baubles: AUTOMATIC_DEFAULT_scala.log
AUTOMATIC_DEFAULT_scala.log
Please consider citing the following papers:
P.R.Evans, "Scaling and assessment
of data quality", Acta Cryst. D62, 72-82
Note that definitions of Rmeas and Rpim in this paper are missing a square-root on the (n/n-1) factor
datasets processed
Dataset: AUTOMATIC/DEFAULT/WAVE1
written as averaged data to output file /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled_WAVE1.mtz
Maximum resolution:
Dataset: AUTOMATIC/DEFAULT/WAVE2
written as averaged data to output file /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled_WAVE2.mtz
Maximum resolution:
Dataset: AUTOMATIC/DEFAULT/WAVE3
written as averaged data to output file /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled_WAVE3.mtz
Maximum resolution:
See Summary Tables in logfile for details
The following tables were found in the logfile:
Correlation of Anomalous Differences between datasets
Correlation of Dispersive Differences between datasets
RMS Anomalous & Dispersive Differences
&&& Scales v rotation range, WAVE1
Analysis against all Batches for all runs , WAVE1
Analysis against resolution , WAVE1
Analysis against intensity, WAVE1
Completeness, multiplicity, Rmeas v. resolution, WAVE1
Correlations within dataset, WAVE1
Axial reflections, axis h, WAVE1
Axial reflections, axis k, WAVE1
Axial reflections, axis l, WAVE1
1, standard deviation v. Intensity, WAVE1
&&& Scales v rotation range, WAVE2
Analysis against all Batches for all runs , WAVE2
Analysis against resolution , WAVE2
Analysis against intensity, WAVE2
Completeness, multiplicity, Rmeas v. resolution, WAVE2
Correlations within dataset, WAVE2
Axial reflections, axis h, WAVE2
Axial reflections, axis k, WAVE2
Axial reflections, axis l, WAVE2
2, standard deviation v. Intensity, WAVE2
&&& Scales v rotation range, WAVE3
Analysis against all Batches for all runs , WAVE3
Analysis against resolution , WAVE3
Analysis against intensity, WAVE3
Completeness, multiplicity, Rmeas v. resolution, WAVE3
Correlations within dataset, WAVE3
Axial reflections, axis h, WAVE3
Axial reflections, axis k, WAVE3
Axial reflections, axis l, WAVE3
3, standard deviation v. Intensity, WAVE3
Current view: summary only
Current view: full logfile
###############################################################
###############################################################
###############################################################
### CCP4 6.1: Scala
version 3.3.15 : 08/04/09##
###############################################################
User: unknown
Run date: 27/10/2009 Run time: 13:38:16
Please reference: Collaborative Computational Project, Number 4. 1994.
&The CCP4 Suite: Programs for Protein Crystallography&. Acta Cryst. D50, 760-763.
as well as any specific reference in the program write-up.
Input commands:
Table of contents of logfile:
*******************************************
SCALA - continuous scaling program
Version: 3.3.15
Phil Evans, MRC LMB, Cambridge, UK
pre@mrc-lmb.cam.ac.uk
*******************************************
$TEXT:Reference: $$ Please reference $$
P.R.Evans, &Scaling and assessment
of data quality&, Acta Cryst. D62, 72-82
Note that definitions of Rmeas and Rpim in this paper are missing a square-root on the (n/n-1) factor
OPENED INPUT MTZ FILE
Logical Name: HKLIN
Filename: /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_sorted.mtz
* Base dataset:
0 HKL_base
* Number of Datasets = 3
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 AUTOMATIC
WAVE1_SWEEP1
2 AUTOMATIC
WAVE2_SWEEP2
3 AUTOMATIC
WAVE3_SWEEP3
* Number of Columns = 18
* Number of Reflections = 1536392
* Missing value set to NaN in input mtz file
* Number of Batches = 1120
* Column Labels :
H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART FLAG BGPKRATIOS
* Column Types :
H H H Y B J Q J Q R R R R R R I I R
* Associated datasets :
0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
Resolution Range :
* Sort Order :
* Space group = 'P 21 21 21' (number
Spacegroup information obtained from library file:
Logical Name: SYMINFO
Filename: /home/pjb/Diamond/CCP4-install/ccp4-6.1.2/lib/data/syminfo.lib
Reciprocal space symmetry:
Space group: &P 21 21 21& Point group: &PG222& Laue group: &mmm&
