The CASP organizers (who have seen the native solved structure of this protein) have told us:

"Regions showing significant deviation: 25-45, 146-156, 187-197."

These are the 3 regions that you'll need to work on, after you thread the Rosetta model using the Alignment Tool.

You'll probably want to freeze the rest of the protein while you initially refine these 3 regions.

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=139

Here is the sequence logo predicted by the SAM server:

H = helix
E = sheet
C = loop (or coil)

The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.

You'll notice that the secondary structure predictions in the regions you need to work on (residues 25-45, 146-156 & 187-197) don't tell you very much!

in the "good" parts?

the chain 25-45 runs right down the middle of the puzzle clashing with everything. Use the cut tool to move it outside.