Starting phenix.real_space_refine on Thu Oct 22 17:40:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vnn_65214/10_2026/9vnn_65214.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vnn_65214/10_2026/9vnn_65214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vnn_65214/10_2026/9vnn_65214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vnn_65214/10_2026/9vnn_65214.map" model { file = "/net/cci-nas-00/data/ceres_data/9vnn_65214/10_2026/9vnn_65214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vnn_65214/10_2026/9vnn_65214.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 1680 2.51 5 N 462 2.21 5 O 546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2688 Number of models: 1 Model: "" Number of chains: 126 Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB G 210 " pdbres="GLY G 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB A 210 " pdbres="GLY A 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB B 210 " pdbres="GLY B 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB C 210 " pdbres="GLY C 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB D 210 " pdbres="GLY D 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB E 210 " pdbres="GLY E 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB F 210 " pdbres="GLY F 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "N" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB N 210 " pdbres="GLY N 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB H 210 " pdbres="GLY H 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB I 210 " pdbres="GLY I 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "J" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB J 210 " pdbres="GLY J 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB K 210 " pdbres="GLY K 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB L 210 " pdbres="GLY L 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "M" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB M 210 " pdbres="GLY M 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "a" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB a 210 " pdbres="GLY a 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "O" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB O 210 " pdbres="GLY O 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "Q" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB Q 210 " pdbres="GLY Q 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "S" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB S 210 " pdbres="GLY S 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "U" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB U 210 " pdbres="GLY U 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "W" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB W 210 " pdbres="GLY W 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "Y" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB Y 210 " pdbres="GLY Y 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "o" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB o 210 " pdbres="GLY o 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "c" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB c 210 " pdbres="GLY c 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "e" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB e 210 " pdbres="GLY e 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "g" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB g 210 " pdbres="GLY g 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "i" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB i 210 " pdbres="GLY i 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "k" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB k 210 " pdbres="GLY k 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "m" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB m 210 " pdbres="GLY m 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "b" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB b 210 " pdbres="GLY b 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB P 210 " pdbres="GLY P 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB R 210 " pdbres="GLY R 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "T" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB T 210 " pdbres="GLY T 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "V" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB V 210 " pdbres="GLY V 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "X" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB X 210 " pdbres="GLY X 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "Z" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB Z 210 " pdbres="GLY Z 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "p" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB p 210 " pdbres="GLY p 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "d" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB d 210 " pdbres="GLY d 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "f" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB f 210 " pdbres="GLY f 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "h" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB h 210 " pdbres="GLY h 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "j" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB j 210 " pdbres="GLY j 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "l" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB l 210 " pdbres="GLY l 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "n" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Unusual residues: {'3FB': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 4, None: 1} Not linked: pdbres="3FB n 210 " pdbres="GLY n 211 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'3FB': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'3FB:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 0.76, per 1000 atoms: 0.28 Number of scatterers: 2688 At special positions: 0 Unit cell: (77.19, 97.11, 32.37, 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 546 8.00 N 462 7.00 C 1680 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 additional links: simple=168, symmetry=0 Simple link: pdb=" C 3FB A 210 " - pdb=" N GLY A 211 " Simple link: pdb=" C 3FB A 216 " - pdb=" N GLY A 217 " Simple link: pdb=" C 3FB B 210 " - pdb=" N GLY B 211 " Simple link: pdb=" C 3FB B 216 " - pdb=" N GLY B 217 " Simple link: pdb=" C 3FB C 210 " - pdb=" N GLY C 211 " Simple link: pdb=" C 3FB C 216 " - pdb=" N GLY C 217 " Simple link: pdb=" C 3FB D 210 " - pdb=" N GLY D 211 " Simple link: pdb=" C 3FB D 216 " - pdb=" N GLY D 217 " Simple link: pdb=" C 3FB E 210 " - pdb=" N GLY E 211 " Simple link: pdb=" C 3FB E 216 " - pdb=" N GLY E 217 " Simple link: pdb=" C 3FB F 210 " - pdb=" N GLY F 211 " Simple link: pdb=" C 3FB F 216 " - pdb=" N GLY F 217 " Simple link: pdb=" C 3FB G 210 " - pdb=" N GLY G 211 " Simple link: pdb=" C 3FB G 216 " - pdb=" N GLY G 217 " Simple link: pdb=" C 3FB H 210 " - pdb=" N GLY H 211 " Simple link: pdb=" C 3FB H 216 " - pdb=" N GLY H 217 " Simple link: pdb=" C 3FB I 210 " - pdb=" N GLY I 211 " Simple link: pdb=" C 3FB I 216 " - pdb=" N GLY I 217 " Simple link: pdb=" C 3FB J 210 " - pdb=" N GLY J 211 " Simple link: pdb=" C 3FB J 216 " - pdb=" N GLY J 217 " Simple link: pdb=" C 3FB K 210 " - pdb=" N GLY K 211 " Simple link: pdb=" C 3FB K 216 " - pdb=" N GLY K 217 " Simple link: pdb=" C 3FB L 210 " - pdb=" N GLY L 211 " Simple link: pdb=" C 3FB L 216 " - pdb=" N GLY L 217 " Simple link: pdb=" C 3FB M 210 " - pdb=" N GLY M 211 " Simple link: pdb=" C 3FB M 216 " - pdb=" N GLY M 217 " Simple link: pdb=" C 3FB N 210 " - pdb=" N GLY N 211 " Simple link: pdb=" C 3FB N 216 " - pdb=" N GLY N 217 " Simple link: pdb=" C 3FB O 210 " - pdb=" N GLY O 211 " Simple link: pdb=" C 3FB O 216 " - pdb=" N GLY O 217 " Simple link: pdb=" C 3FB P 210 " - pdb=" N GLY P 211 " Simple link: pdb=" C 3FB P 216 " - pdb=" N GLY P 217 " Simple link: pdb=" C 3FB Q 210 " - pdb=" N GLY Q 211 " Simple link: pdb=" C 3FB Q 216 " - pdb=" N GLY Q 217 " Simple link: pdb=" C 3FB R 210 " - pdb=" N GLY R 211 " Simple link: pdb=" C 3FB R 216 " - pdb=" N GLY R 217 " Simple link: pdb=" C 3FB S 210 " - pdb=" N GLY S 211 " Simple link: pdb=" C 3FB S 216 " - pdb=" N GLY S 217 " Simple link: pdb=" C 3FB T 210 " - pdb=" N GLY T 211 " Simple link: pdb=" C 3FB T 216 " - pdb=" N GLY T 217 " Simple link: pdb=" C 3FB U 210 " - pdb=" N GLY U 211 " Simple link: pdb=" C 3FB U 216 " - pdb=" N GLY U 217 " Simple link: pdb=" C 3FB V 210 " - pdb=" N GLY V 211 " Simple link: pdb=" C 3FB V 216 " - pdb=" N GLY V 217 " Simple link: pdb=" C 3FB W 210 " - pdb=" N GLY W 211 " Simple link: pdb=" C 3FB W 216 " - pdb=" N GLY W 217 " Simple link: pdb=" C 3FB X 210 " - pdb=" N GLY X 211 " Simple link: pdb=" C 3FB X 216 " - pdb=" N GLY X 217 " Simple link: pdb=" C 3FB Y 210 " - pdb=" N GLY Y 211 " Simple link: pdb=" C 3FB Y 216 " - pdb=" N GLY Y 217 " Simple link: pdb=" C 3FB Z 210 " - pdb=" N GLY Z 211 " Simple link: pdb=" C 3FB Z 216 " - pdb=" N GLY Z 217 " Simple link: pdb=" C 3FB a 210 " - pdb=" N GLY a 211 " Simple link: pdb=" C 3FB a 216 " - pdb=" N GLY a 217 " Simple link: pdb=" C 3FB b 210 " - pdb=" N GLY b 211 " Simple link: pdb=" C 3FB b 216 " - pdb=" N GLY b 217 " Simple link: pdb=" C 3FB c 210 " - pdb=" N GLY c 211 " Simple link: pdb=" C 3FB c 216 " - pdb=" N GLY c 217 " Simple link: pdb=" C 3FB d 210 " - pdb=" N GLY d 211 " Simple link: pdb=" C 3FB d 216 " - pdb=" N GLY d 217 " Simple link: pdb=" C 3FB e 210 " - pdb=" N GLY e 211 " Simple link: pdb=" C 3FB e 216 " - pdb=" N GLY e 217 " Simple link: pdb=" C 3FB f 210 " - pdb=" N GLY f 211 " Simple link: pdb=" C 3FB f 216 " - pdb=" N GLY f 217 " Simple link: pdb=" C 3FB g 210 " - pdb=" N GLY g 211 " Simple link: pdb=" C 3FB g 216 " - pdb=" N GLY g 217 " Simple link: pdb=" C 3FB h 210 " - pdb=" N GLY h 211 " Simple link: pdb=" C 3FB h 216 " - pdb=" N GLY h 217 " Simple link: pdb=" C 3FB i 210 " - pdb=" N GLY i 211 " Simple link: pdb=" C 3FB i 216 " - pdb=" N GLY i 217 " Simple link: pdb=" C 3FB j 210 " - pdb=" N GLY j 211 " Simple link: pdb=" C 3FB j 216 " - pdb=" N GLY j 217 " Simple link: pdb=" C 3FB k 210 " - pdb=" N GLY k 211 " Simple link: pdb=" C 3FB k 216 " - pdb=" N GLY k 217 " Simple link: pdb=" C 3FB l 210 " - pdb=" N GLY l 211 " Simple link: pdb=" C 3FB l 216 " - pdb=" N GLY l 217 " Simple link: pdb=" C 3FB m 210 " - pdb=" N GLY m 211 " Simple link: pdb=" C 3FB m 216 " - pdb=" N GLY m 217 " Simple link: pdb=" C 3FB n 210 " - pdb=" N GLY n 211 " Simple link: pdb=" C 3FB n 216 " - pdb=" N GLY n 217 " Simple link: pdb=" C 3FB o 210 " - pdb=" N GLY o 211 " Simple link: pdb=" C 3FB o 216 " - pdb=" N GLY o 217 " Simple link: pdb=" C 3FB p 210 " - pdb=" N GLY p 211 " Simple link: pdb=" C 3FB p 216 " - pdb=" N GLY p 217 " Simple link: pdb=" C ASN A 215 " - pdb=" N 3FB A 216 " Simple link: pdb=" C ASN B 215 " - pdb=" N 3FB B 216 " Simple link: pdb=" C ASN C 215 " - pdb=" N 3FB C 216 " Simple link: pdb=" C ASN D 215 " - pdb=" N 3FB D 216 " Simple link: pdb=" C ASN E 215 " - pdb=" N 3FB E 216 " Simple link: pdb=" C ASN F 215 " - pdb=" N 3FB F 216 " Simple link: pdb=" C ASN G 215 " - pdb=" N 3FB G 216 " Simple link: pdb=" C ASN H 215 " - pdb=" N 3FB H 216 " Simple link: pdb=" C ASN I 215 " - pdb=" N 3FB I 216 " Simple link: pdb=" C ASN J 215 " - pdb=" N 3FB J 216 " Simple link: pdb=" C ASN K 215 " - pdb=" N 3FB K 216 " Simple link: pdb=" C ASN L 215 " - pdb=" N 3FB L 216 " Simple link: pdb=" C ASN M 215 " - pdb=" N 3FB M 216 " Simple link: pdb=" C ASN N 215 " - pdb=" N 3FB N 216 " Simple link: pdb=" C ASN O 215 " - pdb=" N 3FB O 216 " Simple link: pdb=" C ASN P 215 " - pdb=" N 3FB P 216 " Simple link: pdb=" C ASN Q 215 " - pdb=" N 3FB Q 216 " Simple link: pdb=" C ASN R 215 " - pdb=" N 3FB R 216 " Simple link: pdb=" C ASN S 215 " - pdb=" N 3FB S 216 " Simple link: pdb=" C ASN T 215 " - pdb=" N 3FB T 216 " Simple link: pdb=" C ASN U 215 " - pdb=" N 3FB U 216 " Simple link: pdb=" C ASN V 215 " - pdb=" N 3FB V 216 " Simple link: pdb=" C ASN W 215 " - pdb=" N 3FB W 216 " Simple link: pdb=" C ASN X 215 " - pdb=" N 3FB X 216 " Simple link: pdb=" C ASN Y 215 " - pdb=" N 3FB Y 216 " Simple link: pdb=" C ASN Z 215 " - pdb=" N 3FB Z 216 " Simple link: pdb=" C ASN a 215 " - pdb=" N 3FB a 216 " Simple link: pdb=" C ASN b 215 " - pdb=" N 3FB b 216 " Simple link: pdb=" C ASN c 215 " - pdb=" N 3FB c 216 " Simple link: pdb=" C ASN d 215 " - pdb=" N 3FB d 216 " Simple link: pdb=" C ASN e 215 " - pdb=" N 3FB e 216 " Simple link: pdb=" C ASN f 215 " - pdb=" N 3FB f 216 " Simple link: pdb=" C ASN g 215 " - pdb=" N 3FB g 216 " Simple link: pdb=" C ASN h 215 " - pdb=" N 3FB h 216 " Simple link: pdb=" C ASN i 215 " - pdb=" N 3FB i 216 " Simple link: pdb=" C ASN j 215 " - pdb=" N 3FB j 216 " Simple link: pdb=" C ASN k 215 " - pdb=" N 3FB k 216 " Simple link: pdb=" C ASN l 215 " - pdb=" N 3FB l 216 " Simple link: pdb=" C ASN m 215 " - pdb=" N 3FB m 216 " Simple link: pdb=" C ASN n 215 " - pdb=" N 3FB n 216 " Simple link: pdb=" C ASN o 215 " - pdb=" N 3FB o 216 " Simple link: pdb=" C ASN p 215 " - pdb=" N 3FB p 216 " Simple link: pdb=" C GLY A 209 " - pdb=" N 3FB A 210 " Simple link: pdb=" C GLY B 209 " - pdb=" N 3FB B 210 " Simple link: pdb=" C GLY C 209 " - pdb=" N 3FB C 210 " Simple link: pdb=" C GLY D 209 " - pdb=" N 3FB D 210 " Simple link: pdb=" C GLY E 209 " - pdb=" N 3FB E 210 " Simple link: pdb=" C GLY F 209 " - pdb=" N 3FB F 210 " Simple link: pdb=" C GLY G 209 " - pdb=" N 3FB G 210 " Simple link: pdb=" C GLY H 209 " - pdb=" N 3FB H 210 " Simple link: pdb=" C GLY I 209 " - pdb=" N 3FB I 210 " Simple link: pdb=" C GLY J 209 " - pdb=" N 3FB J 210 " Simple link: pdb=" C GLY K 209 " - pdb=" N 3FB K 210 " Simple link: pdb=" C GLY L 209 " - pdb=" N 3FB L 210 " Simple link: pdb=" C GLY M 209 " - pdb=" N 3FB M 210 " Simple link: pdb=" C GLY N 209 " - pdb=" N 3FB