[modeller_usage] Optimization or Refinement of Homology Model

Modellers,

1) What level of refinement or MD_LEVEL is used as a default?

My top script is like this:

# A sample TOP file for fully automated comparative modeling INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 2 SET ATOM_FILES_DIRECTORY = '/mod6v2/ATOMS'SET ALIGNMENT_FORMAT = 'PIR' SET ALNFILE = 'model.ali' SET KNOWNS = 'template' SET SEQUENCE = 'model' SET STARTING_MODEL=1 SET ENDING_MODEL=10 CALL ROUTINE = 'model'

SUBROUTINE ROUTINE = 'special_restraints' ##there are a number of alpha helical and symmetry restraints ##omitted here for clarity. RETURN END_SUBROUTINE

2) After modelling, if there are "bumps" or poorly defined bond lengths or angles (based on ProCheck output), what is the preferred way of optimizing them?

Thanks for any input,

David