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"despite its deficiencies" is correct and usable in written English.
You can use this phrase to indicate that something has flaws or weaknesses, but it still has some positive qualities or is still able to accomplish something. Example: Despite its deficiencies in graphics and design, the video game received high praise for its engaging gameplay and compelling storyline.
Exact(2)
That longer-term commitment also sends an important message to Afghans that Washington will not abandon them as it did after the Soviets were driven out, and that it is worth taking a chance on their government despite its deficiencies.
Despite its deficiencies, the work, whose short title is Foedera ("Treaties"), is a considerable and valuable achievement.
Similar(57)
Despite all its deficiencies, it was her place on earth.
They failed, but their movement forged the generation responsible for the democratic pact that — despite its many deficiencies and discontinuities — so displeases Mr. Chávez today.
With support, the Afghan government, despite its many deficiencies, looks resilient enough to repel the Taliban from the main cities and economic centres.
Through this newly configured globalised CF, the regulatory architecture of accounting may work to sustain the centrality of finance in a post-GFC economy, despite its many deficiencies.
Despite its methodological deficiencies, the strong prognostic value of mediastinal background-corrected myocardial I-MIBG washout has been repeatedly demonstrated [ 24, 25].
2 7 Despite its many deficiencies and its dependency on political decisions, CED has been considered by many to be the tool to evaluate evolving technologies, but the best approach remains unknown.
Although Rickman's scheme remains in general use, despite recognition of its deficiencies, Sharpe's terms "Geometrical" and "Curvilinear" are very often used in addition to distinguish styles or phases within Rickman's "Decorated".
In fact, the failure of vitamin D3 (cholecalciferol) supplementation to show beneficial effects on body weight or on the course of inflammatory diseases may be due to the persistence of its deficiency despite its administration.
However, the V438F/T504E mutant was able to dimerize despite its substrate-binding deficiency, ruling out the substrate-binding model for dimerization.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com