N 210 " Simple link: pdb=" C GLY O 209 " - pdb=" N 3FB O 210 " Simple link: pdb=" C GLY P 209 " - pdb=" N 3FB P 210 " Simple link: pdb=" C GLY Q 209 " - pdb=" N 3FB Q 210 " Simple link: pdb=" C GLY R 209 " - pdb=" N 3FB R 210 " Simple link: pdb=" C GLY S 209 " - pdb=" N 3FB S 210 " Simple link: pdb=" C GLY T 209 " - pdb=" N 3FB T 210 " Simple link: pdb=" C GLY U 209 " - pdb=" N 3FB U 210 " Simple link: pdb=" C GLY V 209 " - pdb=" N 3FB V 210 " Simple link: pdb=" C GLY W 209 " - pdb=" N 3FB W 210 " Simple link: pdb=" C GLY X 209 " - pdb=" N 3FB X 210 " Simple link: pdb=" C GLY Y 209 " - pdb=" N 3FB Y 210 " Simple link: pdb=" C GLY Z 209 " - pdb=" N 3FB Z 210 " Simple link: pdb=" C GLY a 209 " - pdb=" N 3FB a 210 " Simple link: pdb=" C GLY b 209 " - pdb=" N 3FB b 210 " Simple link: pdb=" C GLY c 209 " - pdb=" N 3FB c 210 " Simple link: pdb=" C GLY d 209 " - pdb=" N 3FB d 210 " Simple link: pdb=" C GLY e 209 " - pdb=" N 3FB e 210 " Simple link: pdb=" C GLY f 209 " - pdb=" N 3FB f 210 " Simple link: pdb=" C GLY g 209 " - pdb=" N 3FB g 210 " Simple link: pdb=" C GLY h 209 " - pdb=" N 3FB h 210 " Simple link: pdb=" C GLY i 209 " - pdb=" N 3FB i 210 " Simple link: pdb=" C GLY j 209 " - pdb=" N 3FB j 210 " Simple link: pdb=" C GLY k 209 " - pdb=" N 3FB k 210 " Simple link: pdb=" C GLY l 209 " - pdb=" N 3FB l 210 " Simple link: pdb=" C GLY m 209 " - pdb=" N 3FB m 210 " Simple link: pdb=" C GLY n 209 " - pdb=" N 3FB n 210 " Simple link: pdb=" C GLY o 209 " - pdb=" N 3FB o 210 " Simple link: pdb=" C GLY p 209 " - pdb=" N 3FB p 210 " Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 29.0 milliseconds 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB 3FB G 210 " pdb=" CB 3FB G 216 " pdb=" CB 3FB A 210 " pdb=" CB 3FB A 216 " pdb=" CB 3FB B 210 " pdb=" CB 3FB B 216 " pdb=" CB 3FB C 210 " pdb=" CB 3FB C 216 " pdb=" CB 3FB D 210 " pdb=" CB 3FB D 216 " pdb=" CB 3FB E 210 " pdb=" CB 3FB E 216 " pdb=" CB 3FB F 210 " pdb=" CB 3FB F 216 " pdb=" CB 3FB N 210 " pdb=" CB 3FB N 216 " pdb=" CB 3FB H 210 " pdb=" CB 3FB H 216 " pdb=" CB 3FB I 210 " pdb=" CB 3FB I 216 " pdb=" CB 3FB J 210 " pdb=" CB 3FB J 216 " pdb=" CB 3FB K 210 " pdb=" CB 3FB K 216 " pdb=" CB 3FB L 210 " pdb=" CB 3FB L 216 " pdb=" CB 3FB M 210 " pdb=" CB 3FB M 216 " pdb=" CB 3FB a 210 " pdb=" CB 3FB a 216 " pdb=" CB 3FB O 210 " pdb=" CB 3FB O 216 " pdb=" CB 3FB Q 210 " pdb=" CB 3FB Q 216 " pdb=" CB 3FB S 210 " pdb=" CB 3FB S 216 " pdb=" CB 3FB U 210 " pdb=" CB 3FB U 216 " pdb=" CB 3FB W 210 " pdb=" CB 3FB W 216 " pdb=" CB 3FB Y 210 " pdb=" CB 3FB Y 216 " pdb=" CB 3FB o 210 " pdb=" CB 3FB o 216 " pdb=" CB 3FB c 210 " pdb=" CB 3FB c 216 " pdb=" CB 3FB e 210 " pdb=" CB 3FB e 216 " pdb=" CB 3FB g 210 " pdb=" CB 3FB g 216 " pdb=" CB 3FB i 210 " pdb=" CB 3FB i 216 " pdb=" CB 3FB k 210 " pdb=" CB 3FB k 216 " pdb=" CB 3FB m 210 " pdb=" CB 3FB m 216 " pdb=" CB 3FB b 210 " pdb=" CB 3FB b 216 " pdb=" CB 3FB P 210 " pdb=" CB 3FB P 216 " pdb=" CB 3FB R 210 " pdb=" CB 3FB R 216 " pdb=" CB 3FB T 210 " pdb=" CB 3FB T 216 " pdb=" CB 3FB V 210 " pdb=" CB 3FB V 216 " pdb=" CB 3FB X 210 " pdb=" CB 3FB X 216 " pdb=" CB 3FB Z 210 " pdb=" CB 3FB Z 216 " pdb=" CB 3FB p 210 " pdb=" CB 3FB p 216 " pdb=" CB 3FB d 210 " pdb=" CB 3FB d 216 " pdb=" CB 3FB f 210 " pdb=" CB 3FB f 216 " pdb=" CB 3FB h 210 " pdb=" CB 3FB h 216 " pdb=" CB 3FB j 210 " pdb=" CB 3FB j 216 " pdb=" CB 3FB l 210 " pdb=" CB 3FB l 216 " pdb=" CB 3FB n 210 " pdb=" CB 3FB n 216 " Number of C-beta restraints generated: 252 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 214 through 215 removed outlier: 5.495A pdb=" N ASP C 214 " --> pdb=" O ASN S 215 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP S 214 " --> pdb=" O ASN T 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'J' and resid 214 through 215 removed outlier: 5.471A pdb=" N ASP J 214 " --> pdb=" O ASN g 215 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ASP g 214 " --> pdb=" O ASN h 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 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: 0.01 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 546 1.29 - 1.36: 252 1.36 - 1.43: 504 1.43 - 1.49: 306 1.49 - 1.56: 954 Bond restraints: 2562 Sorted by residual: bond pdb=" N 3FB j 210 " pdb=" CA 3FB j 210 " ideal model delta sigma weight residual 1.455 1.560 -0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" N 3FB U 210 " pdb=" CA 3FB U 210 " ideal model delta sigma weight residual 1.455 1.560 -0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" N 3FB V 210 " pdb=" CA 3FB V 210 " ideal model delta sigma weight residual 1.455 1.560 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" N 