Sentence examples for maximum likelihood refinement from inspiring English sources

Final rounds of model building for both the structures were carried out using COOT (Emsley and Cowtan, 2004) and refined using PHENIX (Adams et al, 2010) involving restrained maximum likelihood refinement of atomic position and isotropic B-factors.

Manual model rebuilding was performed in Coot (Emsley and Cowtan 2004), and maximum likelihood refinement was performed using REFMAC5 (Murshudov et al. 1997).

Maximum likelihood refinement using REFMAC[53] was carried out using bulk solvent correction (Babinet model).

Iterative structure refinement was carried out using a combination of CNS1.2 [42] and REFMAC5 [43] for simulated annealing, sigma A weighted composite omit electron density calculations, and restrained maximum likelihood refinement.

The best of these (Z score of 10) refined well in maximum-likelihood refinement using REFMAC [15] Rfree of 47% after 20 cycles) and the output built to near completion (342 residues of 411 possible) and an Rfree of 25% using ARP/wARP [16].

The model was refined with Refmac5 [75] using restrained maximum-likelihood refinement and TLS refinement [79].

The methods described are applicable to both least-squares and maximum-likelihood refinement protocols.

A single SpGH38 molecule was then used as a molecular replacement model with the 1.9 Å native dataset in PHASER [60], followed by cycles of maximum-likelihood refinement using REFMAC [61] interspersed with manual corrections of the models using COOT [62].

Several rounds of maximum-likelihood refinement and bulk solvent correction using all data over the whole resolution range were performed.

The free R factor is equivalent to the R factor, but is calculated using 5% of reflections excluded from the maximum-likelihood refinement stages.

Maximum-likelihood refinement using REFMAC [ 23], incorporating TLS (translation, libration screw-rotation) displacement refinement was carried out using a bulk solvent correction (Babinet model with mask) and autoBUSTER with TLS and the weighting fixed at 0.006 [ 21].