Colin Kaepernick did a lot of scrambling against the Indianapolis Colts. His pocket clock was short, and he took off quickly and ran pretty often throughout the game. The 49ers’ offensive line hasn’t been up to snuff so far this season — while the run blocking improved greatly against Indianapolis’ defense, they didn’t protect Kaepernick well when he dropped back to pass on Sunday. Four of the 49ers’ five offensive linemen scored negatively in pass protection against the Colts on Pro Football Focus, with only Anthony Davis in the green (+1.9). The unit allowed seven hurries and two sacks.

Colin KaepernickThe problem with shaky pass protection is that it creates a shaky quarterback. Kaepernick was trained to run early and often for four years at the University of Nevada, but now he’s being trained to pass first, run second and do the latter carefully. His scrambles this year have been considerably less decisive than what we saw in 2012. While that’s probably the right tact, it stalled the offensive on several offensive drives, and at times the illusion of a broken pocket forced Kaepernick to flee and miss open receivers.

First, lets take a look at the cause of the problem.

7:00 2nd Quarter — 1st-and-10

Not all of the protection issues exist solely in Kaepernick’s mind, but they had to start somewhere. Here, the offensive line cost the 49ers a huge gain. They run out of a modified pistol formation and send Kyle Williams across the middle and downfield. Kaepernick never has a chance to let Williams’s route fully develop, and he was staring a gang tackle in the face before he could even set his feet.

The design is brilliant — the corner on Williams ends up bumping into the linebacker who’s staying in to spy Kaepernick. It would have allowed Williams to run completely free, but the pocket deteriorated quickly. Kaepernick couldn’t escape, and the play only netted the 49ers three yards.

Now, let’s look at the effect these plays have on the quarterback.

8:03 1st Quarter — 2nd-and-10

The 49ers came out in a single-back, one tight end, three-wide set with Kaepernick under center. They sent all five out as pass options, but only Kyle Williams got open on the right side.

If Kaepernick had stood in for a split second longer and made his progressions to Williams, the pocket would have stood up and he would have had a chance to hit Williams for a long gain. Instead, he fled the pocket early and scrambled for a 14-yard pick up. It was a positive play, but also an early indication of some yips from the young quarterback.

6:14 1st Quarter — 1st-and-10

Again the 49ers got into a single-back set, this time with two wideouts and two tight ends. Kaepernick dropped back to pass, with Kendall Hunter staying in to help on pass protection. The pocket held up magnificently, and while his first and second reads were blanketed, Vance McDonald popped out in the middle of the field wide open.

The clock simply went off too early for Kaepernick. If he saw McDonald and hit him, the 49ers would have been looking at 1st-and-10 from the 15-yard line … or 6 points.

4:09 4th Quarter — 1st-and-10

The 49ers were down 20-7 at this point, but the Colts’ defense didn’t take their collective (and metaphorical) foot off the gas. For the first play of Kaepernick’s last stand he didn’t scramble, but instead hastily hit his first read: a tightly covered Anquan Boldin.

If he had hung in, he would have seen the safety bite on McDonald’s head fake, leaving the tight end wide open for an easy completion.

The best read for Kaepernick to make right now is the easiest completion, and McDonald was the easy completion there. Limited time in protection has him scrambling and forcing throws. Remember: Kaepernick is still young and learning. He doesn’t have the best targets in the league, but players are getting open. Kaepernick’s passing options should improve when Vernon Davis returns, but even then it’ll be up to him to trust his offensive line, stand in the pocket, and deliver throws under fire.