code: private void updateMultipleAlignment() throws StructureException,
  			RefinerFailedException {
  
  		msa.clear();
  
  		// Override the alignment with the new information
  		Block b = msa.getBlock(0);
  		b.setAlignRes(block);
  		repeatCore = b.getCoreLength();
  		if (repeatCore < 1)
  			throw new RefinerFailedException(
  					"Optimization converged to length 0");
  
  		SymmetryTools.updateSymmetryTransformation(axes, msa);
  	}
docs: This method translates the internal data structures to a
  MultipleAlignment of the repeats in order to use the methods to score
  MultipleAlignments.
  
  @throws StructureException
  @throws RefinerFailedException