Hi Mario
Maintaining the secondary structure of your protein when refining against weak
data can be really challenging.
There are some options, but in the end you might have to accept a fairly large
number of Ramachandran plot outliers.
Try phenix.refine with the keyword
Remember that phi-psi angels are excellent for validation purposes,
but only when they are unrestrained, so if you restrain them you
lose this option.
The above is a very important point!
Having now said that, restraining alpha-helices hydrogen bonding, and
beta-sheet cross-strand
