I've updated the beta files again, they are in the same place. Aside from fixing a few bugs you've managed to still find, I've modified the algorithms as per some of our discussions from beta 4. (Let me know if the CPU is still being taken up during energy minimization like it was for some people before) It should now complete 250 generations in under a week on most machines but we'll have to try to find out. We may make it give up when it gets stuck even faster depending on how this goes. Also, AMD_is_logical's trick will no longer work..
Lastly we've changed it a bit in an attempt to keep helices from unfolding which we experience with beta 4. The fix applied may or may not work so if this fails we have a backup plan (for test # 6) which will almost certainly do the job. This is what was preventing us from getting too close to the correct structure (below 5A).
We intend to run beta 5 for about 1 week and then try the other method for keeping helices after that for another week or so. We are nearing the final release of the new approach however, just a few more tests to tweak the algorithm before we unleash it. Thanks again to all the beta testers for your input and help.
I am going to wipe the beta stats shortly, so please do not start running the new beta until you see the stats have been reset on the beta web site (or else you'll have to start over again anyways).