Dear Friends, 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. 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. Final refined parameters are REMARK Start: r_work = 0.3576 r_free = 0.3345 bonds = 0.009 angles = 1.344 REMARK Final: r_work = 0.2517 r_free = 0.2845 bonds = 0.008 angles = 1.209 at 2.9A resolution Thanking you in advances for all your suggestions... Regards... Raja