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[ccp4bb]: Geometry problems in Refmac

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I'm trying to refine a liganded protein structure in 
Refmac, but the geometry of the ligand keeps going to pot. 
 (In fact, the distortions of the ligand geometry are so 
extreme as to be visible by eye.)  I tried to use the 
ligand sketcher to make a new monomer library entry for 
the ligand, but if anything the distortions have gotten 
worse.  Does anyone have any idea what I might be doing 

-Ben Sandler