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 2.55 High resolution limit 2.45 8.83 2.45 Rmerge (within I+/I-) 0.127 0.057 0.817 Rmerge (all I+ and I-) 0.130 0.058 0.848 Rmeas (within I+/I-) 0.140 0.063 0.898 Rmeas (all I+ & I-) 0.136 0.061 0.888 Rpim (within I+/I-) 0.058 0.027 0.373 Rpim (all I+ & I-) 0.040 0.019 0.263 Rmerge in top intensity bin 0.062 - - Total number of observations 288903 5972 32430 Total number unique 25576 592 2857 Mean((I)/sd(I)) 13.1 23.6 3.5 Mn(I) half-set correlation CC(1/2) 0.998 0.998 0.874 Completeness 100.0 99.7 100.0 Multiplicity 11.3 10.1 11.4 Mean(Chi^2) 1.08 0.72 0.96 Anomalous completeness 100.0 99.9 100.0 Anomalous multiplicity 5.8 5.6 5.8 DelAnom correlation between half-sets -0.270 -0.466 -0.055 Mid-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 Student Department of Chemistry and Biochemistry University 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
