[phenixbb] fixing atoms

Green, Todd green at cbse.uab.edu
Wed Apr 7 13:47:32 PDT 2010

Hello all,

I am refining a structure which contains several uranyl sites. I know the atoms should be there based on peaks in anomalous difference fourier maps, peak heights are greater than 10 sigma. Likewise we have solved the apo-structure before with the same heavy atoms. If I perform simulated annealing, the heteroatoms get pushed as far as 8 angstroms away. The Asp(s) and Glu residues that coordinate the uranyl ion then just move into the region of the map where the U has vacated. The resulting fofc difference map has a huge peak(>11 sigma) where the U should be. I noticed that if I inflate the starting b-factor for the U, the positions will stay put(relatively). What is the best thing to do here? Can I fix their positions, so that this does not happen? How do I do it? I found a post in the archives that says i can use: refine.sites.individual="not element U". Will this work for the SA? I know it works during refinement. Anyway, the data is to 3 angstrom. Here is the result from some SA runs:

following simulated annealing:
no u, starting b-factor for all atoms 20:
Final R-work = 0.2502, R-free = 0.2899
with u starting b-factor 20:
Final R-work = 0.2771, R-free = 0.3094
with u inflated starting b-factor for U:
Final R-work = 0.2682, R-free = 0.2983
After further manual rebuilding and TLS refinement(with u):
Final R-work = 0.2478, R-free = 0.2849

Also, during further refinement(if I reposition the U(s)), some of the U(s) still get displaced and the b-factors get extremely high, some as high as 500. I think this is due to them being displaced though. Other datasets which I have refined with phenix don't exhibit this behavior. Could it have something to do with NCS restraints on the protein?

any suggests?

Thanks in advance-
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