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The refinement consists of full coordinate optimization of all ligand atoms, and any poses that violate the constraints are discarded after the refinement.
This refinement consists of two steps: correspondence point matching and transform estimation.
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At the end of the refinement (consisting of one loop in this work), the final attacked image J is obtained.
Refinement consisted of two cycles of torsion angle annealing followed by B-factor refinements.
Three iterations of weight refinement consisting of 100 runs of 1,700,000 steps were performed for RMSD ST simulations, followed by 100 runs of 900,000,000 steps for data collection.
Two iterations of weight refinement consisting of 100 runs of 600,000 steps were performed for temperature ST simulations, followed by 100 runs of 600,000 steps for data collection.
Refinement consisted of rigid body, simulated annealing, positional and individual B-factor refinement with no sigma cutoff.
Refinement consisted of conjugate gradient minimization and calculation of individual anisotropic displacement and translation/libration/screw (TLS) parameters.
Each cycle of refinement consisted of electron and difference density map inspection and model manipulation together with incorporation of cofactors, waters and ions, followed by REFMAC5 refinement.
The subsequent refinement consisted of alternating rounds of positional minimization, individual restrained thermal factor refinement, both using the MLF maximum likelihood target function, and model building.
The data set used for refinement consisted of 180 frames collected with an oscillation width of 1°, a detector distance of 250 mm, and an exposure time of 1.0 s/frame at 4% transmission.
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