Xinghua: A couple of questions you might ask before reverting to drastic measures: Can you exclude a covalent bond to the protein? How confident are you about the fit, orientation and nature of the ligand? Do you see the same phenomenon in a different dataset, i.e. is it reproducible? It is better to look for an explanation of your experimental findings than to tweak/restrain the refinement to conform to your expectations. At this resolution the occupancy will be tightly coupled to B-factors. You could try and refine an overall occupancy for the ligand. What makes you believe that you have partial occupancy? Residual fofc density? Carsten From: [email protected] [mailto:[email protected]] On Behalf Of [email protected] Sent: Monday, August 10, 2015 10:43 PM To: phenixbb Subject: [phenixbb] ligand refinement Hi everyone, I am refining a structure of protein/ligand complex (2.75 Å) almost to the last stage. However, I found that some atoms of the ligand is too close to the protein (1.2 or 1.3 Å) after refinement. How should I avoid this? Should I use the "nonbonded_distance_cutoff" parameter? What the value should be set to? Another question is that at this resolution is it possible for me to refine the occupancy? Any suggestion is appreciated. Best Xinghua ________________________________ Xinghua Qin Ph.D Department of Physiology The Fourth Military Medical University 169# Changlexi Road Xi'an 710032, China Tel. 86-29-84772779 E-mail: [email protected]mailto:[email protected]