I am refining a structure that showed two positive peaks larger than 8 sigma. I assigned them as Mg ions, since I have them in the crystallization condition and also because it make sense, according to where they are located. 

However when I refine there's still all this green blob around the already properly placed Mg ions. I don't know why, they don't show large thermal factors or anything suspicious...

I'm refining individual sites, individual adps, and TLS groups. 

The resolution I am talking about is 2.5 A. 

Any thoughts on this?

Thank you very much

Best wishes, 

Almudena
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