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Hi Dave, I sounds to me like you are worried about 2 separate things here. A: Am I affecting the geometry of the coordination sites with a restraint file that is innacurate? B:Are my electron density maps biased, and what I am seeing is not really there? AFAIU, if you have a restraint file that is innacurate, lets say it is defining the metal/ ligand angles to be those of a tetrahedron, that would influence the position of your atoms after refinement as the program will try to "obey" the restraint file. The electron density maps, however do not directly take into account your restraints file. With that being said, model bias can be a problem, yes. This is dependent on many factors, and if you have obtained your phases through a molecular replacement solution rather than experimentally (MAD, SAD, etc..) your maps will be particularly susceptible to bias. And if your dealing with a low resolution data set this can become even more of a problem (you dont mention your resolution). If you are working with a 1.2A data set, I would not lose sleep over it. People have spent many hours of thinking and programming to develop ways of eliminating model bias and many programs can calculate electron density maps in a way that your bias is minimized. Always check your difference map (mFo-Dfc), you can calculate omit maps, averaged kick maps, and in the case of metals even an anomalous maps sometimes. All of these would help you put your mind at ease. Hope this helps