To find Cl its worth looking at anomalous maps, especially for home source 
data, since even with partial occupancy Cl is easily located. Also, for well 
ordered Cl ions, B-factor will often refine to lower value than coordinating 
atoms when its incorrectly refined as water. Finally, in a subset of cases 
chemical environment is what you'd expect for an anion, with main chain NH 
groups, Arg/Lys side chains, and or Ser/Thr OH groups coordinating the ion.

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