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<FavorNativeResidue name="" bonus="(1.5 &bool)"/>Adds residue_type_constraints to the pose with the given bonus. The name is a slight misnomer -- the "native" residue which is favored is actually the identity of the residue of the current pose at apply time (-in:file:native is not used by this mover).
Running this mover multiple times will have a cumulative effect. For example, if FavorNativeResidue with a bonus of 1.5 is called twice in the same protocol, after the second instance, the bonus for each residue will be 3.0.
For more flexible usage see FavorSequenceProfileMover (with "scaling=prob matrix=IDENTITY", this will show the same native-bonus behavior).
IMPORTANT NOTE: This mover will update the weights of all of your scorefunctions to the weight provided in "bonus," unless that scorefunction already has a non-zero constraint weight. This may be what you want, but it can also lead to unexpected behavior. For example, if you want to determine the total_score without constraints (e.g. "pure" ref2015) using a SimpleMetric and you define a scorefxn without any constraint weights (e.g. "ref2015.wts"), FavorNativeResidue will add the residue_type_constraint of 1.5 to that scorefunction! If you want to get the same effect without changing your scorefunction weights, use the following mover instead:
<FavorSequenceProfile name="favournative" weight="1.5" use_current="true" matrix="IDENTITY"/>