<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:13px"><div dir="ltr" id="yui_3_16_0_1_1421873316626_31729">Dear ALL</div><div dir="ltr" id="yui_3_16_0_1_1421873316626_31728"><br></div><div class="qtdSeparateBR"><br><br></div><div class="yahoo_quoted" id="yui_3_16_0_1_1421873316626_30996" style="display: block;"><div id="yui_3_16_0_1_1421873316626_30995"><div id="yui_3_16_0_1_1421873316626_30994"><div class="y_msg_container" id="yui_3_16_0_1_1421873316626_30993"><div id="yiv8970247139"><div id="yui_3_16_0_1_1421873316626_30992"><div style="background-color: rgb(255, 255, 255);" id="yui_3_16_0_1_1421873316626_30991"><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" style="color: rgb(0, 0, 0); font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 8px;" dir="ltr"><font size="2" id="yiv8970247139yui_3_16_0_1_1421873316626_20054">when you start you refinement in phenix with ***.sca file, fraction of reflection in test set will be created. under <b>options </b>(bottom) in phenix refine, you could see that fraction of reflection in test set is 0.1 which means 10 %</font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" style="color: rgb(0, 0, 0); font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 8px;" dir="ltr"><font size="2" id="yiv8970247139yui_3_16_0_1_1421873316626_20069">by looking to the PDB header for completely different structures (below) you will find different percentage but always FREE R VALUE TEST SET COUNT is around 3800. so it always take the same 3800 count regardless the number of reflections.</font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" style="color: rgb(0, 0, 0); font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 8px;" dir="ltr"><font size="2"><br></font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" style="color: rgb(0, 0, 0); font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 8px;" dir="ltr"><font size="2" id="yiv8970247139yui_3_16_0_1_1421873316626_20313">When you look in generated mtz file after the refinement, you see under R-free-flags(+) and R-free-flags(-) either 0 or 1. what does 0 or 1 mean?</font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" style="color: rgb(0, 0, 0); font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 8px;" dir="ltr"><font size="2"><br></font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" style="color: rgb(0, 0, 0); font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 8px;" dir="ltr"><font size="2" id="yiv8970247139yui_3_16_0_1_1421873316626_20317">Thank you in advance for explanation.</font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" style="color: rgb(0, 0, 0); font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 8px;" dir="ltr"><font size="2"><br></font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" dir="ltr" style="color: rgb(0, 0, 0); font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif;"><font size="2" id="yui_3_16_0_1_1421873316626_31121">number of reflection : 47312</font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" dir="ltr" style="color: rgb(0, 0, 0); font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif;"><font size="2" id="yui_3_16_0_1_1421873316626_31120">number of reflections (non-anomalous): 24389</font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" dir="ltr" style="color: rgb(0, 0, 0); font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif;"><font size="2" id="yui_3_16_0_1_1421873316626_31112">R value (working set): 0.1673</font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" dir="ltr"><font size="2" id="yui_3_16_0_1_1421873316626_31119">free R value : 0.2084<br></font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" dir="ltr"><font size="2" id="yui_3_16_0_1_1421873316626_31124">free r value test set size (%): 8.21</font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" dir="ltr"><font size="2" id="yui_3_16_0_1_1421873316626_31122">free R value test set count : 3882</font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" dir="ltr"><br></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" dir="ltr"><font size="2" id="yui_3_16_0_1_1421873316626_31137"><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style="">number of reflection : 107005</div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style="">number of reflections (non-anomalous): 56251</div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style="">R value (working set):0.1534 </div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style="">free R value : 0.1997</div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style="">free r value test set size (%): 3.51</div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style="">free R value test set count : 3809</div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style=""><br></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style=""><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style="">number of reflection : 48150</div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style="">number of reflections (non-anomalous): 25296</div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style="">R value (working set): 0.1470</div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style="">free R value : 0.1918</div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style="">free r value test set size (%): 7.98</div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style="">free R value test set count : 3841</div></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style=""><br></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="" dir="ltr" style=""><br></div></font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" style="color: rgb(0, 0, 0); font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 8px;" dir="ltr"><font size="2" id="yui_3_16_0_1_1421873316626_31405">TKDawoD</font></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" style="color: rgb(0, 0, 0); font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 8px;" dir="ltr"><br></div><div id="yiv8970247139yui_3_16_0_1_1421873316626_19750" class="yiv8970247139" style="color: rgb(0, 0, 0); font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 8px;"><br class="yiv8970247139" style=""></div></div></div></div><br><br></div> </div> </div> </div> </div></body></html>