3FB D 210 " pdb=" CA 3FB D 210 " ideal model delta sigma weight residual 1.455 1.560 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" N 3FB i 210 " pdb=" CA 3FB i 210 " ideal model delta sigma weight residual 1.455 1.560 -0.105 2.00e-02 2.50e+03 2.73e+01 ... (remaining 2557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 2708 3.49 - 6.98: 257 6.98 - 10.47: 35 10.47 - 13.96: 18 13.96 - 17.45: 6 Bond angle restraints: 3024 Sorted by residual: angle pdb=" CA 3FB P 210 " pdb=" CCC 3FB P 210 " pdb=" C 3FB P 210 " ideal model delta sigma weight residual 113.17 130.62 -17.45 3.00e+00 1.11e-01 3.39e+01 angle pdb=" CA 3FB O 210 " pdb=" CCC 3FB O 210 " pdb=" C 3FB O 210 " ideal model delta sigma weight residual 113.17 130.61 -17.44 3.00e+00 1.11e-01 3.38e+01 angle pdb=" CA 3FB H 210 " pdb=" CCC 3FB H 210 " pdb=" C 3FB H 210 " ideal model delta sigma weight residual 113.17 130.60 -17.43 3.00e+00 1.11e-01 3.38e+01 angle pdb=" CA 3FB A 210 " pdb=" CCC 3FB A 210 " pdb=" C 3FB A 210 " ideal model delta sigma weight residual 113.17 130.60 -17.43 3.00e+00 1.11e-01 3.37e+01 angle pdb=" CA 3FB d 210 " pdb=" CCC 3FB d 210 " pdb=" C 3FB d 210 " ideal model delta sigma weight residual 113.17 130.59 -17.42 3.00e+00 1.11e-01 3.37e+01 ... (remaining 3019 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 27.95: 1152 27.95 - 55.89: 354 55.89 - 83.83: 126 83.83 - 111.76: 42 111.76 - 139.70: 6 Dihedral angle restraints: 1680 sinusoidal: 1092 harmonic: 588 Sorted by residual: dihedral pdb=" CA 3FB Z 216 " pdb=" C 3FB Z 216 " pdb=" N GLY Z 217 " pdb=" CA GLY Z 217 " ideal model delta harmonic sigma weight residual 180.00 -132.08 -47.92 0 5.00e+00 4.00e-02 9.19e+01 dihedral pdb=" CA 3FB M 216 " pdb=" C 3FB M 216 " pdb=" N GLY M 217 " pdb=" CA GLY M 217 " ideal model delta harmonic sigma weight residual 180.00 -132.12 -47.88 0 5.00e+00 4.00e-02 9.17e+01 dihedral pdb=" CA 3FB n 216 " pdb=" C 3FB n 216 " pdb=" N GLY n 217 " pdb=" CA GLY n 217 " ideal model delta harmonic sigma weight residual -180.00 -132.13 -47.87 0 5.00e+00 4.00e-02 9.17e+01 ... (remaining 1677 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.064: 95 0.064 - 0.124: 52 0.124 - 0.183: 33 0.183 - 0.243: 24 0.243 - 0.302: 6 Chirality restraints: 210 Sorted by residual: chirality pdb=" CA 3FB U 216 " pdb=" N 3FB U 216 " pdb=" CB 3FB U 216 " pdb=" CCC 3FB U 216 " both_signs ideal model delta sigma weight residual False -2.44 -2.74 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA 3FB j 216 " pdb=" N 3FB j 216 " pdb=" CB 3FB j 216 " pdb=" CCC 3FB j 216 " both_signs ideal model delta sigma weight residual False -2.44 -2.74 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA 3FB K 216 " pdb=" N 3FB K 216 " pdb=" CB 3FB K 216 " pdb=" CCC 3FB K 216 " both_signs ideal model delta sigma weight residual False -2.44 -2.74 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 207 not shown) Planarity restraints: 546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA 3FB l 216 " -0.031 2.00e-02 2.50e+03 9.14e-02 8.35e+01 pdb=" C 3FB l 216 " 0.156 2.00e-02 2.50e+03 pdb=" O 3FB l 216 " -0.051 2.00e-02 2.50e+03 pdb=" N GLY l 217 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA 3FB k 216 " -0.031 2.00e-02 2.50e+03 9.11e-02 8.29e+01 pdb=" C 3FB k 216 " 0.156 2.00e-02 2.50e+03 pdb=" O 3FB k 216 " -0.051 2.00e-02 2.50e+03 pdb=" N GLY k 217 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA 3FB E 216 " 0.031 2.00e-02 2.50e+03 9.11e-02 8.29e+01 pdb=" C 3FB E 216 " -0.156 2.00e-02 2.50e+03 pdb=" O 3FB E 216 " 0.051 2.00e-02 2.50e+03 pdb=" N GLY E 217 " 0.074 2.00e-02 2.50e+03 ... (remaining 543 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 331 2.74 - 3.28: 2419 3.28 - 3.82: 4320 3.82 - 4.36: 6252 4.36 - 4.90: 9570 Nonbonded interactions: 22892 Sorted by model distance: nonbonded pdb=" O GLY U 209 " pdb=" O GLY U 211 " model vdw 2.201 3.040 nonbonded pdb=" O GLY D 209 " pdb=" O GLY D 211 " model vdw 2.201 3.040 nonbonded pdb=" O GLY V 209 " pdb=" O GLY V 211 " model vdw 2.202 3.040 nonbonded pdb=" O GLY j 209 " pdb=" O GLY j 211 " model vdw 2.202 3.040 nonbonded pdb=" O GLY i 209 " pdb=" O GLY i 211 " model vdw 2.202 3.040 ... (remaining 22887 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' 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' 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' } 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.800 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 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 : 0.015 0.105 2730 Z= 0.914 Angle : 6.815 39.255 3528 Z= 3.598 Chirality : 0.118 0.302 210 Planarity : 0.007 0.022 378 Dihedral : 33.041 139.698 924 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 99.