Hi Guto,
I would be very cautious with the InnerShell merging statistics as yours.
Rmeas in this shell is higher than Rmeas overall,
which probably means you have a lot of overloads,
(or problems with backstop shadow, which is not so likely
on Diamond nowdays).
And generally InnerShell Rmerge over 5-6% in XDS processing
(Diamond pipelines) is usually an indicator of future problems in
refinement.
Rfree of 25 % at 1.06 A seems to confirm your space group.
In the case of wrong space group or origin (ZANUDA), it would normally be well
over 35 %.
Try to collect data setting transmission/exposure time to lower values.
If this was the only crystal ever explain high-ish value of freeR in the
methods
session as due to overexposure.
For cases like yours I would really like to see Rmeas in the inner shell in
Table 1.
Best wishes,
Misha Isupov
________________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Guto Rhys
[guto.r...@bristol.ac.uk]
Sent: Tuesday, October 9, 2018 6:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset
(1.05 Ang)
Hi all,
I have a 1.05 Angstrom dataset that I was able to phase but the refined model
only has an Rfree of approximately 0.25. The dataset includes 1800 images and,
as the crystal did not suffer significantly from radiation damage, comprises
all 360 deg. Auto-processing pipelines at diamond light source all suggest
I222. I have also indexed the data in iMOSFLM, which has the highest-symmetry
Laue group that is least penalised of I422. Subsequent scaling and merging in
AIMLESS strongly indicates that I222 is the likely space group (see below). I
have ran the refined model through ZANUDA, which has similar R values to lower
symmetry space groups (see below). The output from Phenix Xtriage does not find
any specific crystal pathologies and if twinning is present it is very low (2
to 4%, see below). The difference map suggests that the model accounts for
nearly all the density. Any ideas or direction would be greatly appreciated.
Best,
Guto
AIMLESS Summary
Overall InnerShell OuterShell
Low resolution limit 27.75 27.75 1.07
High resolution limit 1.05 5.75 1.05
Rmerge (within I+/I-) 0.050 0.078 0.466
Rmerge (all I+ and I-) 0.051 0.080 0.536
Rmeas (within I+/I-) 0.055 0.086 0.591
Rmeas (all I+ & I-) 0.054 0.085 0.613
Rpim (within I+/I-) 0.023 0.034 0.359
Rpim (all I+ & I-) 0.017 0.028 0.288
Rmerge in top intensity bin 0.049 - -
Total number of observations 107950 779 1972
Total number unique 11315 88 486
Mean((I)/sd(I)) 19.7 46.2 1.8
Mn(I) half-set correlation CC(1/2) 0.998 0.994 0.796
Completeness 99.1 99.2 90.4
Multiplicity 9.5 8.9 4.1
Anomalous completeness 98.1 100.0 79.1
Anomalous multiplicity 5.0 6.4 2.2
DelAnom correlation between half-sets -0.067 0.286 0.097
Mid-Slope of Anom Normal Probability 0.789 - -
Estimate of maximum resolution for significant anomalous signal = 1.14A, from
CCanom > 0.15
Estimates of resolution limits: overall
from half-dataset correlation CC(1/2) > 0.30: limit = 1.05A == maximum
resolution
from Mn(I/sd) > 1.50: limit = 1.05A == maximum
resolution
from Mn(I/sd) > 2.00: limit = 1.07A
Estimates of resolution limits in reciprocal lattice directions:
Along h axis
from half-dataset correlation CC(1/2) > 0.30: limit = 1.06A
from Mn(I/sd) > 1.50: limit = 1.09A
Along k axis
from half-dataset correlation CC(1/2) > 0.30: limit = 1.11A
from Mn(I/sd) > 1.50: limit = 1.13A
Along l axis
from half-dataset correlation CC(1/2) > 0.30: limit = 1.05A == maximum
resolution
from Mn(I/sd) > 1.50: limit = 1.05A
Anisotropic deltaB (i.e. range of principal components), A^2: 6.40
Average unit cell: 29.12 29.26 55.50 90.00 90.00 90.00
Space group: I 2 2 2
Average mosaicity: 0.36
AIMLESS Laue Group prediction
