AN MTR CREW; DEPARTING KNUQ; MISINTERPED THEIR CLRNC; STARTING A CLB TO 15000 FT UNRESTR; INSTEAD OF ADHERING TO THE SID RESTRS.

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ACFT COMMANDER CALLED FOR CLRNC 1/2 HR BEFORE DEP SITTING IN THE R SEAT. DEP WAS AS FILED: SOUTHLAND 9 DEP; AVENAL TRANSITION; CLB AND MAINTAIN 15000 FT; EXPECT FL290 10 MINS AFTER DEP; CONTACT DEP 121.3; SQUAWK XXXX. READ BACK 'CLRED AS FILED; CLB MAINTAIN 15000 FT; EXPECT FL290 10 MINS AFTER DEP; 121.3; SQUAWK XXXX; OVER.' TAXI FOR TKOF; TKOF RWY 32L. TOOK OFF; CLBED UP; SWITCHED DEP WHEN CLRED BY TWR; CHKED IN WITH DEP; CALLED 'ACFT X TURNING R HDG 090 DEGS; CLBING THROUGH 1400 FT FOR 15000 FT.' BELIEVE I GOT A ROGER. A FEW MOMENTS LATER; APCH CALLED TFC; OUR TCASII CAME UP YELLOW WITH AN ALERT. BOTH PLTS VISUALLY ACQUIRED THE TFC AND CALLED CLBING ABOVE HDG 090 DEGS NO FACTOR. CLB PROFILE WAS CONTINUED. AFTER A FEW MORE MOMENTS; CTLR ASKED FOR OUR DEP. WE REPEATED CLRED AS FILED CLB MAINTAIN 15000 FT EXPECT FL290 10 MINS AFTER DEP. CTLR ASKED US TO LEVEL AT 7000 FT. WE HAD PASSED 7200 FT AND DSNDED BACK TO 7000 FT. CTLR GAVE US A VECTOR AND POINTED OUT ALTS ON THE PLATE THAT WE ROGERED AT THAT TIME; BUT REITERATED THAT WE HAD BEEN CLRED UP TO 15000 FT. CTLR ASKED THAT WE CALL ATC UPON LNDG. REMAINDER OF FLT UNREMARKABLE. CALLED ATC UPON ARR AT DEST AFTER COMPLETE. TOLD HIM WE WERE A MIL CREW. EXPLAINED THE ALT CONFUSION TO ATC AND HE SEEMED TO UNDERSTAND THAT THERE WAS CONFUSION AND THE DEP CALL TO ATC. ATC CONTENDS THAT WHEN CLRED VIA A DEP; DEP ALTS ARE TO BE MAINTAINED EVEN WHEN YOU ARE CLRED TO A HIGHER ALT -- CONFUSING AT BEST. CREW CONTENDS THAT WHEN GIVEN A CLB AND MAINTAIN ALT THAT THIS INFO IS LAST CLRNC GIVEN AND IS EXPECTED TO BE COMPLIED WITH. POSED THIS SCENARIO TO OTHER PLTS WITH THOUSANDS OF HRS OF EXPERIENCE. THEY; TOO; SAID THAT IN THIS SIT THE LAST ALT CLRNC GIVEN WAS TO 15000 FT; AND THAT IS WHAT THEY WOULD CLB TO. IF LOST COM HAD BEEN ENCOUNTERED; WE WOULD HAVE CLBED TO 15000 FT; PUNCHED THE CLOCK; AND THEN AFTER 10 MINS GONE UP TO FL290 ON THE FILED AND CLRED RTE OF FLT AS OUR EXPECTED CLRNC DICTATED. THIS CONFUSION COULD HAVE BEEN AVOIDED AND THE CHAIN BROKEN IN 2 WAYS: 1) WHEN CLRNC WAS GIVEN BY CLRNC DELIVERY; IF AIRCREW IS EXPECTED TO FOLLOW THE DEP ALTS THE CLRNC COULD READ 'ACFT X CLRED VIA THE DEP; THEN AS FILED; EXPECT FL290 10 MINS AFTER DEP....' THIS ALERTS THE AIR CREW THAT THEY ARE FOLLOWING THE SID; EXPECTING FL290 10 MINS DOWN THE ROAD. 2) WHEN THE INITIAL DEP CALL WAS MADE; 'ACFT X CHKING IN; PASSING 1400 FT FOR 15000 FT; TURNING R TO 090 DEGS;' IF THE CTLR HAD COME BACK 'ACFT X; NEGATIVE; LEVEL OFF AT 4000 FT;' THE LINK IN THE CHAIN OF EVENTS WOULD HAVE BEEN BROKEN. I KNOW NOW TO QUESTION ALL ALTS AND CONFIRM CLRED TO ALT AFTER SID COMPLETION. MY HOPE IS THAT THIS EVENT WILL SERVE AS AN EXAMPLE TO HELP OTHERS. I WILL BRIEF THIS SCENARIO IN OUR NEXT PLT TRAINING SESSION SO THAT OTHERS MAY LEARN FROM A CONFUSING SIT. THE IRONY OF THIS EVENT STARTING AT THE NASA FACILITY IS NOT LOST ON ME. THANK YOU FOR YOUR TIME AND ATTN.