Date: 201604
Local time of day: 1201-1800
Location: ZZZZ.Airport, FO
Flight conditions: VMC
Light: Daylight
Aircraft: B747-400
Operator: Air Carrier
Operating under: Part 121
Flight plan: IFR
Mission: Passenger
Flight phase: Climb
Aircraft component: Nose Gear Door
Component problem: Malfunctioning
Reporter organization: Air Carrier
Reporter function: Captain; Pilot Flying
Reporter qualification: Flight Crew Air Transport Pilot (ATP)
Human factors: Workload; Distraction; Confusion; Communication Breakdown
Second reporter function: Pilot Not Flying; First Officer
Anomaly: Aircraft Equipment Problem Less Severe; Deviation - Altitude Overshoot; Deviation / Discrepancy - Procedural Clearance; Deviation / Discrepancy - Procedural Published Material / Policy
Detector: Person Flight Crew
When detected: Aircraft In Service At Gate; In-flight
Result: Air Traffic Control Issued New Clearance; Flight Crew Became Reoriented; Flight Crew Took Evasive Action; Flight Crew Returned To Clearance; Flight Crew Requested ATC Assistance / Clarification; General Maintenance Action
Contributing factors: Aircraft; Procedure; Human Factors; Airport
Primary problem: Aircraft

Narrative: Filed for a SID. Runway 23L (primary) closed. When I input Runway 23R; there were no SIDs available. Clearance Delivery assigned us the SID for 23L (the SIDs don't explicitly state '23L'; but when you look at the depiction; they show the aircraft departing 23L)...I do not think there are any published SIDs for 23R; which is why it was not in our box. Pilot Monitoring (PM) told Clearance Delivery (CD) that we could not fly the SID. CD then told us again that we were cleared on the SID; and told us Departure would send us direct to ZZZ VOR after takeoff. We told CD that we would fly Runway Heading initially. Since we were not flying a SID; I selected VNAV and briefed that I would hand fly the departure.Clearance Delivery cleared us to only FL050. The Transition Altitude was 4;500 feet. I briefed both of those items; but didn't realize the significance of them being so close together during climbout; which may have affected the ability of the Autopilot to level off.When we called tower; the PM again told them that we were not flying the SID. They replied for us to fly the SID. PM repeated again that we were unable; and told them we were flying Runway Heading initially. Tower told us to contact ATC/Departure at 2;000 feet.Takeoff; climb to 2;000 feet and a turn to an assigned heading from Departure were uneventful. I was hand flying as I had briefed. I think we got past Flaps Up; when we heard a loud rumble and felt a vibration. The PO (Pilot Observing) stated that maybe the gear was slow in retracting. I reached over and selected the Gear Synoptic; and saw that the Nose Gear Doors were In Transit. At this point; I realized that we had a non-standard situation that would distract the PM. I called for Left Autopilot Command; and the PM selected it.I was looking over towards the PM; and I heard the aural annunciation for Transition. I looked at my PFD and saw the Altimeter box highlighted. I looked over at the PM and realized he was busy; and wouldn't be selecting STD with me. I called 'Transition' and pushed the button to change the Altimeter to STD. Shortly after this; I heard the Aural Warning; and saw the Altitude Warning. I looked at the altitude readout; which said 5;78x'. I immediately Disconnected the Autopilot and pitched the nose down. When established in the descent; I selected the Left Autopilot Command; and then selected FL CH. When we were level; I reselected VNAV. We did not receive any communication from ATC.When the Warning initially sounded; the PM saw the Altitude Deviation; and then looked at the MCP confirming it was set at 5000'; and asked what happened. He didn't understand how we could be on Autopilot and have flown through the MCP Altitude Target. The PO (Pilot Observer) stated that normally he would be backing me up and watching the Level Off; but he was distracted by the Gear Problem.Gear Situation: There was no EICAS or Status Message. There was the Synoptic Display showing the NG Doors 'In Transit'; and a CMC Present Leg Fault relating to the Nose Gear and a Nose Gear Sensor. The PM placed the Gear Handle in the 'Up' position; and the Nose Gear Doors retracted. We left the Gear Handle UP for the duration of the flight and notified Dispatch/Maintenance via ACARS.The rest of the flight was uneventful. We landed [at our destination]; using the VOR DME XXL approach. It took some time to explain the Nose Gear problem to maintenance after we blocked in.When I fly an RNAV SID or STAR; or a complicated (non-RNAV) SID or STAR; I ALWAYS turn on the autopilot at 250'.When we were given a level off altitude of FL050; with a Transition Level of 4500'; I could have decided to turn on the Autopilot at 250'; because the closeness in time/space of the Transition and the Level Off makes things more complicated. I am used to the problem of descending with the cleared level and the Transition Level being close together; but have not had much experience with the two of them being so closetogether on climbout. I think this may have contributed to the Altitude Deviation; as it may have disrupted the automation to switch from local Altimeter setting to STD so close to the level off altitude.The other thing I could have done on this flight; was after our call to Departure at 2000'; I could have selected STD then; which would have given the automation more time to process the change; and would also be helpful for capturing the correct altitude; especially when the local Altimeter setting was far from Standard. In addition; turning the Autopilot ON at 250' would have given the autopilot more time to process and correctly level off at FL50.As it was; when I realized that we had a problem; I think it was a good idea to turn on the Autopilot; but then should have focused 100% of my attention on Flying the Aircraft; and let my PM and PO work on the problem. After we were level at FL50; and when I had less going on; then I could have checked back in with them.In future; when Pilot Flying (PF); I will:1-Turn the Autopilot ON at 250' whenever we have a 'low level' level off.2-In any abnormal situation; I will either spend all my time focusing on flying the aircraft; or I will give the aircraft to the PM; tell the PM to concentrate 100% on flying the aircraft; and I will manage the abnormal situation.


Second narrative: Prior to departure; clearance attempted to give [a SID]. They were informed unable due to restrictions in FMS system. Clearance acknowledged and said to expect radar vectors.At the hold short; tower cleared the flight for the [SID] again and they were told unable and expecting radar vectors per clearance's instructions. It was stated to tower we plan on flying runway heading initially. Tower acknowledge and said report passing 2;000 feet. We acknowledged back. On climb-out from Runway 23R; Pilot Flying (PF) called for flaps 10. Pilot Monitoring (PM) re-positioned the flaps and called to tower passing 2;000 feet. Tower instructed us to turn to HDG 300 and contact departure. PM read back instructions. While on the heading of 300; several events occurred quickly. Flaps 5 was called; the gear handle was placed in the OFF position; a loud rumble was heard; the PF asked for the AP to CMD; and the PM turned to the OBS in a CRM fashion to work a potential emergency. PF called transition at the required transition altitude. Just as the PM raised the gear handle; the noise stopped and the altitude warning horn sounded. The PM and OBS saw the altitude and simultaneously the PF quickly disengaged the autopilot and corrected back to the assigned altitude of FL050. An observed maximum altitude of FL057 was observed when the climb was arrested and a correction was made. After the correction; PM reported in to departure with heading and altitude and continued the climb. There was no response from ATC. The rest of the flight occurred uneventfully. The autopilot was unable to handle the high rate of climb with a close transition altitude. Suggest a software revision to lessen climb rate when transition altitude is within 2;000 feet of level off altitude or allow crew more latitude on when to change the setting so as to account for sudden situations like this one.


Synopsis: A B747-400 was unable to accept the cleared SID because no SIDs were available in their FMC for the only operational Runway. After hand flying the departure on vectors; the nose gear door did not close so as the First Officer dealt with the gear; the Captain overshot the 5;000 feet level off altitude assignment.