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    Hello,<br>
    <br>
    default setting is 10% with max 2000 reflections. As Georg said,
    0=Work and 1=Test (free). phenix.refine tries its best to figure out
    what are "work" and "free" flags, as different programs have
    different conventions.<br>
    <br>
    Unless you changed the default, I think you get more than 2000 flags
    because Fobs+ and Fobs- are counted as separate reflections (2
    reflections), while each one of the two must have the same flag (for
    example, if Fobs+ is "1" then Fobs- must be "1" too).<br>
    <br>
    Pavel<br>
    <br>
    <br>
    <div class="moz-cite-prefix">On 1/21/15 1:31 PM, Tarek DawoD wrote:<br>
    </div>
    <blockquote
cite="mid:1388758317.2840520.1421875866790.JavaMail.yahoo@jws100145.mail.ne1.yahoo.com"
      type="cite">
      <div style="color:#000; background-color:#fff;
        font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
        Lucida Grande, sans-serif;font-size:8px">
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""
          dir="ltr"><font id="yui_3_16_0_1_1421873316626_20318" size="2">Dear
            ALL</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""
          dir="ltr"><font size="2"><br>
          </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""
          dir="ltr"><font id="yui_3_16_0_1_1421873316626_20054" size="2">when
            you start you refinment 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="yui_3_16_0_1_1421873316626_19750" class="" style=""
          dir="ltr"><font id="yui_3_16_0_1_1421873316626_20069" size="2">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="yui_3_16_0_1_1421873316626_19750" class="" style=""
          dir="ltr"><font size="2"><br>
          </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""
          dir="ltr"><font id="yui_3_16_0_1_1421873316626_20313" size="2">when
            you look in generated mtz file after the refinment, you see
            under R-free-flags(+) and R-free-flags(-)  either 0 or 1.
            what does 0 or 1 mean?</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""
          dir="ltr"><font size="2"><br>
          </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""
          dir="ltr"><font id="yui_3_16_0_1_1421873316626_20317" size="2">thank
            you in advance for explaination.</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""
          dir="ltr"><font size="2"><br>
          </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""
          dir="ltr"><font size="2">TKDawoD</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" size="2"><br>
          </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_20010"
            size="2">----------------------------------------------------------------------------------------------------</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_20008"
            size="2">REMARK   3   NUMBER OF REFLECTIONS             :
            47312     </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_20007"
            size="2">REMARK   3   NUMBER OF REFLECTIONS (NON-ANOMALOUS)
            : 24389     </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_20006"
            size="2">REMARK   3  </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_20005"
            size="2">REMARK   3  FIT TO DATA USED IN REFINEMENT.</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_20000"
            size="2">REMARK   3   R VALUE     (WORKING + TEST SET) :
            0.1673</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_20004"
            size="2">REMARK   3   R VALUE            (WORKING SET) :
            0.1636</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_20003"
            size="2">REMARK   3   FREE R VALUE                     :
            0.2084</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_20002"
            size="2">REMARK   3   FREE R VALUE TEST SET SIZE   (%) :
            8.21  </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_20001"
            size="2">REMARK   3   FREE R VALUE TEST SET COUNT      :
            3882</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_19952"
            size="2">------------------------------------------------------------------------------------------------------</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_19951"
            size="2">REMARK   3   NUMBER OF REFLECTIONS             :
            107005   </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_19950"
            size="2">REMARK   3   NUMBER OF REFLECTIONS (NON-ANOMALOUS)
            : 56251    </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_19949"
            size="2">REMARK   3  </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_19948"
            size="2">REMARK   3  FIT TO DATA USED IN REFINEMENT.</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            id="yui_3_16_0_1_1421873316626_19925" class="" style=""
            size="2">REMARK   3   R VALUE     (WORKING + TEST SET) :
            0.1457</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_19947"
            size="2">REMARK   3   R VALUE            (WORKING SET) :
            0.15.34</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_19946"
            size="2">REMARK   3   FREE R VALUE                     :
            0.1997</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_19945"
            size="2">REMARK   3   FREE R VALUE TEST SET SIZE   (%) :
            3.51 </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            class="" style="" id="yui_3_16_0_1_1421873316626_19944"
            size="2">REMARK   3   FREE R VALUE TEST SET COUNT      :
            3809</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            id="yui_3_16_0_1_1421873316626_19896" size="2">-----------------------------------------------------------------------------------------------------</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            id="yui_3_16_0_1_1421873316626_19895" size="2">NUMBER OF
            REFLECTIONS             : 48150     </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            id="yui_3_16_0_1_1421873316626_19894" size="2">REMARK   3  
            NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 25296     </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            id="yui_3_16_0_1_1421873316626_19897" size="2">REMARK   3  </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            id="yui_3_16_0_1_1421873316626_19893" size="2">REMARK   3
             FIT TO DATA USED IN REFINEMENT.</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            id="yui_3_16_0_1_1421873316626_19892" size="2">REMARK   3  
            R VALUE     (WORKING + TEST SET) : 0.1507</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            id="yui_3_16_0_1_1421873316626_19891" size="2">REMARK   3  
            R VALUE            (WORKING SET) : 0.1470</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            id="yui_3_16_0_1_1421873316626_19890" size="2">REMARK   3  
            FREE R VALUE                     : 0.1918</font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            id="yui_3_16_0_1_1421873316626_19889" size="2">REMARK   3  
            FREE R VALUE TEST SET SIZE   (%) : 7.98  </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><font
            id="yui_3_16_0_1_1421873316626_19888" size="2">REMARK   3  
            FREE R VALUE TEST SET COUNT      : 3841     </font></div>
        <div id="yui_3_16_0_1_1421873316626_19750" class="" style=""><br
            class="" style="">
        </div>
      </div>
      <br>
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      <br>
      <pre wrap="">_______________________________________________
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</pre>
    </blockquote>
    <br>
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