " " NAG L 2 " - " XYP L 3 " " MAN L 6 " - " XYP L 7 " " MAN M 1 " - " AHR M 8 " " NAG M 2 " - " XYP M 3 " " MAN M 6 " - " XYP M 7 " " MAN N 1 " - " AHR N 8 " " NAG N 2 " - " XYP N 3 " " MAN N 6 " - " XYP N 7 " " MAN O 1 " - " AHR O 8 " " NAG O 2 " - " XYP O 3 " " MAN O 6 " - " XYP O 7 " " MAN P 1 " - " AHR P 8 " " NAG P 2 " - " XYP P 3 " " MAN P 6 " - " XYP P 7 " " MAN Q 1 " - " AHR Q 8 " " NAG Q 2 " - " XYP Q 3 " " MAN Q 6 " - " XYP Q 7 " " MAN R 1 " - " AHR R 8 " " NAG R 2 " - " XYP R 3 " " MAN R 6 " - " XYP R 7 " " MAN S 1 " - " AHR S 8 " " NAG S 2 " - " XYP S 3 " " MAN S 6 " - " XYP S 7 " " MAN T 1 " - " AHR T 8 " " NAG T 2 " - " XYP T 3 " " MAN T 6 " - " XYP T 7 " " MAN U 1 " - " AHR U 8 " " NAG U 2 " - " XYP U 3 " " MAN U 6 " - " XYP U 7 " " MAN V 1 " - " AHR V 8 " " NAG V 2 " - " XYP V 3 " " MAN V 6 " - " XYP V 7 " " MAN W 1 " - " AHR W 8 " " NAG W 2 " - " XYP W 3 " " MAN W 6 " - " XYP W 7 " " MAN X 1 " - " AHR X 8 " " NAG X 2 " - " XYP X 3 " " MAN X 6 " - " XYP X 7 " " MAN Y 1 " - " AHR Y 8 " " NAG Y 2 " - " XYP Y 3 " " MAN Y 6 " - " XYP Y 7 " " MAN Z 1 " - " AHR Z 8 " " NAG Z 2 " - " XYP Z 3 " " MAN Z 6 " - " XYP Z 7 " " MAN a 1 " - " AHR a 8 " " NAG a 2 " - " XYP a 3 " " MAN a 6 " - " XYP a 7 " " MAN b 1 " - " AHR b 8 " " NAG b 2 " - " XYP b 3 " " MAN b 6 " - " XYP b 7 " " MAN c 1 " - " AHR c 8 " " NAG c 2 " - " XYP c 3 " " MAN c 6 " - " XYP c 7 " " MAN d 1 " - " AHR d 8 " " NAG d 2 " - " XYP d 3 " " MAN d 6 " - " XYP d 7 " BETA1-4 " MAN D 1 " - " XYP D 5 " " MAN E 1 " - " XYP E 5 " " MAN F 1 " - " XYP F 5 " " MAN G 1 " - " XYP G 5 " " MAN H 1 " - " XYP H 5 " " MAN I 1 " - " XYP I 5 " " MAN J 1 " - " XYP J 5 " " MAN K 1 " - " XYP K 5 " " MAN L 1 " - " XYP L 5 " " MAN M 1 " - " XYP M 5 " " MAN N 1 " - " XYP N 5 " " MAN O 1 " - " XYP O 5 " " MAN P 1 " - " XYP P 5 " " MAN Q 1 " - " XYP Q 5 " " MAN R 1 " - " XYP R 5 " " MAN S 1 " - " XYP S 5 " " MAN T 1 " - " XYP T 5 " " MAN U 1 " - " XYP U 5 " " MAN V 1 " - " XYP V 5 " " MAN W 1 " - " XYP W 5 " " MAN X 1 " - " XYP X 5 " " MAN Y 1 " - " XYP Y 5 " " MAN Z 1 " - " XYP Z 5 " " MAN a 1 " - " XYP a 5 " " MAN b 1 " - " XYP b 5 " " MAN c 1 " - " XYP c 5 " " MAN d 1 " - " XYP d 5 " MAN-SER " MAN D 1 " - " SER A 3 " " MAN E 1 " - " SER A 6 " " MAN F 1 " - " SER A 9 " " MAN G 1 " - " SER A 12 " " MAN H 1 " - " SER A 15 " " MAN I 1 " - " SER A 18 " " MAN J 1 " - " SER A 21 " " MAN K 1 " - " SER A 24 " " MAN L 1 " - " SER A 27 " " MAN M 1 " - " SER B 3 " " MAN N 1 " - " SER B 6 " " MAN O 1 " - " SER B 9 " " MAN P 1 " - " SER B 12 " " MAN Q 1 " - " SER B 15 " " MAN R 1 " - " SER B 18 " " MAN S 1 " - " SER B 21 " " MAN T 1 " - " SER B 24 " " MAN U 1 " - " SER B 27 " " MAN V 1 " - " SER C 3 " " MAN W 1 " - " SER C 6 " " MAN X 1 " - " SER C 9 " " MAN Y 1 " - " SER C 12 " " MAN Z 1 " - " SER C 15 " " MAN a 1 " - " SER C 18 " " MAN b 1 " - " SER C 21 " " MAN c 1 " - " SER C 24 " " MAN d 1 " - " SER C 27 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 17.0 milliseconds 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 54 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 108 1.28 - 1.34: 105 1.34 - 1.41: 0 1.41 - 1.47: 1269 1.47 - 1.54: 1080 Bond restraints: 2562 Sorted by residual: bond pdb=" C3 NAG E 2 " pdb=" O3 NAG E 2 " ideal model delta sigma weight residual 1.403 1.437 -0.034 2.00e-02 2.50e+03 2.97e+00 bond pdb=" C3 NAG S 2 " pdb=" O3 NAG S 2 " ideal model delta sigma weight residual 1.403 1.437 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C3 NAG b 2 " pdb=" O3 NAG b 2 " ideal model delta sigma weight residual 1.403 1.437 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C3 NAG d 2 " pdb=" O3 NAG d 2 " ideal model delta sigma weight residual 1.403 1.437 -0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" C3 NAG c 2 " pdb=" O3 NAG c 2 " ideal model delta sigma weight residual 1.403 1.437 -0.034 2.00e-02 2.50e+03 2.87e+00 ... (remaining 2557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 1761 1.32 - 2.63: 1208 2.63 - 3.94: 367 3.94 - 5.25: 57 5.25 - 6.57: 27 Bond angle restraints: 3420 Sorted by residual: angle pdb=" N SER B 12 " pdb=" CA SER B 12 " pdb=" C SER B 12 " ideal model delta sigma weight residual 110.23 114.85 -4.62 1.45e+00 4.76e-01 1.01e+01 angle pdb=" N SER C 12 " pdb=" CA SER C 12 " pdb=" C SER C 12 " ideal model delta sigma weight residual 110.23 114.78 -4.55 1.45e+00 4.76e-01 9.84e+00 angle pdb=" N SER A 12 " pdb=" CA SER A 12 " pdb=" C SER A 12 " ideal model delta sigma weight residual 110.23 114.56 -4.33 1.45e+00 4.76e-01 8.91e+00 angle pdb=" N SER A 18 " pdb=" CA SER A 18 " pdb=" C SER A 18 " ideal model delta sigma weight residual 110.91 113.77 -2.86 1.17e+00 7.31e-01 5.98e+00 angle pdb=" N SER A 21 " pdb=" CA SER A 21 " pdb=" C SER A 21 " ideal model delta sigma weight residual 110.91 113.69 -2.78 1.17e+00 7.31e-01 5.64e+00 ... (remaining 3415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.93: 2892 6.93 - 13.86: 629 13.86 - 20.79: 129 20.79 - 27.71: 10 27.71 - 34.64: 9 Dihedral angle restraints: 3669 sinusoidal: 3537 harmonic: 132 Sorted by residual: dihedral pdb=" CA GLY B 8 " pdb=" C GLY B 8 " pdb=" N SER B 9 " pdb=" CA SER B 9 " ideal model delta harmonic sigma weight residual 180.00 -156.13 -23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA GLY C 8 " pdb=" C GLY C 8 " pdb=" N SER C 9 " pdb=" CA SER C 9 " ideal model delta harmonic sigma weight residual -180.00 -156.38 -23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLY A 8 " pdb=" C GLY A 8 " pdb=" N SER A 9 " pdb=" CA SER A 9 " ideal model delta harmonic sigma weight residual -180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 3666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 575 0.043 - 0.085: 143 0.085 - 0.128: 160 0.128 - 0.171: 40 0.171 - 0.214: 27 Chirality restraints: 945 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O2 MAN H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.66e+01 chirality pdb=" C1 NAG L 2 " pdb=" O2 MAN L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.66e+01 chirality pdb=" C1 NAG T 2 " pdb=" O2 MAN T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.64e+01 ... (remaining 942 not shown) Planarity restraints: 105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " -0.266 2.00e-02 2.50e+03 2.22e-01 6.17e+02 pdb=" C7 NAG I 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " 0.373 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 2 " 0.259 2.00e-02 2.50e+03 2.17e-01 5.87e+02 pdb=" C7 NAG b 2 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG b 2 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG b 2 " -0.363 2.00e-02 2.50e+03 pdb=" O7 NAG b 2 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.256 2.00e-02 2.50e+03 2.14e-01 5.73e+02 pdb=" C7 NAG M 2 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.359 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.004 2.00e-02 2.50e+03 ... (remaining 102 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1724 2.99 - 3.47: 1296 3.47 - 3.95: 4143 3.95 - 4.42: 4318 4.42 - 4.90: 6926 Nonbonded interactions: 18407 Sorted by model distance: nonbonded pdb=" C2 XYP D 3 " pdb=" O5 XYP D 4 " model vdw 2.515 2.776 nonbonded pdb=" C2 XYP F 3 " pdb=" O5 XYP F 4 " model vdw 2.524 2.776 nonbonded pdb=" C2 XYP P 3 " pdb=" O5 XYP P 4 " model vdw 2.529 2.776 nonbonded pdb=" C2 XYP S 3 " pdb=" O5 XYP S 4 " model vdw 2.529 2.776 nonbonded pdb=" C2 XYP O 3 " pdb=" O5 XYP O 4 " model vdw 2.530 2.776 ... (remaining 18402 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.400 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.014 0.034 2778 Z= 0.718 Angle : 7.413 65.394 4041 Z= 2.486 Chirality : 0.070 0.214 945 Planarity : 0.095 0.222 105 Dihedral : 6.124 34.641 3615 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.33 % Favored : 74.67 % Rotamer: Outliers : 0.00 % Allowed : 51.85 % Favored : 48.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.55 (0.31), residues: 75 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.24), residues: 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01461 / 0.74 ( 2562) covalent geometry : angle 1.87372 / 0.69 ( 3420) link_ALPHA1-4 : bond 0.00973 / 0.69 ( 27) link_ALPHA1-4 : angle 17.63558 / 10.70 ( 81) link_BETA1-2 : bond 0.00903 / 0.64 ( 54) link_BETA1-2 : angle 8.66063 / 5.32 ( 162) link_BETA1-3 : bond 0.00917 / 0.66 ( 81) link_BETA1-3 : angle 9.74293 / 6.12 ( 243) link_BETA1-4 : bond 0.00917 / 0.65 ( 27) link_BETA1-4 : angle 30.18621 / 18.38 ( 81) link_MAN-SER : bond 0.00936 / 0.66 ( 27) link_MAN-SER : angle 37.47486 / 22.97 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.056 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0682 Evaluate side-chains 0 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.2983 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.066546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.061998 restraints weight = 6553.