Jorge Lorenzo was comfortably fastest in Friday afternoon practice at Laguna Seca.
The Yamaha rider set a 1m22.056s on his ninth lap and stayed ahead thereafter, setting a consistently rapid pace and even escaping a wild moment near the end of his final lap without trouble.
Honda had been first and second in the morning, but could not quite match Lorenzo in practice two. Dani Pedrosa was second in the end, 0.141 seconds down on Lorenzo, with his team-mates Casey Stoner and Andrea Dovizioso third and fourth.
It was an all-factory Yamaha and Honda top five as Ben Spies was top American again in fifth, followed by Marco Simoncelli's Gresini Honda.
Best of the rest this time was Suzuki's Alvaro Bautista in a promising seventh.
Pramac's Randy de Puniet was Ducati's quickest rider in eighth, as the factory bikes of Nicky Hayden and Valentino Rossi were only 10th and 11th, behind Tech 3 Yamaha's Colin Edwards. Both works Ducati men used the 2012 chassis GP11.1 in this session.
Newcomer Ben Bostrom still trailed the field, but narrowed the gap slightly as he took his LCR Honda round 4.1s off Lorenzo's pace.
Pos Rider Team/Bike Time Gap 1. Jorge Lorenzo Yamaha 1m22.056s 2. Dani Pedrosa Honda 1m22.197s + 0.141s 3. Casey Stoner Honda 1m22.231s + 0.175s 4. Andrea Dovizioso Honda 1m22.537s + 0.481s 5. Ben Spies Yamaha 1m22.615s + 0.559s 6. Marco Simoncelli Gresini Honda 1m22.803s + 0.747s 7. Alvaro Bautista Suzuki 1m23.056s + 1.000s 8. Randy de Puniet Pramac Ducati 1m23.135s + 1.079s 9. Colin Edwards Tech 3 Yamaha 1m23.183s + 1.127s 10. Nicky Hayden Ducati 1m23.195s + 1.139s 11. Valentino Rossi Ducati 1m23.369s + 1.313s 12. Hector Barbera Aspar Ducati 1m23.424s + 1.368s 13. Cal Crutchlow Tech 3 Yamaha 1m23.707s + 1.651s 14. Karel Abraham Cardion Ducati 1m23.811s + 1.755s 15. Toni Elias LCR Honda 1m23.830s + 1.774s 16. Hiroshi Aoyama Gresini Honda 1m24.590s + 2.534s 17. Loris Capirossi Pramac Ducati 1m24.663s + 2.607s 18. Ben Bostrom LCR Honda 1m26.159s + 4.103s