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Subsequently, the best-modeled protein structure was used for the refinement process.
Landscape representation at different resolutions can be used for the refinement of docking predictions and detection of macro characteristics, like the binding funnel.
On the other hand, it is true that other optimization approaches, like a gradient-based method or the Newton method, may have been used for the refinement stage.
Moreover, it should be stressed the participatory approach adopted in this specific planning exercise, which was used for the refinement of the objectives set by planners and decision-makers ('learning stage'), as well as for refining the proposed alternative scenarios and for setting priorities (weights) at the stage of the evaluation of these scenarios ('evaluation stage') (see Fig. 1).
The native data set was used for the refinement.
Anisotropic scaling, a bulk solvent correction and TLS restraints were used for the refinement.
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The dataset used for the refinements is from Kondratuk D. V. et al. [30] with 49,666 reflections.
First, we performed the PHENIX refinements using a standard protocol the same as we used for the refinements described in the manuscript, with NCS and secondary structure restraints turned on.
A crystallographic information file (CIF) for CeO2 (ICSD: 72155) was obtained from the ICSD database and used for the Rietveld refinement.
The Pauling's half-hydrogen model with an average occupancy of 0.5 for each deuterium atom in water molecules was used for the Rietveld refinement and MEM analysis, and the ordered model was used for MD calculation.
The nonsymmetric quantizer cannot be used for the progressively refinement process, since it is nonsymmetric with respect to the zero value.
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used for the betterment
used for the modification
used for the tuning
used for the finalisation
used for the refining
used for the improvements
used for the perfecting
used for the fine tuning
used for the network
used for the film
used for the rehabilitation
used for the immobilization
used for the study
used for the heart
used for the experiment
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