ViTO: try out this tool. May be helpful. In the below link you will find download link, tutorial and many more things. Here is the link:

http://abcis.cbs.cnrs.fr/VITO/DOC/

All the best

Hi there,

We developed this web server specifically for protein structure refinement. The energy function is the same as used in the SUMMA server, with an additional step for stereochemistry correction. You can read about it in the 'About' page. It did pretty well in CASP.

http://csb.stanford.edu/kobamin

I would also look at the refinement category of CASP and check out other possible tools.

Best

Hi Siva, have you tried 3Drefine?

http://sysbio.rnet.missouri.edu/3Drefine/

Try ModRefiner http://zhanglab.ccmb.med.umich.edu/ModRefiner/

Hi Siva, you can use this server:

https://feig.bch.msu.edu/web/services/prefmd/