Re: [phenixbb] Geometry problem with the ligand

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.