Hi Sudipta,
Your R factors don't look horribly high for an initial build and refinement at 3.2A, assuming you still need to substantially improve your structure ... if your structure is basically complete that's obviously a different matter. First of all I would look at your scaling output to check for twinning (aimless and pointless give very good indications) ... or simply re-run your last refmac job with twin refinement "on" and check the log file to see if the programme finds any twinning.
Regards,
Tony