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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"><B></B></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"><B></B></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"><B></B></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"><B></B></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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