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Hi, I am working on inserting an FMN ligand into my molecule, but after running Refmac5 restrained refinement the bonding distances and angles are broken. I used PRODRG to create the ligand and used Coot to place the ligand into the correct location in the molecule, merged the ligand and molecule coordinates, and saved the file. Then I went to run restrained refinement on the merged coordinates using the "DRGMAC.LIB" file for the refmac library, the rest of the settings were set at the defaults. Initially when the electron density was not very well resolved the ligand was extremely distorted as observed in coot. After I had improved the quality of the electron density map the ligand got less distortion and only had a terminal phosphate group that had improper intramolecular bonding distances. Could someone please tell me how to treat the ligand as a more rigid body? I would like to run a round of restrained refinement without breaking the geometric restraints that should be imposed on my ligand. Thank you for your help, George Feldman