Hi, Everybody, For refinement of ion in my structure, I used phenix.metal_coordination to produce a geometry restraints file elbow.edits. But after including the file in the phenix refinement, the refined pdb has clash between metal and one of the coordinated atoms, as shown in the attachment. I double checked elbow.edits file, the bond restraint between the two clashed atoms is clearly in the file and included in the refinement. Is this a bug in phenix or I did something wrong?
Thanks!
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