Hi Dmitry,
Are you sure the ab initio is a correct solution? To me it looks a little like one of the failure modes we often see, described here: "side view prior" for ab initio?
It doesn’t seem to have many high resolution features - can you clearly see secondary structure in the ab initio, and what settings are you using for ab initio? Are clear secondary structure features present in the 2D classes?
Cheers
Oli