SANTA CLARA, California (AP) — The San Francisco 49ers have had plenty of problems on offense the first five weeks, leading to coach Chip Kelly's decision to bench quarterback Blaine Gabbert for Colin Kaepernick.

Perhaps none of the issues was as glaring as the inability to get the ball downfield.

Gabbert completed just two passes all season that traveled at least 21 yards downfield and his 37.3 rating on deep throws was second worst among all quarterbacks, according to Sportradar.

He badly missed open receivers on deep passes numerous times, including a key interception two weeks ago against Dallas and being wildly off-target on deep throws to Rod Streater and Torrey Smith in last week's loss to Arizona.

With the Niners providing little threat deep, defenses have been able to crowd the line, which has hindered San Francisco's running game and limited opportunities for big runs after the catch.

Deep throws were a big part of Kelly's offense in his three years in Philadelphia when the Eagles were tied for fifth in the NFL with 69 completions on those passes and ranked second in touchdowns with 26, according to Sportradar.

Kaepernick, with his strong arm, had more success on those throws even as he struggled in other aspects last season when he lost his starting job to Gabbert midway through the year. He completed 10 of 26 deep passes for 451 yards, three touchdowns and two interceptions.

The Niners (1-4) hope Kaepernick can hit some of those throws this week against Buffalo when he makes his first start since Nov. 1, 2015.

"I think there's just small things here and there that we need to clean up, we need to correct as a whole," he said. "Hopefully those are things that we progress on this week and it shows Sunday and helps us get a win."

Before Kaepernick could do that, he signed a restructured two-year contract Wednesday. The new deal replaces the previous deal that ran through 2020, takes the Niners off the hook for a $14.5 million injury guarantee for 2017 and gives Kaepernick the right to void the second year and become a free agent in March.

The contract also converts Kaepernick's $2 million roster bonuses this year into guarantees and he can earn an additional $1 million based on meeting certain playing time thresholds, a person familiar with the deal said on condition of anonymity because details were not made public.

ESPN, which first reported the contract, said the Niners will not be able to use the franchise tag on Kaepernick if he opts for free agency.

This is the second time Kaepernick has taken over as starter in San Francisco midway through a season. In 2012, he replaced a concussed Alex Smith and led San Francisco to the Super Bowl where the 49ers lost 34-31 to Baltimore.

With his breakaway speed and cannon arm, Kaepernick looked like the poster child for the new breed of NFL quarterbacks. He led the Niners to road playoff wins in Green Bay and Carolina after the 2013 season before his late interception in the end zone ended a comeback attempt in the NFC title game in Seattle.

He took a step back the following year and then plummeted last year when he threw for only six touchdowns and had five interceptions in eight starts before losing his job.