Results - CDO_step0-10A

Calculations ended successfully.

Input parameters

Project:CDO_step0-10A
High resolution diffraction limits:2.00 Å, 1.90 Å, 1.80 Å, 1.70 Å, 1.60 Å, 1.50 Å, 1.42 Å
Initial structure model:2B5H_edit_refmac1.pdb
Merged diffraction data:CDO_R.mtz
Unmerged diffraction data:XDS_ASCII.HKL
Data with FreeRflag set 0 will be excluded during refinement.

Run details and program versions

Working directory:/public/pairef_datasets/publication_examples/3-3_CDO/pairef_CDO_step0-10A
Run date and time:2020-05-26 10:34:09
user@host:maly@localhost
PAIREF version:1.1.0
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 `2B5H_edit_refmac1.pdb` (5.8.0257) 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 `2B5H_edit_refmac1.pdb` using the installed version of REFMAC5. This could be performed using the arguments --refmac --prerefinement-ncyc

Overall values

R-values
Raw data: CDO_step0-10A_R-values.csv
# Shell      Rwork(init) Rwork(fin) Rwork(diff)   Rfree(init) Rfree(fin) Rfree(diff)
2.00A->1.90A      0.1561     0.1579      0.0018        0.2180     0.2135     -0.0045
1.90A->1.80A      0.1596     0.1607      0.0011        0.2139     0.2088     -0.0051
1.80A->1.70A      0.1671     0.1677      0.0006        0.2160     0.2125     -0.0035
1.70A->1.60A      0.1777     0.1783      0.0006        0.2224     0.2222     -0.0002
1.60A->1.50A      0.1919     0.1920      0.0001        0.2342     0.2345      0.0003
1.50A->1.42A      0.2068     0.2069      0.0001        0.2445     0.2442     -0.0003

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

Rgap
Raw data: CDO_step0-10A_Rgap.csv

Note: The R-values were calculated at 2.00 Å resolution.

Dependence on resolution

Rfree CCfree
Rwork CCwork
Raw data: No_work_free_reflections

Optical resolution

Optical resolution
Raw data: CDO_step0-10A_Optical_resolution.csv

Merging statistics

CC Intensities Comp_Mult Rmerge_Rmeas_Rpim No_reflections

Raw data: CDO_step0-10A_merging_stats.csv

#shell d_max  d_min   #obs  #uniq   mult.  %comp       <I>  <I/sI>    r_mrg   r_meas    r_pim   cc1/2   cc_ano     cc* 
01     41.96   3.98  30502   2013   15.15 100.00     509.9    92.4    0.029    0.030    0.008   1.000   0.444   1.0000
02      3.98   2.83  55734   3335   16.71 100.00     382.3    74.0    0.048    0.049    0.012   1.000   0.178   1.0000
03      2.83   2.31  73318   4261   17.21 100.00     152.2    40.9    0.127    0.131    0.031   0.999   0.046   0.9997
04      2.31   2.00  86730   5014   17.30 100.00     100.2    23.4    0.254    0.261    0.062   0.997   0.009   0.9992
05      2.00   1.90  40614   2360   17.21 100.00      60.5    13.0    0.412    0.425    0.101   0.993  -0.011   0.9982
06      1.90   1.80  48612   2886   16.84 100.00      31.9     6.8    0.577    0.595    0.144   0.976   0.015   0.9939
07      1.80   1.70  60936   3619   16.84 100.00      16.1     3.5    0.854    0.881    0.214   0.933   0.108   0.9825
08      1.70   1.60  65470   4548   14.40 100.00       8.9     1.9    1.251    1.297    0.340   0.783   0.144   0.9372
09      1.60   1.50  60309   5862   10.29 100.00       4.9     0.9    2.023    2.130    0.653   0.441  -0.021   0.7824
10      1.50   1.42  27549   5842    4.72  98.83       2.9     0.3    3.175    3.557    1.527   0.074   0.004   0.3712
		

Statistics vs. cycle

1.90A statistics vs. cycle, flag 00
Log file from refinement at 1.90 Å
Structure model refined at 1.90 Å PDB mmCIF
1.80A statistics vs. cycle, flag 00
Log file from refinement at 1.80 Å
Structure model refined at 1.80 Å PDB mmCIF
1.70A statistics vs. cycle, flag 00
Log file from refinement at 1.70 Å
Structure model refined at 1.70 Å PDB mmCIF
1.60A statistics vs. cycle, flag 00
Log file from refinement at 1.60 Å
Structure model refined at 1.60 Å PDB mmCIF
1.50A statistics vs. cycle, flag 00
Log file from refinement at 1.50 Å
Structure model refined at 1.50 Å PDB mmCIF
1.42A statistics vs. cycle, flag 00
Log file from refinement at 1.42 Å
Structure model refined at 1.42 Å PDB mmCIF

References

Please reference the used software: