"4-4-1. Clearance
a. A clearance issued by ATC is predicated on known traffic and known physical airport conditions. An ATC clearance means an authorization by ATC, for the purpose of preventing collision between known aircraft, for an aircraft to proceed under specified conditions within controlled airspace. IT IS NOT AUTHORIZATION FOR A PILOT TO DEVIATE FROM ANY RULE, REGULATION, OR MINIMUM ALTITUDE NOR TO CONDUCT UNSAFE OPERATION OF THE AIRCRAFT.
b. 14 CFR Section 91.3(a) states: "The pilot-in-command of an aircraft is directly responsible for, and is the final authority as to, the operation of that aircraft." If ATC issues a clearance that would cause a pilot to deviate from a rule or regulation, or in the pilot's opinion, would place the aircraft in jeopardy, IT IS THE PILOT'S RESPONSIBILITY TO REQUEST AN AMENDED CLEARANCE."
(Federal Aviation Administration - Aeronautical Information Manual - Official Guide to Basic Flight Information and ATC Procedures)
Universal Weather, a global trip support services provider, made the Legacy flight plan taking in account fuel efficiency; best time to destination; adequate reserves; alternate ETOPS; airport weather considerations; RVSM airspace; navigation and communications requirements. This plan foresaw from São José dos Campos (SP) to Brasilia (DF), passing through Poços de Caldas (MG), the Legacy aircraft should travel via airway UW2, at 452 miles per hour, at an altitude of 37,000 feet. From Brasilia onward, the Legacy aircraft should have progressed via the UZ6 airway, at 456 miles per hour, at an altitude of 36,000 feet. From the Teres (virtual) compulsory notification point, the Legacy aircraft should have continued progressing on UZ6 airway, at 449 miles per hour, then changing, to the altitude of 38,000 feet. UZ6 airway has traffic in both directions. Aircraft that are traveling from north to south fly at odd levels (FL 290, FL 310, FL 330,... to FL 410), while those that are traveling from south to north fly at even levels (FL 300, FL 320, FL 340,... to FL 400). This plan was electronically submitted by Embraer to the traffic control center. An air traffic controller, in the Flight Plan Room, confirmed the insertion of the referred plan into the system and verified route conflicts by cross referencing it with the flight plans of the ACCs of the other FIRs. Before beginning a flight, the pilot-in-command shall familiarize himself with all available information appropriate to the intended operation. Although there is documentary evidence the crew had marked the flight route on an aeronautic chart of Brazilian air space, as far as everything has been seen, the probably is immense that the pilots did not even become aware of the originally presented flight plan, only coming to worry to about this after embarking on the aircraft, since there are no records of their presence in the AIS Room of the São José dos Campos Aerodrome. A clearance should contain clearance limit, departure procedure, route of flight, altitude data, and other information that are necessary. The clearance was: “November six zero zero x-ray lima, ATC clearance to Eduardo Gomes, flight level three seven zero, direct Poços de Caldas, squawk transponder code four five seven four. After take-off perform Oren departure”. It was clearly incomplete. It didn’t mention the complete route (Brasilia, Teres). The crew kept the route of the requested flight plan, but not levels. The crew acted with low situational awareness, not observing RVSM airspace and fuel efficiency provided by original flight plan.
(Note: this may be a bad translation)