Date: 201602
Local time of day: 0601-1200
Location: ZID.ARTCC, IN
Flight conditions: IMC
Light: Dusk
Aircraft: Regional Jet 900 (CRJ900)
Operator: Air Carrier
Operating under: Part 121
Flight plan: IFR
Mission: Passenger
Flight phase: Climb
Airspace: Class A ZID
ATC / advisory: Center ZID
Reporter organization: Air Carrier
Reporter function: Captain; Pilot Flying
Reporter qualification: Flight Crew Air Transport Pilot (ATP)
Human factors: Workload; Situational Awareness; Distraction
Second reporter function: First Officer; Pilot Not Flying
Anomaly: Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Published Material / Policy; Deviation / Discrepancy - Procedural Clearance
Detector: Person Air Traffic Control
When detected: In-flight
Result: Flight Crew Became Reoriented; Flight Crew Returned To Clearance
Contributing factors: Human Factors
Primary problem: Human Factors

Narrative: After departure; we received instructions to fly a heading for traffic. Once contacting Indianapolis Center; we were told to verify the routing we had received from clearance. The clearance was to fly the FEDRA3 RNAV departure with the SHIPR transition; then direct SKYWA; and then the FILPZ1 arrival into CLT. We read back the clearance which was correct; however; we had deviated off from that route. Obviously; we were not aware of our deviation until center brought it to our attention. Reflecting back on the departure; we were perplexed because we had reviewed the FMS; and could not figure out how we got off course. After calling ATC with regards to the deviation; we were able to figure out exactly what caused the error. We had planned for a departure off of 17L. On our taxi out; we were told expect runway 17R instead. With the change in runways; I called for a Runway Change Checklist. The First Officer (FO) changed the FMS routing; and then ran the new numbers on the ACARS for our performance. The FO did a great job running through the checklist; and operating the FMS on the way out. However; when we did the FMS review on the checklist; we failed to see that the transition part of the departure was missing. I physically saw the new runway; and departure SID in the FMS; however when we negotiated the taxi hotspot; going from the ramp; to taxiway Juliet; to Gulf; to Bravo; I went to heads up outside and did not physically see the transition phase setup in the FMS; I only heard the verbal. With that transition not selected; we ended up cutting the corner going from FEDRA direct to SKYWA; rather than going from FEDRA direct SHIPR; and then to SKYWA therefore getting off our assigned route. After discussing the deviation with the FO; he said; he did not realize when a runway change is put in the FMS; it wipes out the previous transition; he thought the transition transferred over from the prior inputs; being that the transition was not changed; only the runway.I should have physically looked at the transition; and perhaps stopped the checklist or taxi until we were in a location where I could have been a better resource in backing up the sequence of the FMS. The FO exhibits great skills and knowledge of the aircraft. Being in the aircraft for only a few months; it is imperative for the Captain to keep an extra eye on everything; and do our best to keep the workload at a minimum so these items can be trapped before they become an incident.


Second narrative: When departing we were given a runway change. The runway change checklist was executed and the runway was changed in the FMS. We were doing the FEDRA3 SID SHIPR transition; when I put in the runway change the transition SHIPR dropped out of the flight plan. So we did not have the FMS programmed correctly and proceeded to SKYWA early.In the future I will go to the departure page and put in the entire departure with new runway and double check all of the fixes on the chart; instead of just changing the runway.


Synopsis: CRJ-900 flight crew reported a track deviation occurred when they programmed the FMS improperly following a late runway change on taxi out.