This reverts commit e93d9378.

This reverts commit 156499e3.

This reverts commit 55cd0493.

Probability values of hits in HHblits searches using tag v3.2.0 and
the current master branch differ. We therefore only check whether we
find the expected number of hits and check their score in the hope
that the HHblits scores stay consistent in future HHblits releases.

Setting up secondary annotation using PSIPRED is not part of the
basic HHblits installation. Furthermore, HHblits commits
2b0283251f0e05eaf7661b9570b9d01485c5e902
eb88d8ab74e23ecf337756199652b06044ae66aa
c1d86b1953b2f30996e6720273e86696b4c36d62
contain a bugfix which is not available in tag v.3.2.0 but change
the output for the secondary structure annotation.