Reference asymmetric unit: &h&=0 and k&=0 and l&=0&
(change of basis may be applied)
Spacegroup 19 &P 21 21 21&
Original indices for reflection hkl with symmetry number ISYM
Bijvoet positive
Bijvoet negative
Data line--- bins 20
Data line--- run 1 batch 1 to 360
Data line--- run 2 batch 1001 to 1360
Data line--- run 3 batch 2001 to 2400
Data line--- name run 1 project AUTOMATIC crystal DEFAULT dataset WAVE1
Data line--- name run 2 project AUTOMATIC crystal DEFAULT dataset WAVE2
Data line--- name run 3 project AUTOMATIC crystal DEFAULT dataset WAVE3
Data line--- scales rotation spacing 5.000000 secondary 6.000000 bfactor on tails
Data line--- resolution 1.589104
Data line--- cycles 100
Data line--- sdcorrection fixsdb adjust norefine full 2...000000
Data line--- sdcorrection fixsdb adjust norefine partial 2...030000
Data line--- anomalous on
&h3& Input keyworded commands (click for documentation):
1 batch 1 to 360
2 batch 1001 to 1360
3 batch 2001 to 2400
run 1 project AUTOMATIC crystal DEFAULT dataset WAVE1
run 2 project AUTOMATIC crystal DEFAULT dataset WAVE2
run 3 project AUTOMATIC crystal DEFAULT dataset WAVE3
rotation spacing 5.000000 secondary 6.000000 bfactor on tails
RESOLUTION
SDCORRECTION
fixsdb adjust norefine full 2...000000
SDCORRECTION
fixsdb adjust norefine partial 2...030000
&h2&Contents
Final scale factors
Scale factors by batch
Agreement by batch
Agreement by resolution
Agreement by intensity
Completeness & multiplicity
Axial reflections
Analysis of standard deviations
Run number
1 consists of batches :-
Run number
2 consists of batches :-
Run number
3 consists of batches :-
===== Dataset: AUTOMATIC/DEFAULT/WAVE1
* Wavelength and cell extracted from Batch headers, with rms variation:
* Wavelength:
Wavelength:
===== Dataset: AUTOMATIC/DEFAULT/WAVE2
* Wavelength and cell extracted from Batch headers, with rms variation:
* Wavelength:
Wavelength:
===== Dataset: AUTOMATIC/DEFAULT/WAVE3
* Wavelength and cell extracted from Batch headers, with rms variation:
* Wavelength:
Wavelength:
Base dataset for dispersive differences is AUTOMATIC/DEFAULT/WAVE3
PROFILE_FITTED intensities will be used
Fully-recorded and summed partial reflections will be used in scaling
Summed partials will be checked for consistent MPART flags
Maximum number of parts in summed partials equivalent to 5.0 degrees
Summed partials accepted for scaling if total fraction lies between
Partials with missing parts in the middle will be rejected
Overall resolution limits:
In solving least-squares equations:-
Eigenvalue filter limit:
No damping of shifts
At least TWO eigenvalues will be filtered
VARIANCE weights will be used in scaling
Smoothing factors
Maximum fractional distance
Reflections will be excluded from scaling in all runs if:
I .lt. sd(I) *
Reflections judged implausibly large will be rejected from scaling and merging
Maximum normalised F (ie E) for acentric reflection
Maximum normalised F (ie E) for centric reflection
Minimum probability before reflection is rejected
Outlier rejection limits
========================
--| In scaling |--
==== For all observations including I+ & I-
Reflections measured 3 or more times:
maximum deviation from weighted mean of all other observations
Reflections measured twice:
maximum deviation from weighted mean
first refinement cycle to reject outliers
--| In merging |--
==== Within each I+ & I- set ====
Reflections measured 3 or more times:
maximum deviation from weighted mean of all other observations
Reflections measured twice:
maximum deviation from weighted mean
==== For all observations including I+ & I- ====
Maximum deviation will be determined from observed anomalous differences, see below
TAILS parameters for run
1 will be used for run
TAILS parameters for run
1 will be used for run
TAILS parameter A0 fixed
1, spindle axis is closest to a*, angle
2, spindle axis is closest to a*, angle
3, spindle axis is closest to a*, angle
Standard deviations will be adjusted to SdFac * Sqrt[sd(I)**2 + SdB I + (SdAdd I)**2] as follows:-
Layout of scale factors
=======================
Run number
Dataset: AUTOMATIC/DEFAULT/WAVE1
Relative B-factor:
19 factors at intervals of
5.00 on rotation
Along rotation axis:
