[phenixbb] Geometry problem with the ligand

[Pavel Afonine]

Hi John,

> I am working with a 3.0 A dataset, which binds with cAMP. I have 
> refined the dataset with phenix (TLS+Group_adp) and followed by weight 
> optimization. 

 - Did you refine the individual coordinates as well (it is not clear  
from what you are saying above)?
The refinement of TLS and group B-factors only ("TLS+Group_adp") will 
obviously not change the coordinates.

- Also, can you have a look at .geo file to find out how badly the 
actual bond and angle values deviate from the ideal targets for that 
particular ligand? If the deviations are not bad, then it is very likely 
that Molprobity "thinks" of something different when it "looks" at your 
ligand.

Pavel.