[phenixbb] fixing geometry for deposition

Raja Dey rdey at usc.edu
Tue Nov 17 11:37:47 PST 2009

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...

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