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Dear all, I'm am trying to refine an isopeptide link in diubiquitin between a Lys side chain and a Gly 76 C-termini. The link has reasonable geometry (planar amide bond) prior to refinement with refmac 5.2.0019. After refinement, the peptide link is no longer planar. Any ideas how to enforce planarity of the link? Many thanks for any suggestions-- Sarah refmac: MAKE LINK Y link statement (pdb header): LINK NZ LYS X 48 C GLY Y 76 TRANS CIF file for the link (generated with refmac): global_ _lib_name mon_lib _lib_version 4.11 _lib_update 15/04/05 # # --- LIST OF LINKS --- # data_link_list loop_ _chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 _chem_link.name TRANS1 LYS . . GLY . . bond_LYS-NZ_=_GLY-C # ------------------------------------------------------ # # --- DESCRIPTION OF LINKS --- # data_link_TRANS1 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd TRANS1 1 NZ 2 C . 1.260 0.020 # ------------------------------------------------------ ------------------------------------------------------------------------ ----------- Sarah G. Hymowitz Department of Protein Engineering Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080 E-mail: [log in to unmask] Tel: (650) 225 7819 FAX: (650) 225 3734