Hi, following Jonathan's reply, unless you specify "no anomalous" in the input file, Phenix will refine by default against the anomalous data in your input mtz, even if the signal is weak. You should also check how you define the type of mtz
columns to be used in the refinement. There are several options in the data input part of the gui.
Boaz
Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel
On Oct 29, 2019 00:05, Jonathan Cooper <00000c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
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 2.55
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
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
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
