Dear all, I am working on my molecule, but after running
Refmac5 restrained refinement the bonding distances and angles are broken. I used Phenix 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 cif file provided from the phenix to the refmac library,the rest of the settings were set at the defaults. During fitting the model in the 2Fo-Fc map of the ligand there were no issue, but it fitted well and after refinement of the same, the bond breaks and distorted as observed in coot. The resolution is 1.6 Ang. phosphate linkage bond is broken. What could be the best possible reason for this and what can be solution for this ? Could you please suggest what should I do for a complete model for the ligand ? I would like to run a round of restrained refinement without breaking any geometric restraints that should be imposed on my ligand. Thank you for your help in advance, Jeorge
