PAIREF - results poli

VERDICT - suggested cutoff: strict: 2.10 A; benevolent: 2.00 A

Shell	Accepted?	Reason
2.30-2.10 A	Yes	Overall Rfree decreased while using data in the shell 2.30-2.10 A
2.10-2.00 A	Warning	Overall Rfree decreased while using data in the shell 2.10-2.00 A Rfree in high resolution is higher than 0.40 while using data in the shell 2.10-2.00 A Rwork in high resolution is higher than 0.40 while using data in the shell 2.10-2.00 A
2.00-1.90 A	No	Overall Rfree decreased while using data in the shell 2.00-1.90 A Rfree in high resolution is higher than 0.40 while using data in the shell 2.00-1.90 A Rwork in high resolution is higher than 0.40 while using data in the shell 2.00-1.90 A CC1/2 in high resolution is negative or undefined while using data in the shell 2.00-1.90 A But statistics deteriorate in a previous resolution shell.

Shell

Accepted?

Reason

2.30-2.10 A

Yes

Overall Rfree decreased while using data in the shell 2.30-2.10 A

2.10-2.00 A

Warning

Overall Rfree decreased while using data in the shell 2.10-2.00 A
Rfree in high resolution is higher than 0.40 while using data in the shell 2.10-2.00 A
Rwork in high resolution is higher than 0.40 while using data in the shell 2.10-2.00 A

2.00-1.90 A

Overall Rfree decreased while using data in the shell 2.00-1.90 A
Rfree in high resolution is higher than 0.40 while using data in the shell 2.00-1.90 A
Rwork in high resolution is higher than 0.40 while using data in the shell 2.00-1.90 A
CC1/2 in high resolution is negative or undefined while using data in the shell 2.00-1.90 A
But statistics deteriorate in a previous resolution shell.

Input parameters

Project:

poli_ccp4sw2023

High resolution diffraction limits:

2.30 Å, 2.10 Å, 2.00 Å, 1.90 Å

Initial structure model:

poli67_webinar_2-3A.pdb

Merged diffraction data:

poli67_1-9A.mtz

Unmerged diffraction data:

poli67_XDS_ASCII_1-9A.HKL

Weight matrix for REFMAC5:

0.0600

Data with FreeRflag set 0 will be excluded during refinement.

Run details and program versions

Working directory:

/home/martin/Documents/PAIREF_webinar_poli/pairef_poli_ccp4sw2023

Run date and time:

2022-12-21 13:04:18

user@host:

martin@precision

PAIREF version:

1.3.9

REFMAC5 version:

5.8.0403

Python version and executable:

3.7.12 /opt/ccp4/ccp4-8.0/libexec/python3.7

matplotlib version:

3.3.4

WARNING: The version of REFMAC5 used for refinement of the input structure model `poli67_webinar_2-3A.pdb` (5.8.0258) is not the same as the version of REFMAC5 that is now installed and used during paired refinement (5.8.0403). The results from PAIREF could be misleading. Consider refinement of the structure model `poli67_webinar_2-3A.pdb` using the installed version of REFMAC5. This could be performed using the arguments --refmac --prerefinement-ncyc

Overall values

Raw data: poli_ccp4sw2023_R-values.csv

# Shell      Rwork(init) Rwork(fin) Rwork(diff)   Rfree(init) Rfree(fin) Rfree(diff)
2.30A->2.10A      0.2255     0.2232     -0.0023        0.2989     0.2956     -0.0033
2.10A->2.00A      0.2325     0.2315     -0.0010        0.3108     0.3096     -0.0012
2.00A->1.90A      0.2413     0.2422      0.0009        0.3178     0.3166     -0.0012

Note: For each incremental step of resolution from X->Y, the R-values were calculated at resolution X.

Raw data: poli_ccp4sw2023_Rgap.csv

Note: The R-values were calculated at 2.30 Å resolution.

Model statistics - binned values

Optical resolution

Merging statistics

#shell d_max d_min #obs #uniq mult. %comp <I> <I/sI> r_mrg r_meas r_pim r_anom cc1/2 cc_ano cc* 01 47.05 5.13 22367 1948 11.48 99.44 494.1 38.8 0.042 0.044 0.013 0.021 0.999 -0.214 0.9997 02 5.13 3.63 42232 3343 12.63 99.79 203.3 31.7 0.064 0.067 0.019 0.031 0.999 -0.163 0.9997 03 3.63 2.97 57138 4246 13.46 99.95 56.9 14.3 0.151 0.157 0.042 0.072 0.997 -0.166 0.9992 04 2.97 2.57 65007 5014 12.97 99.70 11.3 4.0 0.622 0.648 0.178 0.325 0.951 -0.025 0.9874 05 2.57 2.30 73887 5623 13.14 99.89 3.7 1.3 1.839 1.914 0.523 0.848 0.730 -0.014 0.9187 06 2.30 2.10 83129 6181 13.45 99.92 1.2 0.4 5.812 6.041 1.633 1.518 0.311 0.001 0.6888 07 2.10 2.00 49772 4021 12.38 98.51 0.3 0.1 16.989 17.721 4.963 1.944 0.027 0.008 0.2293 08 2.00 1.90 35920 4046 8.88 81.18 0.1 0.0 41.435 43.993 14.417 2.297 -0.132 -0.016 N/A

Statistics vs. cycle

Log file from refinement at 2.10 Å
Structure model refined at 2.10 Å PDB mmCIF

Log file from refinement at 2.00 Å
Structure model refined at 2.00 Å PDB mmCIF

Log file from refinement at 1.90 Å
Structure model refined at 1.90 Å PDB mmCIF

References

Paired refinement under the control of PAIREF. M. Maly, K. Diederichs, J. Dohnalek, P. Kolenko (2020) IUCrJ 7

Overview of the CCP4 suite and current developments. Collaborative Computational Project, Number 4 (2011) Acta Cryst. D67:235-242

REFMAC5 for the refinement of macromolecular crystal structures. G.N. Murshudov, P. Skubak, A.A. Lebedev, N.S. Pannu, R.A. Steiner, R.A. Nicholls, M.D. Winn, F. Long, A.A. Vagin (2011) Acta Cryst. D67:355-367

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. A.A. Vaguine, J. Richelle, S.J. Wodak (1999) Acta Cryst. D55:191-205

The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework. R.W. Grosse-Kunstleve, N.K. Sauter, N.W. Moriarty, P.D. Adams (2002) J. Appl. Crystallogr. 35:126-136

Linking crystallographic model and data quality. P.A. Karplus & K. Diederichs (2012) Science 336:1030-3

Assessing and maximizing data quality in macromolecular crystallography. P.A. Karplus & K. Diederichs (2015) Cur. Op. in Str. Biology 34:60-68

Better models by discarding data? P.A. Karplus & K. Diederichs (2013) Acta Cryst. D59:1215-1222

Results - poli_ccp4sw2023