[ccp4bb] Rfactor and Rfree not coming below 0.4

[ameya benz]

I am trying to refine my data set collected at 1.9A. The density appears
clean and the fit is also good. In coot, all residues are in green zone in
density fit analysis. Also in Ramachandran plot 89% residues are in allowed
region. Few residues in loop region do not have good density for side
chains. My protein contains about 61% loops and remaining beta sheets , no
alpha helices (predicted from homology model). What could be done to
improve the Rfree and Rfactor?