I believe the answer is: "But no sooner had he made it clear to himself and his friends that she hardly had a good feature in her face, than he began to find it was rendered uncommonly intelligent by the beautiful expression of her dark "
From the lines, It is clear that Darcy initially perceived Elizabeth as ugly, which unusual among females that he usually see in his social standing.
Then, after interracting with ther, he realized that Elizabeth has astounding inner beauty and intellect which altered his perception toward her.
