SANTA CLARA, Calif. -- If your glass is half full, you could have watched the San Francisco 49ers' final organized team activity Thursday and come away impressed with the defense. If your glass is half empty, you might have walked away thinking just how far the offense has to go.

As is always the case at this time of year, when no pads are involved, making sweeping generalizations about any team is a fool's errand. It's particularly true for a team such as the Niners, who are starting fresh with new coach Kyle Shanahan, his staff and a drastically different roster.

New 49ers coach Kyle Shanahan and GM John Lynch, right, got a visit from Stanford coach David Shaw, left, during OTAs on Thursday. AP Photo/Jeff Chiu

The 49ers' offense, which is learning Shanahan's encyclopedic playbook for the first time, has a lot on its plate. But for veterans such as receiver Pierre Garcon, who has played for Shanahan before, that doesn't mean that lagging behind the defense sits well.

"Apparently we can’t run the ball or throw the ball against our defense, so everything is standing out," Garcon said. "They’re doing a good job.

"It is very frustrating, but it’s part of the offseason things that you have to go through. The defense has to work on stuff. The offense has to work on stuff. We have to be ready to react to anything. It’s very frustrating, but it’s just part of the game, and you have got to just keep moving forward."

Among the bumps and bruises that came during Thursday's practice were a handful of "sacks" that drew disappointment from offensive-line coach John Benton, a pair of interceptions that came on passes that deflected off the intended target's hands and a few drops on catchable balls. A short red zone period was particularly difficult for the Niners' offense.

At this point in the offseason program, the 49ers have installed both the offense and defense for the first time. When they reconvene for training camp in late July, they will go through that installation again. The defense was able to get through its initial installation of coordinator Robert Saleh's scheme in five practices, while the offense took a couple more because of how voluminous Shanahan's scheme is.

The difference in complexity as well as volume, combined with the altered personnel working together for the first time, was enough to put the defense clearly ahead of the offense at this point.

"The first time through, I think it’s always hard in a new system," quarterbacks coach Rich Scangarello said. "But I think it’s very similar to when we went through the process in Atlanta. It will take some time; obviously, when we come back for training camp, hearing it again, there will be some familiarity, but I definitely feel like we’re on course."

Shanahan's scheme has a reputation for expansive verbiage that can take some time to grasp. Fullback Kyle Juszczyk, who played in a system with similar concepts in Baltimore, prefers to call the offense thorough instead of complex but says there's good reason for that.

Each player who has discussed early impressions of the offense has made a point to bring up Shanahan's attention to detail. His offense asks all 11 players to take care of a job, and no defender is unaccounted for. That level of detail requires a certain amount of focus on the part of the players.

"I feel like we just kind of take it to that next level where coach Shanahan just has this knack for understanding the complete defense, where we are thinking about all 11 guys on the defense," Juszczyk said. "There’s never a time where we are running to one side of the ball and we don’t have to worry about that corner on the far side. We really just take everything into account."

The good news for the Niners' offense is that there's still plenty of time for things to come together. The 49ers have their mandatory veteran minicamp next week before they depart for the summer. Adding pads during training camp will also undoubtedly help the offensive line and allow for more accurate assessments of what's happening on the practice field.

The bad news is that this is an offense that has ranked near the bottom of the league in recent years, and outside expectations aren't exactly optimistic. After all, Shanahan's scheme took a full year to take hold in Atlanta, and that was with a far more talented group of players.

"There’s a lot of learning going on right now," Juszczyk said. "It’s a new system on both sides of the ball, and there’s a lot of guys that haven’t been in this system before. So it’s really just getting everybody on the same page, and each day you are dealing with a new install. It’s really just about honing in on that day, worrying about the play that’s in front of you and getting everybody to play it."