19 scales at intervals of
No variation of scale with detector coordinate
Spherical harmonic correction on SECONDARY beam direction in camera frame, l-order
6 non-centrosymmetric
Diffuse scattering correction (TAILS), initial parameters:
Run number
Dataset: AUTOMATIC/DEFAULT/WAVE2
Relative B-factor:
19 factors at intervals of
5.00 on rotation
Along rotation axis:
19 scales at intervals of
No variation of scale with detector coordinate
Spherical harmonic correction on SECONDARY beam direction in camera frame, l-order
6 non-centrosymmetric
Diffuse scattering correction (TAILS), initial parameters:
Run number
Dataset: AUTOMATIC/DEFAULT/WAVE3
Relative B-factor:
21 factors at intervals of
5.00 on rotation
Along rotation axis:
21 scales at intervals of
No variation of scale with detector coordinate
Spherical harmonic correction on SECONDARY beam direction in camera frame, l-order
6 non-centrosymmetric
Diffuse scattering correction (TAILS), initial parameters:
===========================================
SURFACE parameters will be TIED to zero (ie restrained to a spherical correction)
with a standard deviation of
0.0010, number of ties =
Tails parameters A1 will be TIED to initial values with a standard deviation of
4.0000, number of ties =
Working array size =
Note that the number of ranges is one less than the number of scale factors
Initial scales for run
Initial scales for run
Initial scales for run
Residual Sum( w Del**2) =
0.269E+06, restraint residual =
, total residual =
Sum( w Del**2) / (m-n) =
2 eigenvalues filtered out, smallest =
-0.780E-10, largest filtered =
Damping factor =
266089 observations used from
24856 independent reflections
Whole reflections rejected (all observations):
Observations rejected:
resolution
B-factors normalised on point
&&&& WARNING: parameter A1.1 is below minimum (
0.0000): reset to
5.0000 and fixed
Mean and maximum shift/sd :
86.326 (parameter
UNKNOWN file opened on unit
Logical name: SCALES, Filename: DEFAULT_final.scales
Residual Sum( w Del**2) =
0.832E+05, restraint residual =
0.228E+09, total residual =
Sum( w Del**2) / (m-n) =
2 eigenvalues filtered out, smallest =
0.154E-04, largest filtered =
Damping factor =
265034 observations used from
24758 independent reflections
Whole reflections rejected (all observations):
Observations rejected:
resolution
Emax limit
B-factors normalised on point
Mean and maximum shift/sd :
32.676 (parameter
Residual Sum( w Del**2) =
0.798E+05, restraint residual =
0.166E+09, total residual =
Sum( w Del**2) / (m-n) =
2 eigenvalues filtered out, smallest =
0.985E-05, largest filtered =
Damping factor =
265060 observations used from
24761 independent reflections
Whole reflections rejected (all observations):
Observations rejected:
resolution
Emax limit
B-factors normalised on point
Mean and maximum shift/sd :
21.381 (parameter
Residual Sum( w Del**2) =
0.756E+05, restraint residual =
0.175E+09, total residual =
Sum( w Del**2) / (m-n) =
2 eigenvalues filtered out, smallest =
0.988E-05, largest filtered =
Damping factor =
265053 observations used from
24761 independent reflections
Whole reflections rejected (all observations):
Observations rejected:
resolution
Emax limit
B-factors normalised on point
Mean and maximum shift/sd :
0.648 (parameter
Residual Sum( w Del**2) =
0.755E+05, restraint residual =
0.176E+09, total residual =
Sum( w Del**2) / (m-n) =
2 eigenvalues filtered out, smallest =
0.998E-05, largest filtered =
Damping factor =
265062 observations used from
24762 independent reflections
Whole reflections rejected (all observations):
Observations rejected:
resolution
Emax limit
B-factors normalised on point
Mean and maximum shift/sd :
0.336 (parameter
Residual Sum( w Del**2) =
0.755E+05, restraint residual =
0.176E+09, total residual =
Sum( w Del**2) / (m-n) =
2 eigenvalues filtered out, smallest =
0.997E-05, largest filtered =
Damping factor =
265062 observations used from
24762 independent reflections
Whole reflections rejected (all observations):
Observations rejected:
resolution
Emax limit
B-factors normalised on point
Mean and maximum shift/sd :
0.182 (parameter
=== Shifts for cycle
Run number
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Run number
