Hello, it looks as though the No observations that phenix is reporting is exactly twice the number of unique reflections. Perhaps phenix is reporting the merging statistics for the Friedel pairs (i.e. F(+) and F(-)) within your merged dataset. Hence the stats look much better than those for the raw data fed to Aimless. I think you should be able to make a perfectly respectable Table 1 with the merging stats from Mosflm/Aimless and the refinement stats from phenix but others will know how to do it properly. On Monday, 28 October 2019, 20:05:52 GMT, Nemanja Vuksanovic <nema...@uwm.edu> wrote: Dear All, I need a bit of help with an issue I am encountering with one of my datasets when using phenix.refine. After processing data with Mosflm I get the following parameters:
Overall InnerShell OuterShell Low resolution limit 65.69 65.69 2.55High resolution limit 2.45 8.83 2.45Rmerge (within I+/I-) 0.127 0.057 0.817 Rmerge (all I+ and I-) 0.130 0.058 0.848Rmeas (within I+/I-) 0.140 0.063 0.898Rmeas (all I+ & I-) 0.136 0.061 0.888Rpim (within I+/I-) 0.058 0.027 0.373Rpim (all I+ & I-) 0.040 0.019 0.263Rmerge in top intensity bin 0.062 - - Total number of observations 288903 5972 32430Total number unique 25576 592 2857Mean((I)/sd(I)) 13.1 23.6 3.5Mn(I) half-set correlation CC(1/2) 0.998 0.998 0.874Completeness 100.0 99.7 100.0Multiplicity 11.3 10.1 11.4Mean(Chi^2) 1.08 0.72 0.96Anomalous completeness 100.0 99.9 100.0 Anomalous multiplicity 5.8 5.6 5.8DelAnom correlation between half-sets -0.270 -0.466 -0.055Mid-Slope of Anom Normal Probability 0.788 - - After molecular replacement with PHASER and then refinement with Phenix.refine, (defauIt settings in both) I generated a TABLE 1 in PHENIX and noticed that the total number of observations has dropped, significantly lowering multiplicity and R factors. Could you perhaps give me your opinion on what might be causing this discrepancy?I'd be happy to provide the mtz file and any other information if needed. Table 1. Data collection and refinement statistics. Wavelength Resolution range 56.89 - 2.451 (2.539 - 2.451) Space group I 2 3 Unit cell 160.9 160.9 160.9 90 90 90 Total reflections 51076 (5030) Unique reflections 25538 (2515) Multiplicity 2.0 (2.0) Completeness (%) 99.96 (100.00) Mean I/sigma(I) 13.37 (3.56) Wilson B-factor 41.08 R-merge 0.0263 (0.1879) R-meas 0.03719 (0.2657) R-pim 0.0263 (0.1879) CC1/2 0.999 (0.895) CC* 1 (0.972) Reflections used in refinement 25532 (2515) Reflections used for R-free 1300 (121) R-work 0.2698 (0.3589) R-free 0.3115 (0.3897) CC(work) 0.908 (0.679) CC(free) 0.885 (0.444) Number of non-hydrogen atoms 2310 macromolecules 2310 Protein residues 286 RMS(bonds) 0.010 RMS(angles) 1.01 Ramachandran favored (%) 96.40 Ramachandran allowed (%) 2.52 Ramachandran outliers (%) 1.08 Rotamer outliers (%) 0.00 Clashscore 8.47 Average B-factor 43.55 Best Regards,Nemanja Vuksanovic -- Graduate StudentDepartment of Chemistry and BiochemistryUniversity of Wisconsin-Milwaukee To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1