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We then performed a controlled paired-refinement, where the starting model was refined using the same refinement protocol against both a full data set and a truncated version (to 2.85 2.95 Å) of the full data set.
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For each crystal form, we used the same refinement protocol.
An average DNAJA1-JD structure was calculated on the basis of the average atom coordinates of the 20 water-refined structures and subsequently minimized using the same explicit water refinement described above.
Each of these re-refined structures was used as the input structure for ensemble refinement, using the same run-time parameters.
(We are assuming that is -dimensional, and using the same symbol for terms of a refinement of the previous central series).
Our dataset was searched for reads that could be grouped in with these families using the same criterion, but employing some additional refinements.
The time points collected involved running 3D classification for 2 rounds and 3D refinement for 6 rounds, using the same number of particles and box sizes listed above: 62,022 particles for classification and 32,533 particles for refinement with box sizes of 240 × 240 pixels.
The auto-refinement procedure was then repeated using the same starting model and C1 symmetry, to check for symmetry artefacts.
Using the same process, continue.
This methodology allows one to use the same communication refinement mechanisms for architectural exploration.
The following theorem shows that the adaptive algorithm reduces the error with the optimal rate and therefore at least as good as any other algorithm which uses the same mesh-refinement.
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