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Cbeta Deviations : 40.00 % 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: -6.07 (0.13), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.62 (0.10), residues: 126 Details of bonding type rmsd/Z covalent geometry : bond 0.01566 / 0.92 ( 2562) covalent geometry : angle 2.37337 / 1.11 ( 3024) link_TRANS : bond 0.01065 / 0.61 ( 168) link_TRANS : angle 17.06757 / 10.13 ( 504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.067 Fit side-chains REVERT: L 213 ASN cc_start: 0.7360 (m110) cc_final: 0.7084 (m-40) REVERT: i 214 ASP cc_start: 0.6746 (t70) cc_final: 0.6539 (t0) REVERT: V 213 ASN cc_start: 0.5158 (m-40) cc_final: 0.4891 (m-40) REVERT: j 214 ASP cc_start: 0.7395 (t70) cc_final: 0.7074 (t0) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1071 time to fit residues: 7.2137 Evaluate side-chains 45 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.132064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119994 restraints weight = 2841.674| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.47 r_work: 0.3400 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.7256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.042 2730 Z= 0.580 Angle : 2.122 18.342 3528 Z= 0.818 Chirality : 0.157 0.518 210 Planarity : 0.005 0.020 378 Dihedral : 31.175 94.669 672 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Cbeta Deviations : 32.86 % 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: -5.48 (0.13), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.17 (0.10), residues: 126 Details of bonding type rmsd/Z covalent geometry : bond 0.01134 / 0.58 ( 2562) covalent geometry : angle 2.18313 / 0.79 ( 3024) link_TRANS : bond 0.00721 / 0.42 ( 168) link_TRANS : angle 1.70817 / 0.94 ( 504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.076 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1128 time to fit residues: 6.7673 Evaluate side-chains 46 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.124429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112092 restraints weight = 2973.421| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.49 r_work: 0.3302 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.7785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.064 2730 Z= 0.739 Angle : 1.921 14.875 3528 Z= 0.756 Chirality : 0.163 0.504 210 Planarity : 0.005 0.011 378 Dihedral : 30.695 91.446 672 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.76 % Allowed : 7.94 % Favored : 87.30 % Cbeta Deviations : 32.86 % 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: -5.14 (0.14), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.11), residues: 126 Details of bonding type rmsd/Z covalent geometry : bond 0.01430 / 0.74 ( 2562) covalent geometry : angle 1.98184 / 0.74 ( 3024) link_TRANS : bond 0.00995 / 0.57 ( 168) link_TRANS : angle 1.50493 / 0.83 ( 504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.097 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 47 average time/residue: 0.1148 time to fit residues: 5.9425 Evaluate side-chains 48 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain M residue 215 ASN Chi-restraints excluded: chain Y residue 215 ASN Chi-restraints excluded: chain Z residue 215 ASN Chi-restraints excluded: chain n residue 215 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.128840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.116595 restraints weight = 2879.231| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.47 r_work: 0.3363 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.7879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 2730 Z= 0.388 Angle : 1.359 9.767 3528 Z= 0.535 Chirality : 0.130 0.396 210 Planarity : 0.003 0.007 378 Dihedral : 31.064 88.272 672 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.76 % Allowed : 7.94 % Favored : 87.30 % Cbeta Deviations : 35.24 % 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: -5.10 (0.15), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.11), residues: 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.39 ( 2562) covalent geometry : angle 1.40037 / 0.52 ( 3024) link_TRANS : bond 0.00504 / 0.29 ( 168) link_TRANS : angle 1.08048 / 0.61 ( 504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.069 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 54 average time/residue: 0.1083 time to fit residues: 6.4690 Evaluate side-chains 56 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain M residue 215 ASN