It is possible that your PO4 has its atoms labeled with the wrong chirality. Yes, I know that PO4 is not chiral when you ignore hydrogen atoms and single/double bonds but adding labels creates an unnatural chriality. Try your refinement again after switching the labels on two oxygen atoms.
Dale Tronrud On 6/22/2015 7:48 AM, ansuman biswas wrote: > 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 >
