Just like Mini-CASP 17 (http://www.youtube.com/watch?v=j5JlXdnrQQs), the native for CASP9 Puzzle 5 is being solved using NMR.

The template we are using for CASP9 Puzzle 5 is 2kru (http://www.rcsb.org/pdb/explore/images.do?structureId=2KRU), which was the native you were trying to reach in Mini-CASP 15.

You can see in this youtube clip that 2kru's tails are floppy (just like Mini-CASP 17). This is often the case with NMR structures and when grading our predictions the CASP9 assessors will ignore these flopping regions.

We don't know exactly how much (if any) of the ends of CASP9 Puzzle 5 will be floppy and ungraded, so we are not trimming them in the puzzle. You should keep in mind, however, that it is very likely that the ends will not be solved and therefore will not be counted in the CASP9 assessments.

So don't waste too much time on the termini with this puzzle, focus on the short loops!

For once, the alignment should really be good from the start and you shouldn't have to move the starting alignment (threading should also be easier with this one), but feel free to experiment!