Alex Boone is expected to report to the San Francisco 49ers by the end of Monday to end his holdout.

Boone will sign a new two-year deal to replace his old contract with an increase in salary and incentives.

The 49ers also will not be able to use their franchise tag on Boone once the new contract has expired, sources said.

Boone originally was scheduled to make up to $4 million over the next two seasons under his previous deal, sources said.

Ray McDonald has been arrested on domestic violence charges.

San Jose police Sgt. Heather Randol confirmed that McDonald, 29, was taken into custody early Sunday after officers responded to a call at 2:48 a.m. PT.

McDonald ranks second among San Francisco 49ers' defensive ends in sacks, snaps and tackles since 2011.

Under the league's newly implemented personal conduct policy, a first domestic-violence offense will result in a six-game ban and a second in a lifetime ban from the NFL.

Alson Smith has been suspended for nine games by the NFL.

Smith will be allowed to remain around the San Francisco 49ers' facility during the suspension, which was very important to the franchise.

Smith already appealed the suspension and lost, making it final.

Smith's suspension is for four games for a violation of substance abuse policy and five games for personal-conduct.

Stevie Johnson has caught just two balls for 11 yards this preseason as he's struggled to develop chemistry with Colin Kaepernick.

Johnson was acquired by the San Francisco 49ers in a draft day trade from the Buffalo Bills.

"There are times that he's going to make a move on a DB, and you have to be ready because he's also making a move that you have to see," Kaepernick said, per The Sacramento Bee. "So I think that's something where it took a little bit longer just to get used to his body language because he had some unorthodox things that he does. But ultimately his separation is there, he's getting open."

"I would say we're getting close," Johnson said. "I can't say we're completely on. It's only been a couple months. It's getting there. I can't say we're clicking right now but we're getting there."

Bill Belichick is ranked as the best coach in the NFL, according to a poll of 30 league insiders.

Pete Carroll and Sean Payton are ranked second and third and are also in their first tier.

"The most important thing to me is the ability to control the offense, the defense and the special teams," a GM said in describing the ideal coach. "You can change and you can coach multiple things and you have the ability to teach almost every position group. Then you can lose any coach you want and replace from within because the head coach is the talent. Belichick is the ultimate model of that."

Belichick commmanded a 1 vote on 28 of 30 ballots.

In Tier 2 are Andy Reid at No. 4, Tom Coughlin at No. 5, Mike McCarthy and Mike Tomlin at No. 6, Jim Harbaugh at No. 8, John Harbaugh at No. 9, John Fox at No. 10 , Jeff Fisher at No. 11, Chip Kelly at No. 12, Bruce Arians at No. 13, Lovie Smith at No. 14 and Mavin Lewis at No. 15.

Tier 3 is led by Chuck Pagano At No. 16, followed by Rex Ryan (17), Mike Smith (18), Gus Bradley (19), Ken Whisenhunt (20), Mike McCoy (20), Marc Trestman (22) and Ron Rivera (23).

Tier 4 features Mike Zimmer (24), Jay Gruden (25), Bill O'Brien (26), Jim Caldwell (27), Doug Marrone (28), Joe Philbin (29), Jason Garrett (30), Mike Pettine (31) and Bruce Allen (32).

Jim Harbaugh likes Blaine Gabbert as the San Francisco 49ers' backup quarterback behind Colin Kaepernick despite his struggles in preseason.

"Blaine is that guy right now," Harbaugh said Friday of the No. 2 quarterback, per The Sacramento Bee's Matt Barrows.

In two preseason games, Gabbert is a combined 11-of-25 passing for 60 yards (2.4 yards per pass) with two interceptions and a 17.9 passer rating.

Colin Kaepernick played through a foot injury in 2013.

Kaepernick revealed to The Sacramento Bee this week that he suffered a chipped bone on his forefoot and a ruptured capsule in the ball of his foot when a Seahawks defender landed on it in a Week 2 loss at Seattle.

After rushing for 87 yards against the Seahawks, Kaepernick didn't clear 20 yards on the ground again for more than a month.

"I noticed it, especially in practice," Jim Harbaugh said in March of Kaepernick's limited mobility. "I think anytime you have a foot, a hand or a finger, it affects you throwing and running."

The San Francisco 49ers lost 34-0 to the Denver Broncos on Saturday in their second successive disappointing preseason game.

“We got to get better,” Jim Harbaugh said. “This is going to be an important week for us -- a big week. We need improvement. And we need to make decisions on who we’re playing with. We’re not going to keep experimenting. We got to tighten this down fast.”

The 49ers managed five first downs during Colin Kaepernick's two possessions, but did not score any points.

Antoine Bethea suffered a concussion in the San Francisco 49ers' preseason loss to the Denver Broncos.

Bethea is the starting safety for the 49ers after signing from the Indianapolis Colts.

Bethea has never missed a regular season game after six seasons.

The San Francisco 49ers may need Patrick Willis to be flexible with his inside linebacker position as they play the first part of the season without NaVorro Bowman.

The 49ers aren't sure who will take Bowman's spot in the starting lineup.

If Michael Wilhoite wins the job, Willis will switch to the "Mike" linebacker, but will remain as the "Jack" linebacker if Chris Borland starts.

“Honestly, I’ve always been a team player,” Willis said, via CSNBayArea.com. “Whatever is going to be best for the defense is whatever coach Vic [Fangio] decides. I’m going to play my very best at either/or. Right now, I’m preparing to play the ‘Mike,’ but if it happens I have to go back to ‘Jack,’ that’s where I’ve played these last three years, so I can hold it down there.”