Kyle Shanahan, who helped to guide the Falcons to the Super Bowl, was named the head coach of the San Francisco 49ers on Monday evening, the team announced.

Shanahan, a contributor to the Falcons’ collapse against New England on Sunday with some late questionable pass-play selections when the team might have better served to run time from the clock, reportedly reached agreement on a six-year contract.

Under Shanahan’s watch, the Falcons led the NFL in scoring this season with 540 total points. He was named the league’s assistant coach of the year while helping quarterback Matt Ryan become the league’s most valuable player.

The offense also broke franchise records in total yards per game (415.8) and yards per play (6.7).

In San Francisco, Shanahan will join recently hired general manager John Lynch, who once played safety for Shanahan’s father, Mike, in Denver.

The Falcons are likely to look outside the organization for Shanahan’s replacement.

A team source said the Falcons will block Shanahan from hiring away one of Dan Quinn’s high-profile assistants, such as assistant head coach/wide receivers coach Raheem Morris, running backs coach Bobby Turner and offensive line coach Chris Morgan.

It is more likely Quinn would allow offensive assistants Mike McDaniel and Mike Lafleur accompany Shanahan. Lafleur, the Falcons quarterbacks coach, previously worked under Shanahan in Houston and Washington. Lafleur could be inclined to leave the organization because the Falcons are not likely to promote him as the offensive play-caller.

As for Shanahan’s replacement, Fox Sports reported last week that the Falcons would consider former Philadelphia, San Francisco and Oregon head coach Chip Kelly, who has evolved into a legitimate candidate.

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