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If you solved by MR, this sounds like the description of a model biased map. Be aware that the density graph in coot needs to be properly scaled (cf. Dale’s response on absolute density scale). Extensions->Refine->Set density graph weight. If you see no parts that are discernably different from the model, with nothing to fix, bias is likely. The reasons can be manifold and cannot be determined from your description. Btw, 11% not allowed Rama is not good. Best, BR From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of ameya benz Sent: Friday, January 20, 2017 10:46 PM To: [log in to unmask] Subject: [ccp4bb] Rfactor and Rfree not coming below 0.4 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?