I am refining a 2.6 A structure using both phenix.refine and refmac5.  Both programs give me similar R and Rfree values.  But the estimated coordinate errors are quite different.

From phenix.refine:

maximum likelihood estimate for coordinate error: 0.42 A

From refmac5:

estimated overall coordinate error:

ESU based on R value: 0.427 A

ESU based on Free R value: 0.293 A

ESU based on maximum likelihood: 0.239 A

I am wondering why they are different.

Jianghai