[ccp4bb]: using minimize.inp in CNS

[Jimson Wong]

Hello all
I am trying to do positional refinement on a model of a protein & DNA complex using  minimize.inp from CNS.  The problem I am having is that after 2 cycles of automatic position refinement the Rfree would start to go up.  This happens almost everytime I try to use minimize.inp to do positional refinement.  Through labourous manual rebuilding and with the help of DM solvent flipping + NCS averaging map the Rfree and Rfactor are both 0.271 at the moment, with only 200 water molecules along with 680 residues.  I could add more water molecules to drive down the Rfree, but I really would l like to be able to use minimize.inp to refine the position of the molecules and so far I cannot do that for some reason.  I have made sure that there were no clashes between non-covalently linked atoms and that their distances are not closer than 2.2A.

Would any experienced CNS users know what it means when the Rfree starts to go up when one uses minimize.inp? 

Jimson