A Petaluma man accused of firing shots out of a car window that left three men dead on a South San Francisco street in 2010 pleaded not guilty Friday to murder, attempted murder, racketeering and other crimes before a federal judge in San Francisco.

More than 50 miles north of the courtroom, bullet holes still marred the grey-blue siding of the east Petaluma home where federal agents launched a pre-dawn raid Thursday that erupted in gunfire, wounding three federal agents.

Victor Flores, 20, of Petaluma, was among 13 men and women apprehended early Thursday during raids at 11 locations in the Bay Area, part of a sweep targeting members and supporters of a South San Francisco street gang.

Federal authorities remained tight-lipped Friday about the events in Petaluma.

Officials declined to reveal details of how the federal agents were wounded inside the home. On Thursday, they said the agents encountered a barrage of bullets sprayed from an assault rifle by an unspecified person. All three agents were expected to survive, they said.

FBI officials were investigating the "circumstances of the shooting," spokeswoman Julianne Sohn said.

Officials also declined to confirm if Flores was arrested at the McNeil Avenue home.

"All I can tell you is what's in the indictment," said Jack Gillund, U.S. Attorney's office spokesman.

The 37-page document outlines the history of the South San Francisco gang and its members, who are accused of waging war on their rivals in the city's Old Town neighborhood.

Flores, known as "Little Creeper," and three other suspected members of the 500 Block/C Street gang are accused of killing three rival gang members in the Dec. 22, 2010 drive-by shooting.

The indictment doesn't explain Flores' connection to Petaluma.

Residents along McNeil Avenue indicated a Latino man in his 20s and his family moved into the home not long ago, perhaps as recent as last November.

Next door, Selina Jones, 18, said the family threw a birthday party for a girl who looked to be about 11 years old and put up a host of Christmas decorations on the lawn soon after they arrived.

Jones said she often spoke with the 20-something man about his dogs, two boxers, one named Tyson.

On Friday, fruit trees in planters with the tags still attached sat in the grass among window screens, broken blinds, clothes and other signs of the confrontation.

The windows, which were shattered during the raid, were boarded Friday.

At about 10 a.m. Friday, animal control officers showed up at the property and asked Jones if she knew the names of the family's dogs. The officers said they found the dogs in a field between Petaluma Valley Hospital and Highway 101, Jones said.

"They asked if I could call them by name, would they come," she said.

Early Friday, an older man who lived at the home returned to pick up some things, Jones said.

"I was shocked. They were really nice," Jones said.