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.063527 restraints weight = 2349.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.064433 restraints weight = 1126.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.064972 restraints weight = 641.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.065286 restraints weight = 409.480| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2778 Z= 0.329 Angle : 2.912 18.315 4041 Z= 0.990 Chirality : 0.058 0.268 945 Planarity : 0.003 0.007 105 Dihedral : 9.769 40.962 3588 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 34.67 % Favored : 65.33 % Rotamer: Outliers : 11.11 % Allowed : 0.00 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.54 (0.27), residues: 75 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.22 (0.20), residues: 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.32 ( 2562) covalent geometry : angle 2.22911 / 0.77 ( 3420) link_ALPHA1-4 : bond 0.00932 / 0.67 ( 27) link_ALPHA1-4 : angle 5.68777 / 3.50 ( 81) link_BETA1-2 : bond 0.01082 / 0.75 ( 54) link_BETA1-2 : angle 3.17389 / 1.97 ( 162) link_BETA1-3 : bond 0.00609 / 0.45 ( 81) link_BETA1-3 : angle 3.41057 / 2.18 ( 243) link_BETA1-4 : bond 0.00911 / 0.62 ( 27) link_BETA1-4 : angle 10.20710 / 6.29 ( 81) link_MAN-SER : bond 0.00567 / 0.41 ( 27) link_MAN-SER : angle 5.68748 / 3.52 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0258 time to fit residues: 0.1508 Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain C residue 3 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 overall best weight: 1.9987 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.061676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.057122 restraints weight = 7176.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.058590 restraints weight = 2576.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.059493 restraints weight = 1232.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.060045 restraints weight = 701.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.060410 restraints weight = 457.474| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.020 2778 Z= 0.295 Angle : 2.570 16.649 4041 Z= 0.871 Chirality : 0.057 0.280 945 Planarity : 0.003 0.007 105 Dihedral : 10.272 42.335 3588 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 29.33 % Favored : 70.67 % Rotamer: Outliers : 11.11 % Allowed : 3.70 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.75 (0.31), residues: 75 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.23), residues: 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.29 ( 2562) covalent geometry : angle 2.07643 / 0.71 ( 3420) link_ALPHA1-4 : bond 0.00839 / 0.61 ( 27) link_ALPHA1-4 : angle 5.08104 / 3.14 ( 81) link_BETA1-2 : bond 0.01084 / 0.76 ( 54) link_BETA1-2 : angle 3.41644 / 2.12 ( 162) link_BETA1-3 : bond 0.00293 / 0.21 ( 81) link_BETA1-3 : angle 3.14878 / 2.00 ( 243) link_BETA1-4 : bond 0.01038 / 0.74 ( 27) link_BETA1-4 : angle 6.90715 / 4.28 ( 81) link_MAN-SER : bond 0.00316 / 0.23 ( 27) link_MAN-SER : angle 5.60105 / 3.47 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0198 time to fit residues: 0.1517 Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain C residue 3 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.056933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.052600 restraints weight = 7918.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.053910 restraints weight = 2996.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.054708 restraints weight = 1488.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.055189 restraints weight = 878.