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SANTA CLARA – Kyle Shanahan doesn’t understand the problem with the 49ers’ red-zone offense. The problem is him.

He thinks his players are the issue. He blamed them on Monday, said they “missed opportunities” he created in the red zone during the 49ers’ 24-16 loss to the Minnesota Vikings.

The 49ers may have missed opportunities Sunday when they scored only one touchdown in four red-zone trips. But, their red-zone issues began way before that. They started when Kyle Shanahan became the head coach. He is the constant in this red-zone equation.

And he won’t do the math. He’s in denial.

“Last year, I think we got better in the red zone as the year went,” Shanahan said Monday.

They didn’t. They got worse. The 49ers’ red-zone-touchdown percentage dropped to 45.5, which put them near the bottom of the league, after Jimmy Garoppolo became the starter Week 13. Before Garoppolo was the starter, the 49ers scored touchdowns 48.2 percent of the time they reached the red zone, which also ranked near the bottom of the league.

Garoppolo is much more talented than his predecessors – Brian Hoyer and C.J. Beathard. Yet, the red-zone offense got worse with Garoppolo. The onus is on Shanahan.

Shanahan is an offensive guru. Some consider him the best offensive coach in the league. How can he make getting to the red zone look so easy and scoring in the red zone look so difficult?

“It’s just the same for every other team in the NFL,” Shanahan lectured. “It gets harder the tighter you get. It always does. That’s every team.”

True. But, it gets especially hard for Shanahan.

He has been a play caller and an offensive coordinator for 10 seasons. During that time, his red-zone offenses have ranked in the top half of the league just three times. He has a history of failure near the goal line.

“You try to get guys as open as possible,” Shanahan explained. “When people aren’t open I always look at myself. Yeah, you need guys to beat man coverage, and those are the type of guys we want here, and I think our guys have done a good job at beating man coverage, but we always look into that.”

He’s looking into the wrong things.

Here are the real reasons Shanahan’s offense underperforms in the red zone.

1. Shanahan doesn’t run the ball enough in the red zone.

Notice Shanahan talked about getting people open and beating man coverage.

He’s too focused on passing. The 49ers need to run the ball more. Last season, they ran 26 times fewer than they passed in the red zone. A huge imbalance, one of the most imbalanced red-zone attacks in the league.

The best red-zone offenses commit to the ground game. Of the 10 teams that scored the most touchdowns in the red zone last season, seven ran more than they passed in that area of the field.

Smart coaches want to run the ball.

Gurus want to pass.

Completing a pass into the end zone shows the guru’s ingenuity. He designed a play that outsmarted the other team. He was the hero.

Running the ball into the end zone does not show ingenuity. It shows the strength, toughness and will of the players. They were the heroes.

Shanahan is a smart coach. He should realize the mistake he’s making and take his ego out of the red-zone drama.

2. Shanahan’s offensive philosophy isn’t suited for the red zone.

His philosophy is all about speed. He stretches the opposing defense horizontally with fast offensive linemen and running backs who run outside-zone plays — the foundation of the 49ers’ running game. And he stretches the defense vertically with fast wide receivers and tight ends who run deep.

Shanahan is a stretcher.

But his philosophy doesn’t work in the red zone. That area is too compact for stretching horizontally or vertically. Fast receivers have nowhere to run. And the outside-zone play doesn’t work. Especially near the goal line.

“That’s why we didn’t run one outside zone inside the 10 (Sunday),” Shanahan said. “The tighter you get, everything gets heavier, everything gets harder and when penetration is bad, it’s tough to get outside.”

Which means the 49ers can’t use their best run play inside the opponent’s 10-yard line. Shanahan admitted it in the previous paragraph. Instead, they have to use other runs they don’t execute as well, go to their second-level run plays. They have to pound the rock up the middle and their small offensive line isn’t built for that.

“You need guys who can run,” Shanahan said. “Some of them happen to be a little bit smaller. That’s not your choice, but you can get by.”

Until you reach the red zone.

3. Shanahan doesn’t use zone reads or run-pass options enough in the red zone.

In that respect, he’s not cutting edge. The rest of the league is using RPOs like crazy and he isn’t. I’ll define RPO below.

Scoring touchdowns in the red zone is difficult because the offense almost never can block all 11 defenders near the goal line. Zone reads and RPOs allow offenses to block a defender without actually blocking him. I’ll explain.

For a zone read, the offense leaves one defensive end unblocked. If the defensive end tries to tackle the running back, the quarterback keeps the ball and runs. If the D-end tries to tackle the quarterback, the quarterback hands off to the running back. This puts the defensive end into a knight fork, which puts the defender in the position of having to choose which offensive player to attack. Simple, but effective in the red zone.

An RPO is a similar concept. The quarterback hands the ball off while reading a linebacker or a safety. If the defensive player pursues the run too aggressively, the quarterback pulls the ball away from the running back and throws a quick six-yard pass to a receiver in the spot that defender vacated. Another knight fork.

In the red zone, a six-yard RPO pass could score six points. It’s a good play. The Eagles used it to win the Super Bowl last season.

Just don’t tell that to Shanahan.

“The RPO questions are getting hilarious,” he said to me, not sounding the least bit amused. “It’s not just you, it’s the whole planet right now. I know Philly had success with them. We definitely tried one yesterday and we wasted a call trying it because it didn’t work.”

That’s because Shanahan didn’t design the play correctly.

He made Garoppolo line up under center, drop back one step and fire blindly to his left, where a defensive end was waiting to knock down the pass. No one blocked the defensive end. All five offensive linemen ran away from him as if the play was an outside zone run to the right. That play had no chance to succeed.

The Eagles run their RPOs differently. Their quarterback lines up in the shotgun, not under center. And if he throws, he fakes a handoff first. Meanwhile, three offensive linemen block for a run play, and the other two block for a pass play. One offensive tackle engages a defensive end in pass protection, so that D-end can’t raise his arms and knock down the ball if the quarterback throws it.

The pass blocking is key. Had Shanahan included it in his RPO, Garoppolo’s throw might have been complete.

Any team like the 49ers that doesn’t run proper RPOs or zone reads in the red zone puts itself at a major disadvantage.

Get with it, Kyle.

Grant Cohn covers the 49ers and Bay Area sports for The Press Democrat and Pressdemocrat.com in Santa Rosa. You can reach him at grantcohn@gmail.com.

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