Laue Group Lklhd NetZc Zc+ Zc- CC CC- Rmeas R- Delta
ReindexOperator
= 1 I m m m *** 0.987 6.25 9.19 2.94 0.92 0.29 0.07 0.49 0.0
[h,k,l]
2 I 1 2/m 1 0.004 4.36 9.32 4.96 0.93 0.50 0.07 0.30 0.0
[-h,-k,l]
3 I 1 2/m 1 0.004 4.14 9.24 5.10 0.92 0.51 0.07 0.30 0.0
[k,-h,l]
4 I 1 2/m 1 0.004 4.05 9.23 5.18 0.92 0.52 0.06 0.31 0.0
[h,-l,k]
5 I 4/m m m 0.000 6.35 6.35 0.00 0.64 0.00 0.22 0.00 0.3
[h,k,l]
6 I 4/m 0.000 0.90 6.83 5.93 0.68 0.59 0.17 0.26 0.3
[h,k,l]
7 P -1 0.000 3.69 9.36 5.67 0.94 0.57 0.06 0.26 0.0
[-h,k,1/2h-1/2k-1/2l]
8 I 1 2/m 1 0.000 0.08 6.40 6.33 0.64 0.63 0.23 0.22 0.3
[-1/2h+1/2k-1/2l,-h-k,-1/2h+1/2k+1/2l]
9 F m m m 0.000 -0.43 6.17 6.60 0.62 0.66 0.24 0.20 0.3
[h+k,-h+k,l]
10 I 1 2/m 1 0.000 0.75 6.89 6.14 0.69 0.61 0.22 0.22 0.3
[-1/2h-1/2k-1/2l,h-k,-1/2h-1/2k+1/2l]
Xtriage Summary
Twinning and intensity statistics summary (acentric data):
Statistics independent of twin laws
<I^2>/<I>^2 : 2.126 (untwinned: 2.0, perfect twin: 1.5)
<F>^2/<F^2> : 0.774 (untwinned: 0.785, perfect twin: 0.885)
<|E^2-1|> : 0.761 (untwinned: 0.736, perfect twin: 0.541)
<|L|>, <L^2>: 0.490, 0.323
Multivariate Z score L-test: 1.303
The multivariate Z score is a quality measure of the given
spread in intensities. Good to reasonable data are expected
to have a Z score lower than 3.5.
Large values can indicate twinning, but small values do not
necessarily exclude it.
Statistics depending on twin laws
-----------------------------------------------------------------------------------
| Operator | type | R_abs obs. | R_abs calc. | Britton alpha | H alpha | ML
alpha |
-----------------------------------------------------------------------------------
| k,h,-l | PM | 0.469 | 0.478 | 0.016 | 0.041 | 0.022
|
-----------------------------------------------------------------------------------
Patterson analyses
- Largest peak height : 13.667
(corresponding p value : 0.04780)
The largest off-origin peak in the Patterson function is 13.67% of the
height of the origin peak. No significant pseudotranslation is detected.
The results of the L-test indicate that the intensity statistics
behave as expected. No twinning is suspected.
Zanuda output
Step 2.
Refinements in subgroups.
There are 5 subgroups to test.
current time: Jan 08 16:20 GMT
expected end of job: Jan 08 16:28 GMT
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| >> 5 | I 2 2 2 | 0.0005 | -- | -- | -- |
---------------------------------------------------------------------
| 1 | P 1 | 0.0731 | 0.3242 | 0.2842 | 0.2768 |
| 2 | C 1 2 1 | 0.0755 | 0.3796 | 0.2899 | 0.2799 |
| 3 | C 1 2 1 | 0.0727 | 0.3385 | 0.2909 | 0.2806 |
| 4 | C 1 2 1 | 0.0729 | 0.3398 | 0.2900 | 0.2813 |
| 5 | I 2 2 2 | 0.0707 | 0.3582 | 0.2976 | 0.2802 |
---------------------------------------------------------------------
| << 1 | P 1 | 0.0731 | 0.3242 | 0.2842 | 0.2768 |
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step 3.
Refinement of the best model.
Candidate symmetry elements are added one by one.
current time: Jan 08 16:25 GMT
expected end of job: Jan 08 16:28 GMT
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
| >> 1 | P 1 | 0.0731 | 0.3242 | 0.2842 | 0.2768 |
---------------------------------------------------------------------
| 1 | P 1 | 0.0730 | 0.3243 | 0.2842 | 0.2768 |
| 4 | C 1 2 1 | 0.0751 | -- | 0.2896 | 0.2826 |
| 5 | I 2 2 2 | 0.0737 | -- | 0.2970 | 0.2801 |
---------------------------------------------------------------------
| << 5 | I 2 2 2 | 0.0737 | -- | 0.2970 | 0.2801 |
---------------------------------------------------------------------
R-factor in the original subgroup is (almost) the best.
The original spacegroup assignment seems to be correct.
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