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Brian Hoyer already comfortable again in Kyle Shanahan's offense

SANTA CLARA, Calif. -- For most members of the San Francisco 49ers offense, last week's start of organized team activities meant the first chance to apply what they've learned about coach Kyle Shanahan's system on the football field.

For quarterback Brian Hoyer, the three workouts were closer to a refresher course than a new beginning.

"It’s definitely easier for me to call the plays this time around," Hoyer said. "I remember last time kind of having to think about it, whereas now I find myself knowing that when Kyle starts to call a play I can kind of put it together. Just hearing it the second time around has helped, and knowing the plays, there are a lot of words; I think calling the play is half the battle, and it’s something I really don’t think about anymore. It comes naturally to me."

As with any coaching and scheme change around the league, there's always going to be an inherent learning curve. Depending on the difficulty of that system, it can be a long, excruciating process. But when the Niners entered free agency looking to make drastic changes to their quarterback depth chart, they targeted Hoyer in large part because of his familiarity with Shanahan's offense.

Hoyer and Shanahan previously worked together with the Cleveland Browns in 2014 when Shanahan was an offensive coordinator. Hoyer started 13 games that season, throwing for 3,326 yards with 12 touchdowns and 13 interceptions for a passer rating of 76.5. That season featured a strong start in which Hoyer led the Browns to a 6-3 record in their first nine games while compiling a 90.4 passer rating.

The Browns and Hoyer fizzled out from there, though, as Hoyer struggled in his next four starts (a 53.1 passer rating) and Cleveland turned to Johnny Manziel. As it turned out, that season would be the last for both Hoyer and Shanahan in Cleveland. Hoyer went on to spend a season in Houston and another in Chicago while Shanahan spent the past two years in Atlanta.

Even as Hoyer experienced some success in leading the Texans to the playoffs and a handful of solid starts last year for the Bears, he often found himself wondering what would happen if he got a chance to fully soak up and then play in Shanahan's offense. Now that he's getting that chance, his enthusiasm to be back on the field is easy to see.

"It’s always great when you get to play football," Hoyer said. "We do so many weeks of Phase 2 that we’re just chomping at the bit to get out there and play, so it’s great. I think for us we are in the beginning stages of building the foundation for this offense. We have got to start from the bottom, learn all the concepts and then, having played for Kyle before, things were very week to week on who we’re playing, but you have got to know the base offense before you can get there.

"I think that’s where we are right now, trying to get timing down with everybody, throwing to different receivers, different plays, just learning that base offense and then hopefully as these next (seven) practices go we keep getting better and putting more in and things start to slow down a little bit."

Other than Shanahan, there might not be a person in the organization who will play a more integral role in that development than Hoyer. Although Hoyer is two years removed from working with his head coach, he was able to jump back into some of his old notes and get back to speaking the language of Shanahan's offense before the offseason program even started.

Hoyer's comfort in the system was apparent in the only practice open to media last week when he was in firm command in the huddle and was unafraid to offer guidance to his teammates. For Hoyer, basic tenets of Shanahan's offense, such as strong sells of play action fake and throwing on the move on rollouts, require nothing more than just knocking off a little bit of rust. In fact, I only counted two balls thrown by Hoyer hitting the ground during team drills, both of which were deep balls.

That's not to say Hoyer doesn't have more to learn and gain in the coming weeks and months before the season starts. One of the primary tasks will involve getting on the same page in terms of timing with his pass catchers, something that has nothing to do with X's and O's and only comes as a product of time.

"For me, thankfully, this is my second go around, but everybody else this is really their first except a few other guys," Hoyer said. "Even for me, being that this is my second time, there’s still things I’m always learning about the offense. Why Kyle is calling the play the way that he is, who he is trying to affect on the defense, and I think when we all get to that point and see it the way he sees it, the better it will be for us."