pdb validation summary letter gives a list of covalent bond angles greater than 6 times standard deviation for dna part of my molecule. I am wondering if someone can tell how to fix that. I used PHENIX to refine my molecule. I did not use any restraints for the dna part.
Do you mean hydrogen-bond restraints? -- At 2.9A the structure would probably be completely distorted if you didn't have any restraints. The 6 times standard deviation should not happen if we use the same restraints as the pdb is expecting. If you send me (off-list) the inputs and the pdb summary letter we'll take a closer look.
Also a few amino acids are listed for which phy and psy fall outside Ramachandran plot. I like to know what is the best way to fix these phy, psy angles.
A few outliers are expected. Did you look at them in coot? Ralf