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All further refinement was performed iteratively using COOT and phenix.refine.refine
Further refinement was performed through computer programming to include only one bacterial isolate of the same identification (genus and species) and susceptibility pattern per patient per calendar year in the analysis.
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Further physical map refinement was performed using the Ends-to-Ends and Singles-to-Ends functions of FPC with stepwise reductions of the Sulston score cutoff values to a final score of 1 e-50.
Further, homology modeling and refinement was performed and the refined modeled structure was used for molecular docking with the immune receptor (TLR-3) present on lymphocyte cells.
After several cycles of 3D classification and refinement, a 2D classification step using the alignment parameters from the 3D refinement was performed to check the alignment accuracy and to further exclude particles liable to misalignment.
Cell parameter refinement was performed by Celref version 3 software.
Rietveld refinement was performed using the FULLPROF SUITE 2005 [27].
Refinement was performed with REFMAC [39], [40].
The final refinement was performed with PHENIX software suit [60].
Model building and refinement was performed with CNS [36].
Initial refinement was performed with CNS [22], and the final cycles of refinement were performed with REFMAC [23].
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