Hi Rajesh,

model bias, in a nutshell, is when you see something in the map that is conveyed by the model (that may not be correct) and not by the data.

I am not sure how one can get an idea about model bias looking at triplet of numbers: Rwork, Rfree and Molprobity percentile. By the way, your Rwork/Rfree look pretty good (given the 2.7A resolution).

Anyway, if everything else: bunch of model and data statistics, local and global model-to-data quality fit all look well (*), and you are still suspecting something isn't right, then you can invest from a few days to a week or so into computing an "Iterative Build OMIT map" as described here:

Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, N. W. Moriarty, P. D. Adams, R. J. Read, P. H. Zwart and L.-W. Hung Acta Cryst. D64, 515-524 (2008)

This map is supposed to be bias free.

Pavel

(*) For more details see here:
http://www.phenix-online.org/presentations/latest/pavel_validation.pdf


I have a structure 2.74 A structure with R/freeR 22.7/27.9%. But the molprobity score is 50th percentile.
If I fix the outliers they wouldn't go away and molprobity score remains same or get worst. 
This structure was solved by molecular replacement using a bacterial protein with 38% identity.
I am wondering if there is an model bias? I have not identified particular region in model for bias.

My questions are: Am I right in thinking if there is model bias based on above info?
I  added my .pdb and .mtz and do SA-composit omit map. This is running from morning and I have feeling that I will get results after thanksgiving. Is this the correct way of doing a omit map for the purpose I mentioned? 
I saw lot of discussions on omit map but couldn't grasp everything and I am sure same questions might have been asked before.
I have couple of classical papers next to me but I need help.  I would appreciate if you could help me out either suggesting me how and what to do or pointing to previous thread over the this BB.