Hi all !!!<br><br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Thanks a lot to all of you for your suggestions...&nbsp; As many of you have guessed it is a problem of Bulk solvent correction. When i generated the pdb file using 0 cycles, the values are very much comparable with 
phenix.refine. Interestingly CNS-1.2 xtal_pdbsubmission gave the same result as phenix.refine. which once again confirms that its a bulk solvent correction problem. <br><br>As Huanwang suggested, pdb_extract could generate submission ready cif file.
<br><br>Once again thanks to all of you... But still i have problem with rmsd_bonds. I am using phenix.refine version 2007_05_29_2026 . Refmac gave rmsd_bonds 0.009 and rmsd_angles1.211 but phenix gave rmsd_bonds 0.006 &amp; rmsd_angles&nbsp; 
0.793.<br><br>regards<br>John<br>