Date: 201511
Local time of day: 0601-1200
Location: SFO.Airport, CA
Weather elements / visibility: clear
Light: Dawn
Aircraft: Light Transport; Low Wing; 2 Turbojet Eng
Operator: Corporate
Operating under: Part 91
Flight plan: IFR
Mission: Passenger
Flight phase: Initial Climb
Airspace: Class B NCT
Reporter organization: Corporate
Reporter function: Captain
Reporter qualification: Flight Crew Air Transport Pilot (ATP)
Human factors: Confusion
Anomaly: Deviation - Altitude Excursion From Assigned Altitude; Deviation / Discrepancy - Procedural Clearance; Deviation / Discrepancy - Procedural Published Material / Policy; Deviation / Discrepancy - Procedural FAR
Detector: Person Air Traffic Control
When detected: In-flight
Result: Air Traffic Control Issued New Clearance
Contributing factors: Human Factors
Primary problem: Human Factors

Narrative: We were scheduled for departure from SFO. We received our clearance which was the NITE 3 RNAV Departure with the GRTFL transition; climb via the SID OED as filed. We loaded the departure and Dlt. plan into the FMS along with FL 190 into the altitude alerter which is the altitude for the NITE 3. Before taxi we both reviewed the NITE 3 departure and verified the FMS had the correct information; speeds; altitudes; and headings. This early it wasn't very busy yet so we requested with ground control a departure off of 28R to save the long taxi time all the way over to 01R (usually 15 minutes or more). Ground control gave us taxi instructions to 28R intersection Echo for the takeoff runway; then as we were taxing ground control gave us a new departure clearance. The new clearance was; change departure to the SNTNA 2 RNAV departure climb via the SID. I was in the right seat working the radios and within seconds we were on taxiway Charlie; I told the pilot flying 'my heads down I'm changing the box'. I entered the new runway 28R along with the new SID SNTNA 2. It looked almost identical to the NITE 3 at first glance: 284 degree heading a couple of right turns and then out to GRTFL. We ran our checklists and arrived at taxiway Echo holding short of 28R; ground told us we would have to hold short for a few minutes. The pilot flying picked up his iPad and started to review the departure procedure. We were cleared for takeoff before he finished his review; which would have caught the altitude change in the departure procedure; which was 3;000 feet instead of 19;000 feet. Also there was a procedure off of 28R on the NITE3 that went to 19;000 feet. So to put it mildly we had 19;000 feet stuck in our brain; so to speak. The aircraft was lightly loaded; temperature was cool; sky clear; so we climbed rapidly and were handed over to Norcal departure. I told them we were climbing out of 2;000FT. for FL 190. 15 seconds later the controller came back and gave us a squawk. I told him we were. 36 seconds later the controller came back with 'radar contact 4 west of the airport; what was your assigned altitude?' I replied 190. He said we should have been assigned 3;000 and then cleared us to 10;000. Then he asked if we didn't get the except and maintain 3;000 portion of that clearance? I said no they never gave it to us. That was the last we heard about it till we were handed of to Oakland center and we received the dreaded call this number when you land; which we did. In the mean time we thoroughly reviewed the SNTNA 2 and saw the 3;000Ft. altitude restriction at that point we realized the confusion we had with departure control. We discussed the situation with the Tracon manager explained our being rushed and not having enough time to review the SID and brief it. She told us there were no traffic conflicts; but it would still have to be investigated.My recommendation is two part. First when given a last minute change the controller should also state the altitude restrictions. Second the charts should be reformatted and the altitude restrictions placed in big letters under the name of the SID along with the runways that are already listed at the top of some of the SIDs. As important as an altitude is they should be printed in RED!There were probably several contributing factors creating the incident. One was it was early in the morning at least for us as a crew. I'm not sure of the controller's schedule. The biggest issue was being rushed; which is never good. We only had 6 minutes from brake release to lift off; that's not a big deal in this aircraft; but with runway changes; plus a departure change; it appears it was just a little too much for highly experienced crew. I'm guessing between the both of us were looking at 40;000 plus hours of experience. Something is seriously wrong with the system for this to happen to a well-trained experienced crew seriously concerned about the safety of the system in this critical information is being presented to crews. Something MUST be changed.




Synopsis: After requesting and receiving a different runway for takeoff; crew was assigned a different departure procedure. Crew failed to notice the different final altitude clearance of the new departure.