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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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</blockquote>
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