SANTA CLARA, Calif. (AP) — Brandon Aiyuk’s long contract dispute with San Francisco came to an end Thursday when the star receiver agreed on a four-year contract to stay with the 49ers.

A person familiar with the deal says the sides came to the agreement Thursday after Aiyuk missed his second straight practice despite being cleared by team doctors to participate. The person spoke on condition of anonymity because the deal hadn’t been announced.

NFL Network first reported the agreement that will pay Aiyuk $120 million over four years with $76 million in guarantees.

Aiyuk had refused to practice all offseason as part of a contract “hold in” with the team, saying he had a back injury. Coach Kyle Shanahan and general manager John Lynch said he was cleared by doctors before Wednesday’s practice but Aiyuk still didn’t join, risking possible fines.

Aiyuk had requested a trade earlier in the summer but no team that Aiyuk wanted to go to was willing to give the Niners what they wanted and pay Aiyuk the salary he sought.

But that was all settled when Aiyuk and the 49ers came to an agreement 11 days before the season opener against the New York Jets on Sept. 9.

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That leaves San Francisco with one remaining prominent hold out with All-Pro left tackle Trent Williams still staying away from the team as he seeks a new deal.

Aiyuk had been set to play on the fifth-year option worth about $14.1 million this season but now becomes the latest receiver to cash in with a long-term deal.

Eleven receivers before Aiyuk had signed contracts worth at least $70 million already this offseason, with Justin Jefferson’s four-year, $140 million extension with Minnesota setting the top of the market. Aiyuk is the sixth receiver with an average annual contract of at least $30 million.

Aiyuk had been a key part of San Francisco’s offense last season as he formed a great connection with quarterback Brock Purdy. Aiyuk had 75 catches and a career-high 1,375 yards last season with seven touchdowns as he earned second-team All-Pro honors.

He put up those numbers on an offense that passed at the second-lowest rate in the NFL last season and had several other star playmakers like Deebo Samuel, George Kittle and All-Pro running back Christian McCaffrey.

Aiyuk’s 12.8 average yards receiving per target were the highest mark for any player with at least 75 targets in a season since Jordy Nelson averaged 13.2 for Green Bay in 2011.

Purdy’s 120.5 passer rating when targeting Aiyuk ranks the best of any QB-pass catcher combination with at least 125 attempts over the past two seasons, according to Sportradar.

Aiyuk has 269 catches for 3,931 yards and 25 TDs in four seasons since being drafted 25th overall in 2020 but has taken off since Purdy became quarterback, with eight of his 11 100-yard receiving games in his career coming with Purdy as starter.

The 36-year-old Williams is owed $20.05 million this season under the six-year, $138.1 million deal he signed in 2021.

Williams’ average annual value of just over $23 million has been surpassed by five offensive linemen since he became the richest player at the position when he signed the deal. Tristan Wirfs, Penei Sewell and Christian Darrisaw all got deals this offseason worth at least $26 million a year.

“Everyone knows Trent is a captain, a Hall of Famer, the big dog of the team,” cornerback Charvarius Ward said. “Damn near everybody is scared of him. We miss him a little bit, but like I said, somebody has to step up to be a captain to replace what’s missing with those guys not here.”

NOTES: S Talanoa Hufanga took part in individual drills as he works his way back from an ACL injury last November. He is expected to be back playing some time in September. ... The 49ers made two additions to their practice squad, signing WR Terrace Marshall Jr. after the 2021 second-round pick was cut by Carolina and bringing back RB Ke’Shawn Vaughn, who was cut by San Francisco on Tuesday. The Niners needed extra bodies at running back with Christian McCaffrey (calf) and Isaac Guerendo (groin) dealing with injuries. ... Among the other 49ers players not participating in the open portion of practice were DL Yetur Gross-Matos (knee), WR Jauan Jennings (oblique), LB Dee Winters and G Aaron Banks (pinky).

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