Changing default values for -loops:outer_cycles to 5 and -loops:max_kic_perturber_samples to 2000
since our tests using the 45 loops benchmark set have shown considerable loop modeling performance
increases with these values.
These have already been the recommended values for next generation KIC, which is currently also
the recommended loop modeling protocol to use (I updated the documentation wiki for the loop
modeling app accordingly and will upload it once the server becomes accessible again).
Due to trajectory changes originating from changing the default values for those two
parameters, I expect the following list of integration tests to change:
rosetta_scripts_loops
antibody_H3
UBQ_E2_thioester_extra_bodies
kinematic_looprelax
KIC_refine
SnugDock
next_generation_KIC
AnchoredDesign
The following integration tests have already failed before and are not affected by this commit:
torsion_restricted_sampling
centroid_disulfide_scores
No other test changes expected.