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Run number
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
Parameter:
Old value:
New value:
&h3&Final scale factors
************************************************************************************************************************
Final scale factors:
====================
============ Run
1 =============
Relative B-factors:
Scales -- smoothed, individual, (sd):
Diffuse scattering correction (TAILS)
Half-width (A**-1):
Fraction at zero theta:
Fraction slope:
Fraction at maximum resolution:
(resolution
Spherical harmonic expansion coefficients in SECONDARY beam frame
0.000 -0.001
0.000 -0.001
0.000 -0.001
0.000 -0.001
0.000 -0.001
0.001 -0.001
0.000 -0.001
0.001 -0.001
0.000 -0.001 -0.001
0.002 -0.001
0.000 -0.001
0.000 -0.001
============ Run
2 =============
Relative B-factors:
Scales -- smoothed, individual, (sd):
Diffuse scattering correction (TAILS)
Half-width (A**-1):
Fraction at zero theta:
Fraction slope:
Fraction at maximum resolution:
(resolution
Tails parameters linked to run
Spherical harmonic expansion coefficients in SECONDARY beam frame
0.000 -0.001
0.000 -0.001
0.000 -0.001
0.000 -0.001
0.000 -0.001
0.000 -0.001 -0.001
0.000 -0.001
0.001 -0.001
0.002 -0.001
============ Run
3 =============
Relative B-factors:
Scales -- smoothed, individual, (sd):
Diffuse scattering correction (TAILS)
Half-width (A**-1):
Fraction at zero theta:
Fraction slope:
Fraction at maximum resolution:
(resolution
Tails parameters linked to run
Spherical harmonic expansion coefficients in SECONDARY beam frame
-0.001 -0.002 -0.002 -0.002 -0.003 -0.002
0.000 -0.001 -0.001 -0.002
0.000 -0.001
0.001 -0.001
0.002 -0.001
0.002 -0.002
0.002 -0.002 -0.001
-0.001 -0.002
0.000 -0.002
0.001 -0.001 -0.003
END PLOT: Picture number
END PLOT: Picture number
END PLOT: Picture number
================================================================================
================================================================================
================================================================================
------ Analysis Pass ------
================================================================================
================================================================================
================================================================================
Fully-recorded and summed partial reflections will be used in analysis
Summed partials will be checked for consistent MPART flags
sets with consistent MPART flags will be accepted
sets with inconsistent MPART flags will be tested on the total fraction
Summed partials must contain not more than
Summed partials accepted if total fraction lies between
Partials with missing parts in the middle will be accepted
Outliers will be omitted from output file
Reduced indices hkl will be output (ie reduced to asymmetric unit as in input file)
Outliers with two observations will be kept
===========================
Normal probability analysis
====== Run number:
1, Partials ======
Slope Intercept
Data within expected delta 0.90:
Update of SDcorrection parameters:
initial values:
changed to:
====== Run number:
2, Partials ======
Slope Intercept
Data within expected delta 0.90:
Update of SDcorrection parameters:
initial values:
changed to:
====== Run number:
3, Partials ======
Slope Intercept
Data within expected delta 0.90:
Update of SDcorrection parameters:
initial values:
changed to:
==========================================
================================================
Normal probability analysis of anomalous differences
====== Anomalous differences ======
Slope Intercept
Data within expected delta 0.90:
Outlier rejection limits limits for I+ v I- have been adjusted by a factor
1.262 (AnomProbSlope)
==== For all observations including I+ & I- ====
Reflections measured 3 or more times:
maximum deviation from weighted mean of all other observations
Reflections measured twice:
maximum deviation from weighted mean
================================================================================
================================================================================
================================================================================
