Molecular replacement with multiple different models

Advances in molecular-replacement procedures: theREVANpipeline

TheREVANpipeline aiming at the solution of protein structuresviamolecular replacement (MR) has been assembled. It is the successor toREVA, a pipeline that is particularly efficient when the sequence identity (SI) between the target and the model is greater than 0.30. TheREVANandREVAprocedures coincide when the SI is >0.30, but differ substantially in worse conditions. To treat these cases,REVANcombines a variety of programs and algorithms (REMO09,REFMAC,DM,DSR,VLD,free lunch,Coot,Buccaneerandphenix.autobuild). The MR model, suitably rotated and positioned, is first refined by a standardREFMACrefinement procedure, and the corresponding electron density is then submitted to cycles ofDM–VLD–REFMAC. The nextREFMACapplications exploit the better electron densities obtained at the end of theVLD–EDM sections (a procedure called vector refinement). In order to make the model more similar to the target, the model is submitted to mutations, in whichCootplays a basic role, and it is then cyclically resubmitted toREFMAC–EDM–VLDcycles. The phases thus obtained are submitted tofree lunchand allow most of the test structures studied by DiMaioet al.[(2011),Nature (London),473, 540–543] to be solved without using energy-guided programs.