49ers remain ‘confident’ they will resolve holdout with star defensive end Nick Bosa

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SANTA CLARA, Calif. — The San Francisco 49ers held their first padded practice Monday without their most important defensive player and little indication that Nick Bosa will end his holdout and join the team soon.

General manager John Lynch said he remains in contact with Bosa’s agent Brian Ayrault as the two sides try to come to an agreement on a long-term deal that could make Bosa the richest defensive player in NFL history.

“I don’t like not having one of our best players here,” Lynch said. “We’ve got a really good track record that I’m proud of as a group of having our players in. But I also understand it and understand that we’re going to have to exhibit some patience and understand that ultimately this thing will work out. I’m very confident in that and we’re just going to have to have that right mix of urgency and patience.”

The 49ers have had a strong history of rewarding their own stars, giving lucrative extensions the past three summers to tight end George Kittle, linebacker Fred Warner and receiver Deebo Samuel.

Bosa’s contract should top all of those after he won Defensive Player of the Year in 2022 and has consistently been one of the top defensive ends in the league when healthy since being drafted second overall in 2019.

Bosa led the NFL with 18 1/2 sacks last season when he was named the league’s top defensive player and has 43 in 51 career games. He is currently under contract on the fifth-year option for $17.9 million this season.

Rams defensive tackle Aaron Donald is the only defensive player with a contract worth at least $30 million a year after signing a three-year, $95 million extension last offseason. Bosa could top that with his new deal.

By holding out of camp, Bosa is subject to fines of $40,000 a day and could be fined a game check for each exhibition game he misses. But because he’s still on a rookie deal, the 49ers have the option of waiving those fines, which Lynch said the team plans to do.

“That’s not going to get him in here,” Lynch said about a fine. “We’re both striving for the same thing, so we’ll focus on that.”

Bosa typically stays away from the team for the voluntary portion of the offseason and always reports in top shape each summer after months of workouts back home in Florida.

Lynch said he has no doubt Bosa is working to stay in shape but knows it will be important to get him back with enough time to make sure he is in top form to start the season.

“I don’t know what that right time period, we’ve talked a lot about it internally, but I think that’s important to give yourself the best chance to not only play at the highest level, but to stay healthy and get yourself primed and ready, calloused to play,” Lynch said.

Even with Bosa holding out, the Niners still have a deep defensive line group after adding Javon Hargrave as an interior rusher next to Arik Armstead as a free agent this offseason.

Javon Kinlaw, a 2020 first-round pick, is finally healthy this camp and showing flashes as a defensive tackle, and second-year edge rusher Drake Jackson bulked up after wearing down as a rookie.

Clelin Ferrell, Kerry Hyder Jr. and Austin Bryant have also gotten more opportunities early in camp but the Niners know they will need Bosa if the unit wants to be dominant once again.

“This is definitely a great group and we’re not even all the way together yet. We don’t have our guy here yet,” Armstead said. “We have a great group. We have to keep grinding, keep getting better and see where it takes us in the season. But we always have that responsibility. They invest up front and we know that a lot of games will be on our shoulders to go out there and win. We accept that challenge to get to work and go out there and play as hard we can.”

NOTES: There was one big scuffle on the first day with pads that led to a brief halt of practice. … LT Trent Williams didn’t take part in team drills for a second straight day. … LB Dre Greenlaw had an interception against Brock Purdy in team drills. … Backup QBs Trey Lance and Sam Darnold both had strong practices.

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