Colin Kaepernick lost his starting job partly because he lost his nerve.

On Thursday, offensive coordinator Geep Chryst was even more direct than head coach Jim Tomsula was a day earlier in discussing how Kaepernick’s crumbling psyche led to his benching.

“Maybe with perspective, Kap can breathe a little bit and say, ‘I want to get back to what my core principles are, which was I enjoyed this game,’ and make it about the sport and not about all of the outside expectations or outside criticisms, or really your own expectations or your own criticisms,” Chryst said. “You don’t want to fail in front of everybody. It’s really that fundamentally simple. And so, you shift to ‘I need to protect this throw. I need to protect my teammates.’”

This season, Kaepernick has mentioned making “protective throws,” which are throwaways that have no chance to be intercepted. Kaepernick has thrown only five interceptions this season, but also has failed to consistently push the ball downfield: He ranks 23rd in the NFL in completions of 20-plus yards (19) after eight starts.

In the first seven regular-season starts of his career in 2012, Kaepernick had 32 completions of 20-plus yards.

“You’re a young player, you come in, you’re looking for opportunities to make plays to win,” Chryst said. “Now it’s flipped a little bit and it’s ‘I don’t want to make a mistake’ that provides an opportunity for the team to lose. It sounds (like) semantics, but I think that there may be some of that going in. You don’t want to hurt the team.”

Injury report: Left guard Alex Boone (knee) did not practice after he was limited in Wednesday’s session. Rookie Ian Silberman or Brandon Thomas , a 2014 third-round pick, would make his first career start if Boone if sidelined for Sunday’s game against the Falcons.

Three other starters did not practice: wide receiver Anquan Boldin (hamstring), running back Carlos Hyde (foot) and cornerback Kenneth Acker (chest, concussion).

Eric Branch is a San Francisco Chronicle staff writer.