[phenixbb] Questions about molecular replacement.

Yuan Cheng ycheng at email.unc.edu
Thu Aug 27 07:54:46 PDT 2009

    I am working on solving a protein structure using phenix.automr. 
There is likely four monomers in a ASU based on phenix.xtriage.I am 
using a search model with 30% identity with my protein. After finding 
three monomers in a ASU, the LLG is 1740 and R factor is 56%. After 
finding the fourth monomer, the LLG increased to 2080,but the R factor 
also increased to 58%. I have several question here:
    1) how much should LLG and R factor be if the model from molecular 
replacement is correct? I guess the answer might not be a exact number. 
But I am still wondering what should be the correct range.
    2) Whether R factor and LLG should always be positively correlated?

    I used phenix.refine to refine the model with 3 monomers and the 
model with 4 monomers in a ASU. The Rwork and Rfree are similar for 
these two models,47% and 53% respectively. I think that one more monomer 
should either improve or ruin the model.I don't quite understand why one 
extra monomer doesn't matter too much here. In addition, do you think it 
is worthy to keep doing model building and refinement in consideration 
such high R factors.
   All you suggestions and opinions will be greatly appreciated!


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