Metrolink only runs in Southern California. The closest any Metrolink train gets to Nevada is San Bernardino, about 185 miles away!
If I had to guess, I'd say that scene was shot on the Antelope Valley Line, somewhere in Soledad Canyon around Agua Dolce Canyon.
And if I'm not mistaken, the engine is an EMD F59PH; the number appears to be 861. This particular engine was involved in an accident in 2000, a tractor-trailer got stuck on the tracks and was struck by the train. The truck's load crushed the cab and injured the engineer. She was still able to radio the next train which stopped just 60 feet from the wreck.