PAIREF - results project

Run details and program versions

Working directory:

/public/pairef_datasets/tutorial_poli67/pairef_project

Run date and time:

2021-03-11 12:29:32

user@host:

malyma@localhost

PAIREF version:

1.2.2

REFMAC5 version:

5.8.0258

Python version and executable:

2.7.15 /protein2/phenix/phenix-1.16-3546/build/../conda_base/bin/python2.7

matplotlib version:

2.2.3

WARNING: The version of REFMAC5 used for refinement of the input structure model `poli67_edit12_2-3A_refmac1.pdb` (5.8.0158) is not the same as the version of REFMAC5 that is now installed and used during paired refinement (5.8.0258). The results from PAIREF could be misleading. Consider refinement of the structure model `poli67_edit12_2-3A_refmac1.pdb` using the installed version of REFMAC5. This could be performed using the arguments --refmac --prerefinement-ncyc

Overall values

Raw data: project_R-values.csv

# Shell      Rwork(init) Rwork(fin) Rwork(diff)   Rfree(init) Rfree(fin) Rfree(diff)
2.30A->2.10A      0.2266     0.2288      0.0022        0.2962     0.2970      0.0008
2.10A->2.00A      0.2374     0.2383      0.0009        0.3111     0.3107     -0.0004
2.00A->1.90A      0.2479     0.2476     -0.0003        0.3160     0.3169      0.0009

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

Raw data: project_Rgap.csv

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

Dependence on resolution

Optical resolution

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

Project:	project
High resolution diffraction limits:	2.30 Å, 2.10 Å, 2.00 Å, 1.90 Å
Initial structure model:	poli67_edit12_2-3A_refmac1.pdb
Merged diffraction data:	poli67_1-9A.mtz
Data with FreeRflag set 0 will be excluded during refinement.

Results - project

Input parameters