Hi!
For this case the simplest way is probably to run a HF calculation with symm=off in a small AO basis set and to use the resulting SCFDENSITY file as a better initial guess for the HF in the final AO basis, performed with symm=on. This can be done with the scfiguess=restart option.
As long as the system size does not get much larger you can ignore the symmetry to avoid such complications.
Bests,
Peter
