Conservative mistake-free offense. A persistent running game. A defense that stonewalls running backs and produces turnovers at key moments.

The formula that has worked so well for coach Jim Harbaugh and the 49ers the past two seasons was run to near perfection Sunday. The catch: It was the visiting Colts and not the 49ers who had the right balance.

While Andrew Luck and Indianapolis' low-frills offense were piecing together long drives and gobbling up the clock Harbaugh and the 49ers continued to drift farther away from the path that got them to the NFC Championship Game during the 2011 season. They had the league's fewest turnovers that year were a defensive brick wall when it came to opponents' running games and were aided by strong special teams. The three units worked in concert.

The 49ers are discovering this season what happens when they don't mesh.

The offense suffered from terrible field position in Sunday's 27-7 loss.

The 49ers averaged 12 yards on three kickoff returns and their average offensive possession began at the 19-yard line.

Colin Kaepernick and the offense converted only 25 percent of third downs and the team had to punt seven times. The defense was solid through three and a half quarters but could not sustain it at the end. For the second game in a row the 49ers gave up more than 170 rushing yards and the Colts scored three touchdowns on the ground.

Asked whether the offense is still trying to find the right formula after switching from safe-and-steady Alex Smith to Kaepernick Harbaugh on Monday said "It's evolving. Are there changes? Yes."

"Football's not easy. There are struggles" continued Harbaugh whose team is 1-2 and plays the St. Louis Rams – a team it could not beat last season – on the road Thursday night. "That's one of the things you enjoy about the game that there are struggles. We've got some adversity there's no question about it. And we'll also have the rare opportunity of staring adversity in the face and whipping it. That's our goal."