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.055503 restraints weight = 589.869| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.024 2778 Z= 0.354 Angle : 2.736 14.473 4041 Z= 0.926 Chirality : 0.059 0.290 945 Planarity : 0.003 0.006 105 Dihedral : 11.988 59.589 3588 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 34.67 % Favored : 65.33 % Rotamer: Outliers : 11.11 % Allowed : 14.81 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.86 (0.29), residues: 75 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.46 (0.22), residues: 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.36 ( 2562) covalent geometry : angle 2.35003 / 0.80 ( 3420) link_ALPHA1-4 : bond 0.01173 / 0.84 ( 27) link_ALPHA1-4 : angle 5.21622 / 3.27 ( 81) link_BETA1-2 : bond 0.00741 / 0.52 ( 54) link_BETA1-2 : angle 3.48780 / 2.17 ( 162) link_BETA1-3 : bond 0.00252 / 0.18 ( 81) link_BETA1-3 : angle 3.00491 / 1.91 ( 243) link_BETA1-4 : bond 0.00738 / 0.53 ( 27) link_BETA1-4 : angle 6.59817 / 4.15 ( 81) link_MAN-SER : bond 0.00358 / 0.25 ( 27) link_MAN-SER : angle 5.20432 / 3.29 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0118 time to fit residues: 0.0905 Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain C residue 3 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.4650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.058529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.054070 restraints weight = 7761.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.055440 restraints weight = 2900.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.056272 restraints weight = 1438.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.056773 restraints weight = 852.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.057100 restraints weight = 572.299| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.021 2778 Z= 0.299 Angle : 2.460 12.604 4041 Z= 0.835 Chirality : 0.054 0.277 945 Planarity : 0.002 0.005 105 Dihedral : 11.793 56.147 3588 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 34.67 % Favored : 65.33 % Rotamer: Outliers : 11.11 % Allowed : 29.63 % Favored : 59.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.87 (0.29), residues: 75 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.47 (0.22), residues: 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.30 ( 2562) covalent geometry : angle 2.11609 / 0.73 ( 3420) link_ALPHA1-4 : bond 0.01033 / 0.75 ( 27) link_ALPHA1-4 : angle 4.74584 / 2.98 ( 81) link_BETA1-2 : bond 0.00806 / 0.57 ( 54) link_BETA1-2 : angle 3.31774 / 2.08 ( 162) link_BETA1-3 : bond 0.00293 / 0.22 ( 81) link_BETA1-3 : angle 2.81749 / 1.79 ( 243) link_BETA1-4 : bond 0.00841 / 0.60 ( 27) link_BETA1-4 : angle 5.95206 / 3.74 ( 81) link_MAN-SER : bond 0.00323 / 0.23 ( 27) link_MAN-SER : angle 3.68481 / 2.30 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0246 time to fit residues: 0.1877 Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain C residue 3 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.9317 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.060468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.055814 restraints weight = 7656.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.057173 restraints weight = 2965.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.058017 restraints weight = 1507.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.058546 restraints weight = 907.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.058782 restraints weight = 617.127| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 2778 Z= 0.263 Angle : 2.298 11.101 4041 Z= 0.781 Chirality : 0.051 0.268 945 Planarity : 0.002 0.006 105 Dihedral : 11.317 59.745 3588 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 29.33 % Favored : 70.67 % Rotamer: Outliers : 11.11 % Allowed : 37.04 % Favored : 51.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.88 (0.28), residues: 75 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.47 (0.21), residues: 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.26 ( 2562) covalent geometry : angle 2.00799 / 0.69 ( 3420) link_ALPHA1-4 : bond 0.00859 / 0.62 ( 27) link_ALPHA1-4 : angle 4.21539 / 2.67 ( 81) link_BETA1-2 : bond 0.00740 / 0.52 ( 54) link_BETA1-2 : angle 3.08640 / 1.93 ( 162) link_BETA1-3 : bond 0.00291 / 0.21 ( 81) link_BETA1-3 : angle 2.69642 / 1.71 ( 243) link_BETA1-4 : bond 0.00669 / 0.47 ( 27) link_BETA1-4 : angle 5.30282 / 3.34 ( 81) link_MAN-SER : bond 0.00272 / 0.19 ( 27) link_MAN-SER : angle 3.09407 / 1.93 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0120 time to fit residues: 0.0918 Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain C residue 3 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 overall best weight: 2.9653 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.056325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.051809 restraints weight = 8014.