The R and Rfree after refining domain 1 are 39% and 44%. The density is good for the existing model but disconnected in the missing part of the structure in which I can hardly place any residue.
2) Is there any other method to improve the density of the missing structure? I tried several MR probes of the second barrel fixing the first one but all failed.
I would run ARP/wARP with the starting model being the domain you have already placed by molecular replacement, after refinement. Its the easiest and it coudl work with 2.2 A data.
If that fails, you can also try to run PIRATE before ARP/wARP to get a better map, possibly using as 'templates' the homologous structures, and start ARP/wARP from the PIRATE phases, possibly using them as restraints in refinement.
Or use the RESOLVE mode for molrep solutions and let it do the work. A.