Chi-restraints excluded: chain Y residue 215 ASN Chi-restraints excluded: chain m residue 215 ASN Chi-restraints excluded: chain Z residue 215 ASN Chi-restraints excluded: chain n residue 215 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.124083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112138 restraints weight = 2934.346| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.47 r_work: 0.3298 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.7875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.063 2730 Z= 0.726 Angle : 1.868 11.976 3528 Z= 0.739 Chirality : 0.164 0.498 210 Planarity : 0.004 0.010 378 Dihedral : 30.576 92.166 672 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.76 % Allowed : 7.94 % Favored : 87.30 % Cbeta Deviations : 32.38 % 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: -5.03 (0.16), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.12), residues: 126 Details of bonding type rmsd/Z covalent geometry : bond 0.01405 / 0.73 ( 2562) covalent geometry : angle 1.92393 / 0.72 ( 3024) link_TRANS : bond 0.00997 / 0.58 ( 168) link_TRANS : angle 1.48625 / 0.82 ( 504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.073 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 48 average time/residue: 0.1079 time to fit residues: 5.6866 Evaluate side-chains 50 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain M residue 215 ASN Chi-restraints excluded: chain Y residue 215 ASN Chi-restraints excluded: chain m residue 215 ASN Chi-restraints excluded: chain Z residue 215 ASN Chi-restraints excluded: chain n residue 215 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.129436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117250 restraints weight = 2901.679| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.48 r_work: 0.3373 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.7961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 2730 Z= 0.385 Angle : 1.331 9.845 3528 Z= 0.524 Chirality : 0.129 0.396 210 Planarity : 0.003 0.008 378 Dihedral : 30.962 88.079 672 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.76 % Allowed : 8.73 % Favored : 86.51 % Cbeta Deviations : 35.24 % 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: -5.04 (0.16), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.13), residues: 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.39 ( 2562) covalent geometry : angle 1.37110 / 0.51 ( 3024) link_TRANS : bond 0.00508 / 0.30 ( 168) link_TRANS : angle 1.06091 / 0.60 ( 504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 1.879 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.1139 time to fit residues: 6.9532 Evaluate side-chains 57 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain M residue 215 ASN Chi-restraints excluded: chain Y residue 215 ASN Chi-restraints excluded: chain m residue 215 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 9.9990 overall best weight: 9.9990 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.124385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112317 restraints weight = 2901.735| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.48 r_work: 0.3299 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.7962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.066 2730 Z= 0.722 Angle : 1.842 11.865 3528 Z= 0.728 Chirality : 0.162 0.488 210 Planarity : 0.004 0.011 378 Dihedral : 30.595 91.516 672 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.17 % Allowed : 10.32 % Favored : 86.51 % Cbeta Deviations : 32.86 % 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: -5.01 (0.17), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.13), residues: 126 Details of bonding type rmsd/Z covalent geometry : bond 0.01397 / 0.72 ( 2562) covalent geometry : angle 1.89840 / 0.71 ( 3024) link_TRANS : bond 0.00993 / 0.57 ( 168) link_TRANS : angle 1.45852 / 0.82 ( 504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.106 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.1160 time to fit residues: 6.2031 Evaluate side-chains 48 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain M residue 215 ASN Chi-restraints excluded: chain Y residue 215 ASN Chi-restraints excluded: chain m residue 215 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.129103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.116733 restraints weight = 2928.763| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.51 r_work: 0.3364 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.8019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 2730 Z= 0.385 Angle : 1.331 9.924 3528 Z= 0.522 Chirality : 0.128 