<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>I got the following error when I added a NAG-ASN link in the def file.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>/nfs/home/jzhu/xiao/x61b/phenix6/temp/x61b.pdb</DIV><DIV> Monomer Library directory:</DIV><DIV> "/nfs/home/jzhu/phenix-1.3b-rc3/ext_ref_files/mon_lib"</DIV><DIV> Total number of atoms: 46651</DIV><DIV> apply_cif_link:</DIV><DIV> data_link: NAG-ASN</DIV><DIV> mod_id_1: DEL-O1</DIV><DIV> mod_id_2: DEL-HD22</DIV><DIV> residue_selection_1: chain S and resname NAG and resid 1001</DIV><DIV> residue_selection_2: chain A and resname ASN and resid 15</DIV><DIV> Number of models: 1</DIV><DIV> Model: 0</DIV><DIV> Number of conformers: 1</DIV><DIV> Conformer: " "</DIV><DIV> Number of atoms: 46651</DIV><DIV> Number of chains: 8</DIV><DIV> Number of residues, atoms: 909, 13713</DIV><DIV> Unexpected atoms: {'ASN%DEL-HD22,HD22': 1}</DIV><DIV> Classifications: {'peptide': 909}</DIV><DIV> Modifications used: {'DEL-HD22': 1, 'NH3': 1}</DIV><DIV> Link IDs: {'PTRANS': 59, 'TRANS': 847, 'PCIS': 2}</DIV><DIV> Chain breaks: 3</DIV><DIV> Number of residues, atoms: 601, 8947</DIV><DIV> Classifications: {'peptide': 601}</DIV><DIV> Modifications used: {'NH3': 1}</DIV><DIV> Link IDs: {'PTRANS': 28, 'TRANS': 569, 'PCIS': 3}</DIV><DIV> Chain breaks: 2</DIV><DIV> Number of residues, atoms: 898, 13559</DIV><DIV> Classifications: {'peptide': 898}</DIV><DIV> Modifications used: {'NH3': 1}</DIV><DIV> Link IDs: {'PTRANS': 59, 'TRANS': 836, 'PCIS': 2}</DIV><DIV> Chain breaks: 3</DIV><DIV> Number of residues, atoms: 602, 8954</DIV><DIV> Classifications: {'peptide': 602}</DIV><DIV> Modifications used: {'NH3': 1}</DIV><DIV> Link IDs: {'PTRANS': 28, 'TRANS': 570, 'PCIS': 3}</DIV><DIV> Chain breaks: 2</DIV><DIV> Number of residues, atoms: 642, 642</DIV><DIV> Classifications: {'water': 642}</DIV><DIV> Link IDs: {None: 641}</DIV><DIV> Number of residues, atoms: 31, 780</DIV><DIV> Unusual residues: {'MAN': 7, 'NAG%DEL-O1': 1, 'NAG': 23}</DIV><DIV> Classifications: {'undetermined': 31}</DIV><DIV> Modifications used: {'DEL-O1': 1}</DIV><DIV> Link IDs: {None: 30, 'NAG-ASN': 1}</DIV><DIV> Unresolved non-hydrogen bonds: 30</DIV><DIV> Unresolved non-hydrogen angles: 60</DIV><DIV> Unresolved non-hydrogen chiralities: 30</DIV><DIV> Number of residues, atoms: 16, 16</DIV><DIV> Unusual residues: {' MG': 2, ' CA': 14}</DIV><DIV> Classifications: {'undetermined': 16}</DIV><DIV> Link IDs: {None: 15}</DIV><DIV> Number of residues, atoms: 4, 40</DIV><DIV> Unusual residues: {'IMD': 4}</DIV><DIV> Classifications: {'undetermined': 4}</DIV><DIV> Link IDs: {None: 3}</DIV><DIV> Number of atoms with unknown nonbonded energy type symbols: 1</DIV><DIV> "HD22 ASN A 15 "</DIV><DIV> Time building chain proxies: 32.54, per 1000 atoms: 0.70</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Sorry: Fatal problems interpreting PDB file:</DIV><DIV> Number of atoms with unknown nonbonded energy type symbols: 1</DIV><DIV> Please edit the PDB file to resolve the problems and/or supply a</DIV><DIV> CIF file with matching restraint definitions, along with</DIV><DIV> apply_cif_modification and apply_cif_link parameter definitions</DIV><DIV> if necessary (see phenix.refine documentation).</DIV><DIV> Also note that phenix.elbow is available to create restraint</DIV><DIV> definitions for unknown ligands.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Couldn't figure out what went wrong. Can somebody help me? Thanks.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Jianghai</DIV><DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>+++++++++++++++++++++++++++++++</DIV><DIV>Jianghai Zhu, Ph.D</DIV><DIV>CBR Institute for Biomedical Research</DIV><DIV>Department of Pathology</DIV><DIV>Harvard Medical School</DIV><DIV>200 Longwood Ave., Boston, MA 02115</DIV><DIV>Ph: 617-278-3211</DIV><DIV>Fx: 618-278-3232</DIV><DIV>+++++++++++++++++++++++++++++++</DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN></SPAN></SPAN></SPAN> </DIV><BR></DIV></BODY></HTML>