Non-crystallographic symmetry (NCS) can (and in many cases should) be included in refinement. In CNS two models for NCS are available:
Non-crystallographic symmetry is defined with the CNS auxiliary file ncs.def. This has sections for strict NCS and NCS restraints (either one or the other can be used at a given moment). Here we will perform a simulated annealing for a model with NCS restraints with two molecules in the asymmetric unit. The model consists of a dimer and the definition of NCS related atoms that is used internally to superimpose the protomers and generate restraints that maintain similarity between the two protomers. The NCS restraints are defined with the CNS task file ncs_restrain.def. To use NCS restraints requires that coordinates are known for all the protomers. In this case the two molecules in the dimer were located by molecular replacement. The relationship between protomers is defined by the use of atom selections:
The NCS restraint weight determines how strongly the protomers are restrained to be similar. A value of 300 to 500 results in protomers that are close to identical after superposition. A value of 10 puts very little weight on the NCS restraints and large deviations between related molecules are allowed. It is best to begin refinement with a high weight (300) and use the free R-value the determine if a lower weight is appropriate. After the NCS restraints have been defined a round of simulated annealing is performed:
cns_solve < anneal_restrain.inp > anneal_restrain.out [41 minutes]
Note that the model consists of residues 109 through 220 in each protomer. However, it is clear from the electron density map that the first 10 residues are in very different conformations in the two protomers. Therefore these residues are excluded from the NCS restraints.