Lynch, Shanahan hold 'positive' discussion with Kaepernick

Lynch, Shanahan hold 'positive' discussion with Kaepernick

General manager John Lynch confirmed during a radio interview that he and 49ers coach Kyle Shanahan met with quarterback Colin Kaepernick at his office Wednesday morning at the team headquarters in Santa Clara.

“I would characterize it as just a really positive discussion,” Lynch said during an appearance on KNBR, confirming a CSNBayArea.com report the sides met for the first time since Lynch and Shanahan were hired in their new roles.

Lynch said he and Shanahan have committed to being completely honest with Kaepernick, who can opt out of his contract to become an unrestricted free agent as early as next week.

Lynch did not divulge the topics of conversation. He said a commitment was also made to Kaepernick to not speak publicly about the specifics of their conversations.

“I do think that there are some things that are sacred,” Lynch said. “We did have a great discussion and I think Colin left excited and we left excited.

“And I think as Kyle and I believe, the evaluation process is still very much fluid. We’ve only been on the job a couple of weeks and I can tell you we both very much enjoyed being around Colin, and he seems like he’s in a real good place.”

Source: Kaepernick visits 49ers headquarters

Source: Kaepernick visits 49ers headquarters

Quarterback Colin Kaepernick, who faces an uncertain future with the 49ers, visited team headquarters in Santa Clara on Wednesday morning, according to a league source.

Kaepernick was likely there to meet with 49ers general manager John Lynch and coach Kyle Shanahan for the first time since they were hired to replace Trent Baalke and Chip Kelly.

On Feb. 9, Lynch said Kaepernick “reached out” to him shortly after he was hired as general manager. Lynch said he and Kaepernick planned on meeting in the near future.

Earlier this week, Lynch said he would have open and honest communication with Kaepernick about the club’s plan at the quarterback position.

“The one thing we will do very well with Kap is we’ll communicate,” Lynch said Tuesday on 95.7 The Game. “And I think that’s very important for both sides. Like everything else, that process is well in the works. We’ll continue to do that and we’ll be very up-front with him, in terms of what we’re thinking and we’ll want to know what he’s thinking, as well.”

Kaepernick and the 49ers agreed to a restructured contract in October. The sides tore up the final four years of Kaepernick’s contract and replaced it with a deal that enables Kaepernick to opt out to become an unrestricted free agent in March. Kaepernick's non-guaranteed scheduled pay is $14.9 million for the 2017 season.

Kaepernick does not currently have agent representation, according to the NFL Players Association.

He started 11 games last season after replacing Blaine Gabbert in the starting lineup and bounced back with a solid statistical season. Kaepernick threw 16 touchdown passes and just four interceptions for a passer rating of 90.7. He also rushed for 468 yards and a career-best 6.8-yards per carry.

Paraag Marathe: My job is to stay in my lane, help the coach and GM

Paraag Marathe: My job is to stay in my lane, help the coach and GM

SANTA CLARA – As team executives Jed York and Paraag Marathe traveled the country during the 49ers’ search to fill their head coach and general manager positions, there was plenty of criticism that followed them at every stop.

York, the CEO, has been held accountable by the local media and on social media, as he publicly welcomed, in recent seasons when the 49ers fell from the NFC Championship game to 8-8, 5-11 and 2-14 under three different head coaches.

A year ago, Marathe officially was replaced as team president and became the 49ers’ chief strategy officer and executive vice president of football operations. His duties with the football team have not changed.

In fact, York and Marathe roles with the organization took on a much-greater significance after the decision was made to fire coach Chip Kelly and general manager Trent Baalke.

The 49ers interviewed six head-coach candidates and 10 individuals who were considered for the general manager position.

Along the way, New England offensive coordinator Josh McDaniels bowed out, likely because his top choice to be his general manager partner, Nick Caserio, opted to remain as the Patriots’ chief of personnel. Then-Kansas City executive Chris Ballard declined an interview and another serious candidate, Green Bay’s Brian Gutekunst, removed his name from consideration to remain with the Packers on a new contract.

After more than a month, the 49ers finalized the hirings of general manager John Lynch and head coach Kyle Shanahan, who officially accepted the job the day after the Atlanta Falcons’ crushing defeat in Super Bowl 51.

“Nothing speaks better to the process than the quality of the two men that we hired,” Marathe told CSNBayArea.com. “I can’t tell you, just in the last two weeks even, how inspiring it’s been to be at work, just seeing these guys work together and how they’ve already transformed the building.”

