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.
For example, the Valine at residue 7 is highly predicted to be part of a helix. However, the Valines at residues 61, 73 & 86 are predicted to be part of a sheet!
The above predictions are already on the starting model (based on the horizontal lines in the above figure).
The structure prediction starts with QEIPAG and ends with QIRIDKINE. However, the first 3 segments and last 4 segments have been removed from the puzzle. This means the structure prediction is off by 3. I'm sure there will be recipes posted shortly that will reapply the correct predictions. Thanks to drumpeter and frood for noticing.
Thank you for catching this mistake!
I will repost the puzzle once the new SS predictions come back. You will be able to load in manually saves from this puzzle.
More details here: http://fold.it/portal/node/994549
Sorry for this mistake!