I am trying to link my sugar molecule (FUC-GAL-NGA-FUC), Lewis y, for phenix.refine, but I keep on getting an error message. I am a beginner at this so I just don’t know how to make the links.

For , example, I am using this:

refinement.pdb_interpretation {

  apply_cif_link {

    data_link = BETA1-2

    residue_selection_1 = chain C and resname GAL and resid 224

    residue_selection_2 = chain C and resname FUC and resid 223

  }

  apply_cif_link {

    data_link = BETA1-3

    residue_selection_1 = chain C and resname GAL and resid 224

    residue_selection_2 = chain C and resname NGA and resid 225

  }

  apply_cif_link {

    data_link = BETA1-3

    residue_selection_1 = chain C and resname NGA and resid 225

    residue_selection_2 = chain C and resname FUC and resid 226

     Number of atoms: 46

      Number of conformers: 1

      Conformer: ""

        Number of residues, atoms: 4, 46

          Unusual residues: {'GAL%DEL-HO2%DEL-HO3': 1, 'NGA%DEL-O1%DEL-HO3': 1, 'FUC%DEL-O1': 2}

          Unexpected atoms: {'NGA%DEL-O1%DEL-HO3,O1L': 1, 'NGA%DEL-O1%DEL-HO3,O': 1}

          Classifications: {'undetermined': 4}

          Modifications used: {'DEL-HO2': 1, 'DEL-HO3': 2, 'DEL-O1': 3}

          Link IDs: {None: 3}

          Unresolved non-hydrogen bonds: 3

          Unresolved non-hydrogen angles: 6

          Unresolved non-hydrogen dihedrals: 4

          Unresolved non-hydrogen chiralities: 2

          Unresolved apply_cif_link angles: 1

          Unresolved apply_cif_link chiralities: 1

  Number of atoms with unknown nonbonded energy type symbols: 2

    "HETATM 5649  O   NGA C 225 .*.     O  "

    "HETATM 5655  O1L NGA C 225 .*.     O  "

  Time building chain proxies: 2.31, per 1000 atoms: 0.41

Sorry: Fatal problems interpreting PDB file:

  Number of atoms with unknown nonbonded energy type symbols: 2

  Please edit the PDB file to resolve the problems and/or supply a

  CIF file with matching restraint definitions, along with

  apply_cif_modification and apply_cif_link parameter definitions

  if necessary (see phenix.refine documentation).

  Also note that phenix.elbow is available to create restraint

  definitions for unknown ligands.

Any help and direction would be appreciated.

Grant