I got the following error when I added a NAG-ASN link in the def file.

/nfs/home/jzhu/xiao/x61b/phenix6/temp/x61b.pdb

  Monomer Library directory:

    "/nfs/home/jzhu/phenix-1.3b-rc3/ext_ref_files/mon_lib"

  Total number of atoms: 46651

  apply_cif_link:

    data_link: NAG-ASN

      mod_id_1: DEL-O1

      mod_id_2: DEL-HD22

    residue_selection_1: chain S and resname NAG and resid 1001

    residue_selection_2: chain A and resname ASN and resid 15

  Number of models: 1

  Model: 0

    Number of conformers: 1

    Conformer: " "

      Number of atoms: 46651

      Number of chains: 8

        Number of residues, atoms: 909, 13713

          Unexpected atoms: {'ASN%DEL-HD22,HD22': 1}

          Classifications: {'peptide': 909}

          Modifications used: {'DEL-HD22': 1, 'NH3': 1}

          Link IDs: {'PTRANS': 59, 'TRANS': 847, 'PCIS': 2}

          Chain breaks: 3

        Number of residues, atoms: 601, 8947

          Classifications: {'peptide': 601}

          Modifications used: {'NH3': 1}

          Link IDs: {'PTRANS': 28, 'TRANS': 569, 'PCIS': 3}

          Chain breaks: 2

        Number of residues, atoms: 898, 13559

          Classifications: {'peptide': 898}

          Modifications used: {'NH3': 1}

          Link IDs: {'PTRANS': 59, 'TRANS': 836, 'PCIS': 2}

          Chain breaks: 3

        Number of residues, atoms: 602, 8954

          Classifications: {'peptide': 602}

          Modifications used: {'NH3': 1}

          Link IDs: {'PTRANS': 28, 'TRANS': 570, 'PCIS': 3}

          Chain breaks: 2

        Number of residues, atoms: 642, 642

          Classifications: {'water': 642}

          Link IDs: {None: 641}

        Number of residues, atoms: 31, 780

          Unusual residues: {'MAN': 7, 'NAG%DEL-O1': 1, 'NAG': 23}

          Classifications: {'undetermined': 31}

          Modifications used: {'DEL-O1': 1}

          Link IDs: {None: 30, 'NAG-ASN': 1}

          Unresolved non-hydrogen bonds: 30

          Unresolved non-hydrogen angles: 60

          Unresolved non-hydrogen chiralities: 30

        Number of residues, atoms: 16, 16

          Unusual residues: {' MG': 2, ' CA': 14}

          Classifications: {'undetermined': 16}

          Link IDs: {None: 15}

        Number of residues, atoms: 4, 40

          Unusual residues: {'IMD': 4}

          Classifications: {'undetermined': 4}

          Link IDs: {None: 3}

  Number of atoms with unknown nonbonded energy type symbols: 1

    "HD22 ASN A  15 "

  Time building chain proxies: 32.54, per 1000 atoms: 0.70

Sorry: Fatal problems interpreting PDB file:

  Number of atoms with unknown nonbonded energy type symbols: 1

  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.

Couldn't figure out what went wrong.  Can somebody help me?  Thanks.

Jianghai