[phenixbb] a question related to autobuild

Dear All, Today I have tried to use phenix autobuild, I find in the built model, some residues in the PDB has been changed to simple residues. Will you please introduce to me the theory behind this? In addition, what will be the difference between Rebuild-in-place "auto", "true"and "false"? Especially the difference between Rebuild-in-place "true"and "false"? Cheers, Dialing