I am doing the molecular replacement to solve a membrane protein structure(transmembrane and soluble domain). The structure of the soluble domain is known, 200AAs. And there is a homology structure of transmembrane domain, 350AAs. I used the polyalanine model of the homologous model of transmembrane domain to do the first search.  I got a solution with TFZ 16. Then used the partial solution to do the second search with the soluble domain as the model.I also got a solution with TFZ about 15. The density map showed I got the right solution. And the simple rigid body refinement yielded a Rfactor/Rfree 0.29/0.32. Then I used the polyalanine model and the soluble domain as the starting model to do the phenix autobuild. But it seemed that Autobuild didn't replace the alanine with the real sequence AAs. I tried to set the rebuild in place to false but I still got the same result. The Autobuild even didn't change any amino aside reside from the starting model. I hope you could figure out the problem for me. Thank you in advance!

Best regards,

Jie