You didn’t tell us where your model came from but 10 cycles of TLS and 10 cycles of restrained refinement is not enough for a refinement to converge if you just picked your test set. Try resetting your B-factor and doing 30-40 cycles refinement in REFMAC.
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of wtempel
Sent: Tuesday, June 30, 2015 18:59
To: [log in to unmask]
Subject: [ccp4bb] Rfree below Rwork
my question concerns refinement of a structure with 6-fold NCS (local automatic restraints in REFMAC) against 2.8 A data. The size of my free set is 1172 selected in thin resolution shells (SFTOOLS) and corresponding to 4.3 % of reflections.
A refmac run of 10 cycles of TLS and 10 cycles of CGMAT starts out at Rfree/Rcryst 0.271/0.272. After the 10th TLS cycle I have 0.227/0.224. Yes, Rfree < Rcryst. At the end of CGMAT I have 0.2072/0.2071.
I understand that NCS stresses the independence assumption of the free set. Am I correct in believing that Rfree *may* be smaller than Rcryst even in the absence of a major mistake? My hope is that the combined wisdom of ccp4bb followers can point out my possible mistake, suggest tests that I may perform to avoid them and, possibly, arguments in defense of a crystallographic model with Rfree < Rcryst.