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Hi Carsten,<br>
<br>
they have to match exactly, if they don't then there is something
wrong somewhere...<br>
<br>
I just did a few refinement runs and I can't reproduce this. What is
the command that results in this inconsistency between R-factors?<br>
<br>
Pavel.<br>
<br>
On 5/30/11 11:07 AM, Schubert, Carsten [PRDUS] wrote:
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<title>Inconsistent R-factors in PDB file</title>
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<p dir="LTR"><span lang="en-us"><font face="Calibri">Hi,</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Calibri">Not sure if
this has been asked before but recently I notice</font></span><span
lang="en-us"><font face="Calibri">d phenix seems to report
inconsistent R-values after each refinement</font></span><span
lang="en-us"><font face="Calibri">.</font></span><span
lang="en-us"> <font face="Calibri">The</font></span><span
lang="en-us"> <font face="Calibri">final</font></span><span
lang="en-us"> <font face="Calibri">values reported in the</font></span><span
lang="en-us"> <font face="Calibri">screen</font></span><span
lang="en-us"> <font face="Calibri">output after refinement
match the values reported in the</font></span><span
lang="en-us"> <font face="Calibri">‘</font></span><span
lang="en-us"><font face="Calibri">Quick Facts</font></span><span
lang="en-us"><font face="Calibri">’</font></span><span
lang="en-us"><font face="Calibri"> section, but are not
matched by the values in the PDB deposition section.
Attached is an example:</font></span></p>
<p dir="LTR"><span lang="en-us"></span><span lang="en-us"></span></p>
<p dir="LTR"><span lang="en-us"></span><span lang="en-us"><font
face="Courier New">...</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
******************** REFINEMENT SUMMARY: QUICK FACTS
*******************</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
Start: r_work = 0.1907 r_free = 0.2151 bonds = 0.004 angles
= 0.727</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
Final: r_work =</font></span><span lang="en-us"></span><span
lang="en-us"><b> <font face="Courier New">0.1838</font></b></span><span
lang="en-us"></span><span lang="en-us"><font face="Courier
New"> r_free =</font></span><span lang="en-us"></span><span
lang="en-us"><b> <font face="Courier New">0.2141</font></b></span><span
lang="en-us"></span><span lang="en-us"><font face="Courier
New"> bonds = 0.005 angles = 0.832</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
************************************************************************</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">...</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK IF
THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE
UP.</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 REFINEMENT.</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 PROGRAM : PHENIX (phenix.refine: 1.7.1_743)</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 AUTHORS : Adams,Afonine,Chen,Davis,Echols,Gopal,</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 :
Grosse-Kunstleve,Headd,Hung,Immormino,Ioerger,McCoy,</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 :
McKee,Moriarty,Pai,Read,Richardson,Richardson,Romo,</font></span></p>
<p dir="LTR"><span lang="en-us"></span><span lang="en-us"></span><span
lang="de"><font face="Courier New">REMARK 3 :
Sacchettini,Sauter,Smith,Storoni,Terwilliger,Zwart</font></span></p>
<p dir="LTR"><span lang="en-us"></span><span lang="en-us"><font
face="Courier New">REMARK 3</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 REFINEMENT TARGET : ML</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 </font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 DATA USED IN REFINEMENT.</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.950 </font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.113 </font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 MIN(FOBS/SIGMA_FOBS) : 1.33 </font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 COMPLETENESS FOR RANGE (%) : 92.21 </font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 NUMBER OF REFLECTIONS : 29410 </font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 </font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 FIT TO DATA USED IN REFINEMENT.</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 R VALUE (WORKING + TEST SET) : 0.1894</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 R VALUE (WORKING SET) :</font></span><span
lang="en-us"></span><span lang="en-us"><b> <font
face="Courier New">0.1877</font></b></span><span
lang="en-us"></span><span lang="en-us"></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 FREE R VALUE :</font></span><span
lang="en-us"></span><span lang="en-us"><b> <font
face="Courier New">0.2122</font></b></span></p>
<p dir="LTR"><span lang="en-us"></span><span lang="en-us"><font
face="Courier New">REMARK 3 FREE R VALUE TEST SET SIZE
(%) : 6.74 </font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Courier New">REMARK
3 FREE R VALUE TEST SET COUNT : 1982 </font></span><span
lang="en-us"></span><span lang="en-us"> </span></p>
<p dir="LTR"><span lang="en-us"></span></p>
<p dir="LTR"><span lang="en-us"><font face="Calibri">For regular
work I really don</font></span><span lang="en-us"><font
face="Calibri">’</font></span><span lang="en-us"><font
face="Calibri">t care as long as the values are consistent
and tell me if the refinement reached convergence, but for a</font></span><span
lang="en-us"><font face="Calibri"> deposition it matters a bit
more. So w</font></span><span lang="en-us"><font
face="Calibri">hich values should I report</font></span><span
lang="en-us"><font face="Calibri"> for a paper?</font></span></p>
<p dir="LTR"><span lang="en-us"><font face="Calibri">Cheers,</font></span></p>
<p dir="LTR"><span lang="en-us"> <font face="Calibri">Carsten</font></span></p>
<p dir="LTR"><span lang="en-us"></span></p>
<p dir="LTR"><span lang="en-us"></span></p>
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</pre>
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