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In the first step of refinement, the global parameters, such as background and scale factors, were refined.
We perform an additional step of refinement to further improve the load balance for the rare cases when the load is not evenly balanced.
At each step of refinement we add values for the numerical flux at the new grid-points which are the centers of the coarser cells.
The validity of each step of refinement and rebuilding was monitored by Rwork and Rfree.
Gradient-based minimization is often employed for the last step of refinement of initial models.
(E ) Summed power spectra of filaments with less than 5° of out-of-plane tilt in the last step of refinement.
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The model building process is based on iterative steps of refinement and validation.
The resulting datasets require several steps of refinement before being suitable for statistical analysis.
This model was subsequently subjected to iterative steps of refinement in Phenix and manual model building in Coot.
At the final steps of refinement restrained anisotropic temperature factors for the protein atoms were introduced and this step reduced Rfactor and Rfree by 2.4% and 1.5% respectively.
To overcome the above mentioned shortcomings, a modified RBH, not restricted to the top hits alone and extended to include steps of refinement and validation was used (see Materials and Methods).
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