We report results of an all-sky search for periodic gravitational waves with frequency between 50 and 510 Hz from isolated compact objects, e.g., neutron stars. A new hierarchical multistage approach is taken, supported by the computing power of the Einstein@Home project, allowing us to probe more deeply than ever before. 16 million subthreshold candidates from the initial search [LIGO Scientific and Virgo Collaborations, Phys. Rev. D 94, 102002 (2016)] are followed up in four stages. None of those candidates is consistent with an isolated gravitational wave emitter, and 90% confidence level upper limits are placed on the amplitudes of continuous waves from the target population. Between 170.5 and 171 Hz, we set the most constraining 90% confidence upper limit on the strain amplitude h0 at 4.3×10-25, while at the high end of our frequency range, we achieve an upper limit of 7.6×10-25. These are the most constraining all-sky upper limits to date and constrain the ellipticity of rotating compact objects emitting at 300 Hz at a distance D to less than 6×10-7 [D100 pc].