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[ccp4bb]: Refining Ions - Mn+2 Vs Mg+2...

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I am trying to incorporate ions into my model. 
We know from previous data that we have Mn+2 ions in our structure. Most of us 
in the lab who have tried to refine the ions as Mn+2 in CNS 
(as per CNS tutorial) find that the R-factor and R-free increase (as much as 
1% sometimes) and have continued to refine them as waters.
It's the same situation whether it's Mn+2 or Mn.
However, when I tried to refine all my Mn+2 as Mg+2 (by mistake), 
I found that the program handles it nicely and that there is a nice drop in 
R-factor and R-free.
So, I am currently refining Mn+2 as Mg+2. 
Is there any explanation to what might be going on ? Does something need to be 
done differently to refine them as Mn+2 ions.
Any words of wisdom/advice/suggestions/criticisms ?
Thanks very much,

Rajeswari Edayathumangalam
Dept. of Biochemistry & Molecular Biology
Colorado State University
Fort Collins, CO 80523 USA