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The chemistry between Chip Kelly and Colin Kaepernick

Slowly but steadily, they’re finding ways to work together and it’s paying off

NFL: New Orleans Saints at San Francisco 49ers Kyle Terada-USA TODAY Sports

The San Francisco 49ers losing streak is setting records, even as they play tough against strong teams such as New England and Miami. This has obscured a key development: the dramatic improvement in Colin Kaepernick's play, recently noted by the likes of Scott Van Pelt ("Kaepernick played really, really well") and Ian Rapoport.

It's been a crazy 2016 for Kap: trade demands, “arm fatigue,” political controversy, and a slow recovery from three surgeries. General manager Trent Baalke renegotiated Kap's contract, removing his injury guarantee for next season but also giving the quarterback the right to opt-out this spring and go elsewhere.

Yet, underneath all the controversy, head coach Chip Kelly was working on Kap's comeback, getting him up to speed on the new system and publicly supporting his political stances (as did owner Jed York). Without making a big deal about it, Kelly and Kaepernick have both been modifying their approaches for an effective collaboration.

A lot of people have speculated about Kaepernick being perfect for Chip’s system, and frankly I was skeptical at the beginning of this year — mostly because it seemed like lazy thinking. Chip likes the zone read play, and Kap is mobile, and Marcus Mariota was mobile for Chip at Oregon, so bingo! Super Bowl!

Except that most of Chip’s quarterbacks have not been mobile, from Darron Thomas (who took Oregon to the National Championship Game against Auburn) to Nick Foles and Sam Bradford in Philadelphia. Mike Vick, the fastest QB in NFL history, may have been Chip’s least successful QB.

From the moment Chip was hired by the Eagles in 2013, pundits kept pontificating about how much he needs a mobile quarterback. But his biggest NFL success came with Foles, whose 40 yard dash time (5.12) was worse than most of his offensive line. Chip has made it clear that minimizing turnovers and executing the scheme by getting the ball out quickly to the open receiver is much more important to him than wheels.

Kap did not set the league on fire when he finally got his start in Week 6, but even in his first game he erred on the side of avoiding interceptions (as opposed to 2015, when he had 5 INTs to his 6 TDs). This is a huge deal for Chip. Kaepernick shares many of Mike Vick’s best traits, his foot speed and arm strength, while adding the prototypical QB height and low interception percentage that Vick lacked.

And he has been getting better every game. Ask Chip:

“He’s made a progression from game to game ... in everything; his pocket presence, his accuracy, understanding and knowledge of protections, in all that stuff.”

Against Miami, Kap even got past his maddening tendency to lose accuracy in the second half of games, this year.

On the flip side, Kelly has made a number of changes that suit his QB. For the first time in his career, Kelly is running a lot of pistol, the formation that made Kaepernick famous both at the University of Nevada and in San Francisco.

The Niners aren’t playing at the same tempo Chip’s Eagles did, either. They’re taking 24.45 seconds between plays, compared to 21.95 for the 2014 Birds. This takes pressure off of everyone in the offense, as well as making the scheme less predictable.

The way they are slowing down is also important. Against some — but not all — opponents, the team uses what Jennifer Lee Chan calls “the Meerkat offense.” (They didn’t use it against Miami, for example.) In the Meerkat, the team still lines up fast (to force the defense to declare its formation), then relaxes and looks to the sideline for a different play call. Oscar Aparicio of the Better Rivals podcast notes that this is common in college but rare in the NFL.

Kap has been criticized for a limited ability to read NFL defenses; the Meerkat approach (and less obvious variations) give Kelly a chance to audible to a different play or offer suggestions if the team lines up fast enough, since the helmet speaker stays on until 15 seconds are left in the snap count.

Kap has also taken advantage of deeper routes built into the plays that Kelly has been calling all year, but that Gabbert passed up for quick dump offs. Aparicio points to the “Mesh” concept, a Chip Kelly favorite that Oscar’s pod partner David Neumann charted way back in February.

Against Miami, Kap connected with Garrett Celek on the curl aspect of this route (#4 on the diagram). Aparicio told me that:

Gabbert would have hit one of the two crossing routes [2 and 3] and gotten the ball out quick. If you look at average time to throw, Gabbert is about .5 seconds faster, which doesn’t sound like a long time but is an eternity in the pocket.

Kap, though, lets the crossers clear, quickly checks left, then comes back then hits the TE (his 4th read) for a much longer gain. Celek fumbles, but hey, it’s the 49ers after all.

And after all that, Kaepernick’s ability to run actually has fit Chip’s scheme perfectly. They aren’t running many zone read plays — just enough to keep defenders guessing (and hesitating), which is the point. But Kaepernick has been masterful in punishing man coverage with scrambles of 10 to 30 yards, and finishing those runs with the perfect slides you might expect from a former baseball star.

He’s averaging 62 yards per game this year, compared to less than 33 during his Harbaugh-era heyday, and Kelly’s spread formations are a big reason why. On Tuesday, Kap told reporters:

‘There’s more opportunities for that, especially being in three-receiver sets most of the time, a lot more space out there. So, scramble lanes are bigger. When we do run zone-read, there’s more space there as well.”

The next step will be if and when defenses decide to shut down these runs by switching to zone coverage or assigning a linebacker to spy on Kaerpernick. Kap will have to punish such moves by by taking advantage of the thinner pass coverage, or defenses will have an easy method for shutting him down.

Scott Frost, the UCF coach who was Chip’s WR coach at Oregon and later the Duck’s OC, has been watching the Niners practice at his facility this week. He told Matt Maiocco:

“...looking at the numbers [Kaepernick] put up [against Miami] and his ability to run and throw the ball, I think it’s a good match for what coach Kelly’s offense asks for. I have no doubt, with some time, Chip will get those guys going.”

If he gets the chance. No one knows whether Jed York is ready to fire Baalke (Kap’s nemesis) or if Kaepernick would stay even if he did. Thursday, Kap put his San Jose house up for sale. He may have just decided that he’d prefer living in Noe Valley or Walnut Creek, but it certainly maximizes his bargaining power going into what is effectively free agency.

It’s hard to imagine a better quarterback that the Niners could get for next season, given the questionable draft class. Even with a shaky receiving corps currently led by three castoffs from other teams -- Kerley, Streater, and Harper -- Kaepernick is blossoming in Kelly’s system as the two slowly adapt to each other. If he gets better talent on the other end of his passes, there’s a lot of room for continued improvement.