42"></a>00442       A_my_IK.<a class="code" href="classSimSite3D_1_1IK__tests.html#fac5e4fb00a62ec37cc72f53ebb20cfd">run</a>(A_model, *dset_site, &amp;(*top_align), db_struct_id, std::cout);
<a name="l00443"></a>00443     
<a name="l00444"></a>00444     <span class="comment">// Clear the given map holding the "unrefined" alignments and insert</span>
<a name="l00445"></a>00445     <span class="comment">// the refined alignment and its score</span>
<a name="l00446"></a>00446     tier2_score_mmi aligns_iter = 