Why does AutoBuild bomb and say “Corrupt gradient calculations”?
If an atom is placed very near a special position then sometimes refinement will fail and an error message starting with “Corrupt gradient calculations” is printed out. If the starting PDB file has the atom near a special position, then the best thing to do is move it away from the special position. If AutoBuild builds a model that has this problem, then it may be easier to rerun the job, specifying “ignore_errors_in_subprocess=True” which should allow it to continue past this error (by simply ignoring that refinement step). You can also try setting correct_special_position_tolerance=0 (to turn off the check) or correct_special_position_tolerance=5 (to check over a wider range of distances from the special position; default=1).