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.053104 restraints weight = 3076.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.053924 restraints weight = 1565.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.054394 restraints weight = 936.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.054703 restraints weight = 644.407| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.024 2778 Z= 0.348 Angle : 2.597 12.552 4041 Z= 0.881 Chirality : 0.057 0.291 945 Planarity : 0.002 0.005 105 Dihedral : 12.200 59.357 3588 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.67 % Favored : 61.33 % Rotamer: Outliers : 11.11 % Allowed : 37.04 % Favored : 51.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.96 (0.27), residues: 75 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.53 (0.21), residues: 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.35 ( 2562) covalent geometry : angle 2.30598 / 0.79 ( 3420) link_ALPHA1-4 : bond 0.01279 / 0.92 ( 27) link_ALPHA1-4 : angle 4.85109 / 3.08 ( 81) link_BETA1-2 : bond 0.00654 / 0.46 ( 54) link_BETA1-2 : angle 3.35611 / 2.10 ( 162) link_BETA1-3 : bond 0.00283 / 0.20 ( 81) link_BETA1-3 : angle 2.82087 / 1.80 ( 243) link_BETA1-4 : bond 0.00653 / 0.46 ( 27) link_BETA1-4 : angle 5.82640 / 3.66 ( 81) link_MAN-SER : bond 0.00321 / 0.23 ( 27) link_MAN-SER : angle 3.48418 / 2.18 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0201 time to fit residues: 0.1548 Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain C residue 3 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.5317 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.061038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.056355 restraints weight = 7631.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.057757 restraints weight = 2969.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.058609 restraints weight = 1512.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.059144 restraints weight = 911.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.059498 restraints weight = 616.992| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 2778 Z= 0.241 Angle : 2.237 10.724 4041 Z= 0.761 Chirality : 0.050 0.264 945 Planarity : 0.002 0.005 105 Dihedral : 11.342 62.249 3588 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 29.33 % Favored : 70.67 % Rotamer: Outliers : 11.11 % Allowed : 37.04 % Favored : 51.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.91 (0.27), residues: 75 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.50 (0.20), residues: 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.24 ( 2562) covalent geometry : angle 1.95423 / 0.67 ( 3420) link_ALPHA1-4 : bond 0.00740 / 0.54 ( 27) link_ALPHA1-4 : angle 4.09248 / 2.59 ( 81) link_BETA1-2 : bond 0.00774 / 0.55 ( 54) link_BETA1-2 : angle 3.12875 / 1.96 ( 162) link_BETA1-3 : bond 0.00331 / 0.24 ( 81) link_BETA1-3 : angle 2.65455 / 1.68 ( 243) link_BETA1-4 : bond 0.00688 / 0.48 ( 27) link_BETA1-4 : angle 5.15933 / 3.25 ( 81) link_MAN-SER : bond 0.00291 / 0.21 ( 27) link_MAN-SER : angle 2.56781 / 1.58 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0119 time to fit residues: 0.0909 Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain C residue 3 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.2983 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.064321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.059583 restraints weight = 7222.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.061145 restraints weight = 2629.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.062075 restraints weight = 1264.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.062635 restraints weight = 717.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.062959 restraints weight = 467.992| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2778 Z= 0.222 Angle : 2.075 9.856 4041 Z= 0.707 Chirality : 0.046 0.252 945 Planarity : 0.001 0.004 105 Dihedral : 10.334 59.781 3588 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 29.33 % Favored : 70.67 % Rotamer: Outliers : 11.11 % Allowed : 37.04 % Favored : 51.