I am unable to refine three alternate conformations of a residue provided in PDB file prefixed before resname as A,B and C in Phenix dev-1370. When I make it two alternate conformations it runs OK.

Also I am not able to refine two loop confirmations, the refinement somehow puts both in the major 2Fo-Fc map peak and makes the almost same, even though the starting loop has different trace.Turning off siulated annealing or making temp. lower or just doing 1 cycle is not doing any good.

Any suggestions will be helpful.