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This is the test for jd2 (the old newJD, the second job distributor for mini).  The integration test is not intended for any computation, it tests that the newJD correctly determines what outputs to make and puts them in the right place.  The actual PDB files themselves and their atom placements don't much matter, what matters is which files get made.  FILELIST in this directory describes the list.  Also look for proper "extra scores" at the bottom of the PDBs with greek letters and gibberish numbers (to test the extra scores output functions.)  

The test DELIBERATELY ends with an error state.  This is to test that the jd2 properly notices a bad input signal and cancels those jobs accordingly.  

Also note that some outputs are missing from the sequence - this is on purpose to test the bad result signals.  