CAPT OF MDT OVERSHOT ASSIGNED CLB ALT.

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CAPT'S LEG FROM SEA TO PDX. HE WAS HAND FLYING ACFT ON RAW DATA; THEN SELECTED THE FLT DIRECTOR. I NOTICED THAT ALT CAPTURE MODE WASN'T PROGRAMMED BUT SINCE HE WAS HAND FLYING I DECIDED TO WAIT UNTIL HE ENGAGED THE AFCS (AUTOMATIC FLT CTL SYS) BEFORE TELLING HIM THAT HE HADN'T YET SELECTED THE ALT CAPTURE. AT SOME POINT HE TURNED ON THE AUTOPLT AND I MISSED IT. OUR CLRNC WAS TO LEVEL OFF AT 13000 FT. PASSING 12000 FT; I MADE MY REQUIRED CALL OF '1000 TO GO' AND HE ACKNOWLEDGED IT. THEN I REPLACED DEP CHARTS INTO BINDER AND PULLED OUT ARR CHARTS FOR PORTLAND. WHEN I LOOKED AT THE ALTIMETER; WE WERE CLBING THROUGH 13600 FT MSL. I SAID SOMETHING TO THE CAPT AND HE SWORE AND STARTED US DOWN TO 13000 FT. 2 SECONDS LATER ATC QUERIED WHAT ALT HAD WE BEEN CLRED TO? I REPLIED THAT WE WERE LEVELING AT 13000 FT. TCASII SHOWED NO TFC WITHIN 20 NM ABOVE US. I HAVE NOW SEEN HOW IMPORTANT IT IS THAT ALL OTHER TASKS WAIT UNTIL AFTER THE LAST 1000 FT OF AN ALT CAPTURE HAVE PASSED. THE REASON THAT I DIDN'T SAY SOMETHING ABOUT THE SETUP RIGHT AWAY WAS BECAUSE IT WAS THE FIRST TRIP (SECOND DAY) I HAVE FLOWN WITH THIS CAPT AND I DIDN'T WANT TO COME ACROSS AS AN 'INSTRUCTOR PLT' POINTING OUT MISTAKES WITHOUT GIVING HIM THE CHANCE TO CATCH IT HIMSELF.