。
It's not that he can't run fast.
Literal
He [topic-は] run [nominalizer-のが] fast-not [it's not the case that-わけではない].
A double-negative softening construction. ~わけではない 'it's not the case that, it's not that' denies a strong claim while leaving room for a more nuanced one ('he can run fast, just not consistently / there's another issue'). The inner structure 走るのが速い 'fast at running' uses the nominalizer の to turn 走る into a noun phrase, with 速い as the predicate. The outer 速くないわけではない wraps this claim in a hedged denial.