A standard method override allows HMRC, or the Charity, to impose a special method. It applies, in addition to other conditions, if the overhead recovery rate gives a substantially different result from that based on the use or intended use of the purchases received in making taxable supplies. “Substantial” means more than £50,000 (or more than 50 per cent of overhead input tax if over £25,000).

For further information see Chapter 5 of HMRC VAT Notice 706: Partial Exemption.