Set tolerance to 5 for non-topoaa modules

[sverhoeven]

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As discussed at i-VRESSE/haddock3-webapp#140 (comment) change the default of tolerance so users with easy expertise level have a successful run.

[amjjbonvin]

The tolerance for topoaa should remain 0 otherwise the entire workflow might fail / not do what is expected.
Also I would make consistent (i.e. same value, e.g. 5) for flexref, mdref and emref.

[sverhoeven]

All tolerance parameter have default of 5 except topoaa which stays at 0.