lazy update of em2d states to make sure they aren't near thresholds. They probably could be modified to not use pdbs as input for some

git-svn-id: https://svn.salilab.org/imp/trunk@17331 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
bump the time limit on various em tests and move them out of subdirectories as it is kind of pointless

git-svn-id: https://svn.salilab.org/imp/trunk@17332 e91f8c7b-0e32-4433-a9ac-4502d39a4eab