0.393 210 Planarity : 0.003 0.009 378 Dihedral : 30.909 88.703 672 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.17 % Allowed : 10.32 % Favored : 86.51 % Cbeta Deviations : 35.24 % 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: -5.05 (0.16), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.12), residues: 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.39 ( 2562) covalent geometry : angle 1.37361 / 0.51 ( 3024) link_TRANS : bond 0.00509 / 0.30 ( 168) link_TRANS : angle 1.04062 / 0.60 ( 504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.096 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 55 average time/residue: 0.1134 time to fit residues: 6.8925 Evaluate side-chains 57 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain M residue 215 ASN Chi-restraints excluded: chain Y residue 215 ASN Chi-restraints excluded: chain m residue 215 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.124392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112220 restraints weight = 3004.358| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.51 r_work: 0.3296 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.7989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.061 2730 Z= 0.722 Angle : 1.843 12.074 3528 Z= 0.729 Chirality : 0.162 0.484 210 Planarity : 0.004 0.011 378 Dihedral : 30.578 91.315 672 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.17 % Allowed : 10.32 % Favored : 86.51 % Cbeta Deviations : 33.81 % 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: -5.01 (0.16), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.12), residues: 126 Details of bonding type rmsd/Z covalent geometry : bond 0.01397 / 0.72 ( 2562) covalent geometry : angle 1.89804 / 0.72 ( 3024) link_TRANS : bond 0.01000 / 0.58 ( 168) link_TRANS : angle 1.46736 / 0.82 ( 504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.059 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.1194 time to fit residues: 6.3640 Evaluate side-chains 46 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain M residue 215 ASN Chi-restraints excluded: chain Y residue 215 ASN Chi-restraints excluded: chain m residue 215 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.127965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115758 restraints weight = 2933.600| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.50 r_work: 0.3351 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.8017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.040 2730 Z= 0.454 Angle : 1.437 10.327 3528 Z= 0.564 Chirality : 0.136 0.413 210 Planarity : 0.003 0.009 378 Dihedral : 30.759 89.766 672 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.17 % Allowed : 10.32 % Favored : 86.51 % Cbeta Deviations : 35.24 % 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: -5.04 (0.16), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.12), residues: 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00876 / 0.46 ( 2562) covalent geometry : angle 1.48346 / 0.56 ( 3024) link_TRANS : bond 0.00604 / 0.35 ( 168) link_TRANS : angle 1.11433 / 0.64 ( 504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.062 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 53 average time/residue: 0.1174 time to fit residues: 6.8631 Evaluate side-chains 55 residues out of total 126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain M residue 215 ASN Chi-restraints excluded: chain Y residue 215 ASN Chi-restraints excluded: chain m residue 215 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 10.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.124514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112362 restraints weight = 2947.284| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.50 r_work: 0.3302 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.8000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.061 2730 Z= 0.723 Angle : 1.844 12.215 3528 Z= 0.730 Chirality : 0.162 0.485 210 Planarity : 0.004 0.010 378 Dihedral : 30.571 91.229 672 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.17 % Allowed : 10.32 % Favored : 86.51 % Cbeta Deviations : 33.33 % 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: -5.02 (0.16), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.12), residues: 126 Details of bonding type rmsd/Z covalent geometry : bond 0.01399 / 0.72 ( 2562) covalent geometry : angle 1.89911 / 0.72 ( 3024) link_TRANS : bond 0.00996 / 0.58 ( 168) link_TRANS : angle 1.46914 / 0.82 ( 504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 670.87 seconds wall clock time: 12 minutes 13.16 seconds (733.16 seconds total)