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.89 (0.26), residues: 75 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.48 (0.20), residues: 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.22 ( 2562) covalent geometry : angle 1.83054 / 0.63 ( 3420) link_ALPHA1-4 : bond 0.00638 / 0.46 ( 27) link_ALPHA1-4 : angle 3.64561 / 2.33 ( 81) link_BETA1-2 : bond 0.00772 / 0.55 ( 54) link_BETA1-2 : angle 2.79236 / 1.75 ( 162) link_BETA1-3 : bond 0.00348 / 0.25 ( 81) link_BETA1-3 : angle 2.59794 / 1.64 ( 243) link_BETA1-4 : bond 0.00541 / 0.38 ( 27) link_BETA1-4 : angle 4.53551 / 2.88 ( 81) link_MAN-SER : bond 0.00290 / 0.21 ( 27) link_MAN-SER : angle 2.30095 / 1.41 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0173 time to fit residues: 0.1384 Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain C residue 3 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.6657 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.057936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.053193 restraints weight = 8009.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.054587 restraints weight = 3061.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.055428 restraints weight = 1547.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.055950 restraints weight = 926.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.056288 restraints weight = 631.959| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.023 2778 Z= 0.319 Angle : 2.443 11.896 4041 Z= 0.828 Chirality : 0.054 0.288 945 Planarity : 0.002 0.005 105 Dihedral : 11.379 61.409 3588 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 32.00 % Favored : 68.00 % Rotamer: Outliers : 11.11 % Allowed : 37.04 % Favored : 51.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.01 (0.24), residues: 75 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.58 (0.19), residues: 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.32 ( 2562) covalent geometry : angle 2.18350 / 0.75 ( 3420) link_ALPHA1-4 : bond 0.01181 / 0.85 ( 27) link_ALPHA1-4 : angle 4.43294 / 2.83 ( 81) link_BETA1-2 : bond 0.00620 / 0.43 ( 54) link_BETA1-2 : angle 3.15719 / 1.98 ( 162) link_BETA1-3 : bond 0.00278 / 0.20 ( 81) link_BETA1-3 : angle 2.71761 / 1.73 ( 243) link_BETA1-4 : bond 0.00573 / 0.40 ( 27) link_BETA1-4 : angle 5.36042 / 3.39 ( 81) link_MAN-SER : bond 0.00292 / 0.20 ( 27) link_MAN-SER : angle 3.00499 / 1.87 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 150 Ramachandran restraints generated. 75 Oldfield, 0 Emsley, 75 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.0178 time to fit residues: 0.1279 Evaluate side-chains 3 residues out of total 27 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 0 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain C residue 3 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.2987 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.062286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.057536 restraints weight = 7362.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.058999 restraints weight = 2823.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.059899 restraints weight = 1428.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.060442 restraints weight = 849.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.060783 restraints weight = 573.794| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 2778 Z= 0.228 Angle : 2.134 10.344 4041 Z= 0.727 Chirality : 0.047 0.256 945 Planarity : 0.002 0.004 105 Dihedral : 10.748 64.204 3588 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.67 % Favored : 73.33 % Rotamer: Outliers : 11.11 % Allowed : 37.04 % Favored : 51.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.92 (0.25), residues: 75 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.51 (0.19), residues: 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.22 ( 2562) covalent geometry : angle 1.86953 / 0.64 ( 3420) link_ALPHA1-4 : bond 0.00635 / 0.46 ( 27) link_ALPHA1-4 : angle 3.84317 / 2.44 ( 81) link_BETA1-2 : bond 0.00820 / 0.58 ( 54) link_BETA1-2 : angle 2.97214 / 1.87 ( 162) link_BETA1-3 : bond 0.00373 / 0.27 ( 81) link_BETA1-3 : angle 2.62309 / 1.66 ( 243) link_BETA1-4 : bond 0.00648 / 0.46 ( 27) link_BETA1-4 : angle 4.78559 / 3.02 ( 81) link_MAN-SER : bond 0.00238 / 0.17 ( 27) link_MAN-SER : angle 2.34048 / 1.44 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 378.19 seconds wall clock time: 7 minutes 31.31 seconds (451.31 seconds total)