Dear Matt, Your data past 2.5A is awfully weak, and wont contribute much to any map you calculate. Each term at the outer resolution will have a very low weight. I sometimes cling to the belief that the weak data may help the B factor refinement, but there isnt much evidence of that. There is a feeling that once I/SigI is << 1 the data is no use.. Looking at those statistics I would cut the resolution to 2.75.
What does the I2 data processing report suggest as the cut off? Eleanor On Fri, 30 Sept 2022 at 17:21, Andrew Purkiss < a.purk...@mail.cryst.bbk.ac.uk> wrote: > Is the data anisotropic? This would explain the strange processing > statistics beyond 3.0 Angstrom. If using Dials directly it is worth > looking for abnormalities with the reciprocal lattice viewer. > > I've seen similar issues with the completeness being low, when data is > weak in one direction, despite reflections being reported in the > scaling output. > > It may also be worth running some analysis of the data with Staraniso > (https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi) to try to > help. > > Andy > > > > > Quoting Martin Malý <martin.m...@ibt.cas.cz>: > > > Dear Matt, > > > > thank you for asking. I am bit confused how you set up the PAIREF > > run. In paired refinement, data are added step by step - going to > > higher resolution, i.e. lower d_hkl. So the merged data in the > > PAIREF input should not be cut to much. The data statistics look > > from DIALS quite strange, there is very good completeness and CC1/2 > > for high resolution shells, but very poor <I/sigma> and Rmeas. > > > > I would suggest to refine the model at 3 A to be safe. Then, run > > PAIREF with the initial resolution 3 A and using the cutoffs 2.8, > > 2.6, 2.4 and 2.2 A. Diffraction data must be up to 2.2 A in that > > case, no truncation to 2.4 A as you mentioned previously. > > > > I hope it will help. Please feel free to ask and let me know if it > > was successful. > > > > Best regards, > > Martin > > > > > > On 30. 09. 22 17:29, Matt McLeod wrote: > >> Hi all, > >> > >> I am having a bit of trouble with PAIREF. I am trying to determine > >> the resolution cutoff of a dataset which has a high Rwork > >> (0.223)/free (0.275)value for the resolution (2.24A). I have > >> truncated this data further to 2.4A and the R values get better but > >> the electron density maps do not improve whatsoever. When I put > >> this data into PAIREF I get this message. > >> > >> WARNING: There are only 40 < 50 free reflections in the resolution > >> shell 2.75-2.70 A. Values of statistics Rfree and CCfree in this > >> shell could be misleading. Consider setting thicker resolution > >> shells. > >> > >> This error occurs for all resolution bins. Looking at the pdb log > >> of the refined structure (where the data looks quite reasonable, > >> maybe not a 2.3 dataset but not much worse). > >> > >> REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). > >> REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK > >> RFREE CCWORK CCFREE > >> REMARK 3 1 60.08 - 4.28 1.00 4135 213 0.1646 > >> 0.2213 0.940 0.901 > >> REMARK 3 2 4.28 - 3.40 1.00 4095 201 0.1951 > >> 0.2672 0.928 0.857 > >> REMARK 3 3 3.40 - 2.97 1.00 4099 204 0.2736 > >> 0.3303 0.861 0.739 > >> REMARK 3 4 2.97 - 2.70 1.00 4026 212 0.3486 > >> 0.3508 0.726 0.551 > >> REMARK 3 5 2.70 - 2.51 0.78 3178 154 0.4027 > >> 0.4062 0.637 0.594 > >> REMARK 3 6 2.50 - 2.36 0.29 1154 60 0.4118 > >> 0.3984 0.647 0.547 > >> REMARK 3 7 2.36 - 2.24 0.01 29 1 0.3366 > >> 0.4089 0.343 0.000 > >> > >> Where I assume NFree is the issue, but doesn't suggest that there > >> arent enough reflections. There needs to be a higher cutoff as the > >> completeness goes to pot, but the scaling log from DIALS suggested > >> it was at least a good starting point. > >> > >> Statistics by resolution bin: > >> d_max d_min #obs #uniq mult. %comp <I> > >> <I/sI> r_mrg r_meas r_pim cc1/2 cc_ano > >> 118.81 5.97 10436 1577 6.62 99.94 797.6 > >> 22.8 0.110 0.120 0.046 0.992* -0.397 > >> 5.97 4.74 9602 1549 6.20 100.00 491.7 > >> 10.0 0.172 0.188 0.075 0.979* -0.240 > >> 4.74 4.14 10410 1528 6.81 100.00 513.5 > >> 10.3 0.191 0.207 0.079 0.978* -0.281 > >> 4.14 3.76 10833 1551 6.98 100.00 324.7 > >> 6.9 0.238 0.257 0.098 0.969* -0.419 > >> 3.76 3.49 10956 1526 7.18 100.00 207.5 > >> 4.6 0.259 0.280 0.105 0.975* -0.271 > >> 3.49 3.29 10899 1546 7.05 100.00 133.4 > >> 3.1 0.272 0.294 0.111 0.966* -0.258 > >> 3.29 3.12 9565 1528 6.26 99.93 86.9 > >> 2.0 0.314 0.343 0.136 0.935* -0.346 > >> 3.12 2.99 9256 1519 6.09 100.00 57.1 > >> 1.3 0.354 0.387 0.154 0.932* -0.354 > >> 2.99 2.87 9317 1524 6.11 100.00 43.6 > >> 1.0 0.403 0.441 0.177 0.934* -0.198 > >> 2.87 2.77 10087 1549 6.51 100.00 30.9 > >> 0.7 0.455 0.494 0.192 0.923* -0.116 > >> 2.77 2.69 10157 1524 6.66 100.00 26.4 > >> 0.6 0.503 0.546 0.210 0.927* -0.132 > >> 2.69 2.61 10351 1541 6.72 100.00 19.3 > >> 0.4 0.613 0.665 0.255 0.925* -0.155 > >> 2.61 2.54 10121 1504 6.73 100.00 15.5 > >> 0.4 0.735 0.797 0.306 0.906* -0.088 > >> 2.54 2.48 10510 1539 6.83 100.00 12.4 > >> 0.3 0.932 1.009 0.385 0.857* 0.006 > >> 2.48 2.42 10432 1519 6.87 100.00 11.2 > >> 0.2 0.972 1.052 0.399 0.829* -0.111 > >> 2.42 2.37 10596 1532 6.92 100.00 10.2 > >> 0.2 1.095 1.184 0.447 0.844* -0.083 > >> 2.37 2.32 10577 1535 6.89 100.00 8.9 > >> 0.2 1.259 1.361 0.514 0.825* -0.082 > >> 2.32 2.28 10217 1513 6.75 100.00 7.8 > >> 0.2 1.421 1.540 0.587 0.725* -0.056 > >> 2.28 2.24 9702 1521 6.38 100.00 6.4 > >> 0.1 1.683 1.834 0.721 0.600* -0.001 > >> 2.24 2.20 9551 1538 6.21 100.00 6.1 > >> 0.1 1.895 2.071 0.826 0.603* -0.041 > >> 118.64 2.20 203575 30663 6.64 99.99 142.0 > >> 3.3 0.222 0.241 0.093 0.989* -0.265 > >> > >> > >> > >> Does anyone have any insight into where PAIREF is getting hung up? > >> I am welcome to any other suggestions with regards to handling this > >> dataset to determine resolution cutoff. I can also supply any > >> other log files that may be useful > >> > >> Matt > >> > >> ######################################################################## > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > >> > >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > >> available at https://www.jiscmail.ac.uk/policyandsecurity/ > > > > ######################################################################## > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