Marathe joined the “49ers Insider Podcast” for a wide-ranging interview that touched on his personal life, as well as his responsibilities during his 16 years with the 49ers. The entire 43-minute podcast can be heard here.

Marathe has remained behind the scenes working for the 49ers mostly on contract and salary-cap matters. There has been mystery about his role while working with head coaches Steve Mariucci, Dennis Erickson, Mike Nolan, Mike Singletary, Jim Harbaugh, Jim Tomsula, Kelly and, now, Shanahan.

At one point during the search, Pro Football Talk, citing “thinking inside league circles,” described Marathe as being viewed as an “impediment” to the 49ers' ability to attract top candidates for their openings.

“It’s unfortunate that’s out there, if that’s out there,” Marathe said. “I won't say it’s something that doesn’t bother me at all. Of course, it stings. But I do know, I try to keep my head down and do a good job and support the people who are here. All I try to do is earn their respect and their trust on what I do. I feel like I’ve been able to do that. I think the individuals that you would talk to, if you talked to them, they’d probably tell you the same thing.

“I’m not trying to be anything other than what I am, which is a support to the coach and the GM.”

This offseason, former 49ers coach candidate Adam Gase told CSNBayArea.com one of the reasons he really wanted the head-coaching position in 2015 was because of his relationship with York and Marathe.

Arizona executive Terry McDonough, a finalist for the 49ers’ GM job, went out of his way to compliment Marathe shortly after he learned Lynch was hired.

“When I was done with that first interview, I said, ‘This is a guy I would want to partner with, along with Jed and whoever the new head coach might be,’” McDonough said of Marathe.

A source close to McDaniels reached out to CSNBayArea.com to dispel any notion that McDaniels’ decision to remain with the Patriots was any reflection on those running the 49ers’ search. McDaniels stated he was impressed with York, Marathe and Brian Hampton, the team’s director of football administration and analytics.

The roles of Marathe and the organization’s use of analytics have been a topic of intrigue for years. Marathe said his role is merely to support the individuals on the football side to provide the team with any kind of advantage.

“My job is to keep my head down, stay my lane, do my job and help the head coach and GM as much as I can," he said.

Marathe added, "Coach Harbaugh, as you know, was looking for every advantage. One thing why he has so much success, he’s always looking for every advantage he can get. He used to use that NASCAR example, if you can figure out how to go 1 mph faster.

"So anything that helped him, we would go through. We’d talk after other games in the league about, ‘Hey, that team, they had one minute left. How many plays do you think they could’ve gotten off in that time? I thought six. Well, I thought seven.’ We’d go through it and talk through it. So, yeah, they were receptive, and it was good.”

Marathe said Lynch and Shanahan have already asked for his opinions on the feasibility of some of the upcoming decisions the organization must make during the offseason.

“I come at it from a different perspective, which is from the salary cap and contract side of things and also just having seen a lot over the years, in terms of how deals get made or how trades happen,” Marathe said.

Without specifying a position of inquiry, such as quarterback, Marathe said he has already provided Lynch and Shanahan with reference material for what it has taken to acquire players in past NFL trades.

“Here are all the other examples of when this position was traded for, and what people gave up to trade,” Marathe said. “That would establish the range for us if we are curious about a player at that position. And then we have a discussion from there.”

As the 49ers prepare for free agency, Marathe said the personnel department and coaching staff will rank the players by position. Then, Marathe will come up with comparable players and provide a range of what he anticipates a player will command on the open market. That leads to more discussion about which players are seen as better fits when considering football and finances.

“It’s my job to keep our cap as flexible as possible,” Marathe said. “But from a football standpoint, making decisions on players, that’s those two guys . . . I’m not good at that. That’s what they’re really good at, and that’s who I take my direction from.”

The 49ers have approximately $80 million in salary cap space entering the offseason. But that does not necessarily mean the 49ers will be willing to pay above market value to attract any players.

“I think there are times when you want to be a little bit more aggressive, versus maybe not be as aggressive,” Marathe said.

“The beauty of how the salary cap works, you can roll over the room to future years. There won’t ever be a salary cap dollar that’s unspent. We’ll always spend it. It just may not be this month. It could be next month or it could be next year. We’ll spend ever dollar. It doesn’t change the values. The values are still driven by what the market dictates.”