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The solution was then subjected to multiple rounds of refinement using the Refine module of PHENIX.
The structure was then refined in an iterative procedure via refinement using the software Refmac 5.02 [22] and manually rebuilding using Quanta2006 (Accelrys).
Protein models were refined by rigid body refinement and restrained refinement using Buster.
The structure was refined using iterative cycles of model building and refinement using COOT and phenix.refine, respectively.
Each of these re-refined structures was used as the input structure for ensemble refinement, using the same run-time parameters.
The structure was refined using COOT and iterative steps of manual rebuilding and positional refinement using Phenix.
The models were refined by several cycles of manual rebuilding with COOT, followed by refinement using REFMAC.
The structures were refined by iterative rounds of manual building in Coot 3.0 and refinement using the ccp4i program refmac5 [ 74].
Repeated cycles of refinement using REFMAC5 (ref. 35) and model building using COOT36 were performed.
Several cycles of map fitting and refinement using the program Refmac5 ref. 41) led to convergence.
After that, we perform a landmark detection refinement using the model 2.
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