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Dear CCP4 users, I am working on a protein from a hyperthermophilic archaeon. I have collected mutliple X-Ray datasets, both from home source and synchrotron and always found a clear density for tetrahedral geometry, co-ordinated by two histidines and one lysine. I tried fitting phosphate there, but its geometry always gets distorted after each refinement cycle (Refmac 5.8.0073). Also I found some short contacts between the coordinated residues and phosphate which were very difficult to remove. I am attaching a figure with the density and phosphate. Kindly suggest - 1. if this may be a possible modification of any of the associated residues, and the code of the modified residue to be used. 2. If the ligand requires separate restraints during refinement, I am using the "restrained refinement" option available at the top of the GUI for refmac. Thanking you,yours sincerely,Ansuman Biswas,PhD student,Dept. of Physics,IISc