------ Final Pass for statistics of merging ------
================================================================================
================================================================================
================================================================================
Intensity bins, WILSON mode, mid-bin intensity =
UNKNOWN file opened on unit
Logical name: ROGUES, Filename: ROGUES
UNKNOWN file opened on unit
Logical name: ANOMPLOT, Filename: ANOMPLOT
UNKNOWN file opened on unit
Logical name: NORMPLOT, Filename: NORMPLOT
UNKNOWN file opened on unit
Logical name: ROGUEPLOT, Filename: ROGUEPLOT
********************************************************************************
********************************************************************************
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Correlation coefficients for anomalous & dispersive differences between different datasets
==========================================================================================
Datasets:-
AUTOMATIC/DEFAULT/WAVE1
AUTOMATIC/DEFAULT/WAVE2
AUTOMATIC/DEFAULT/WAVE3
====== Correlation of anomalous differences
$TABLE: Correlation of Anomalous Differences between datasets:
$GRAPHS: Anom CCs v resln -
WAVE WAVE WAVE(base)
N 1/resol^2 dmax
1st dataset
2nd dataset
For inline graphs use a Java browser
Correlation of Anomalous Differences between datasets
(Numbers in brackets)
(40740) (42358)
====== Correlation of dispersive (isomorphous) differences
All dispersive differences are relative to the &base& dataset AUTOMATIC/DEFAULT/WAVE3
$TABLE: Correlation of Dispersive Differences between datasets:
$GRAPHS: Dispersive CCs v resln -
WAVE WAVE WAVE(base)
N 1/resol^2 dmax
1st difference
WAVE1-WAVE3
2nd difference
WAVE2-WAVE3
For inline graphs use a Java browser
Correlation between datasets of Dispersive Differences from base set
(Numbers in brackets)
WAVE2-WAVE3
WAVE1-WAVE3
$TABLE: RMS Anomalous & Dispersive Differences:
$GRAPHS: RMS DelAnom v resln -
WAVE WAVE WAVE(base) :N:2, 4, 6, 8:
: RMS Dispersive diffs v resln -
WAVE WAVE WAVE(base) :N:2,10,12: $$
N 1/resol^2 dmax
WAVE1-WAVE3
WAVE2-WAVE3
For inline graphs use a Java browser
Relative anomalous differences for each dataset, and ratio of rms values
These are approximately the ratios of f&
Ratio of RMS
Relative dispersive differences from base dataset for each dataset, and ratio of rms values
Base dataset is
AUTOMATIC/DEFAULT/WAVE3
These are approximately the ratios of the differences in f'
Ratio of RMS
WAVE1-WAVE3
WAVE2-WAVE3
--------------------------------------------------------------------------------
OPENED INPUT MTZ FILE
Logical Name: HKLIN
Filename: /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_sorted.mtz
********************************************************************************
********************************************************************************
Statistics for dataset
AUTOMATIC/DEFAULT/WAVE1
UNKNOWN file opened on unit
Logical name: CORRELPLOT_WAVE1, Filename: CORRELPLOT_WAVE1
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
WRITTEN OUTPUT MTZ FILE
Logical Name: /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled_WAVE1.mtz
Filename: /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled_WAVE1.mtz
* Base dataset:
0 HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 AUTOMATIC
* Number of Columns = 9
* Number of Reflections = 50943
* Missing value set to NaN in input mtz file
* Column Labels :
H K L IMEAN SIGIMEAN I(+) SIGI(+) I(-) SIGI(-)
* Column Types :
H H H J Q K M K M
* Associated datasets :
0 0 0 1 1 1 1 1 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
Resolution Range :
* Sort Order :
* Space group = 'P 21 21 21' (number
Number of observations read
Number of unique reflections read
Number of observations output
Number of outliers rejected
Number of observations rejected on Emax limit
Number of observations outside resolution limits :
(observations outside resolution limits are omitted from the output file)
Numbers of observations (including parts of reflections) marked in the FLAG column
By default all flagged observations are rejected
Observations may be counted in more than one category
MaxAccepted
BGratio too large
PKratio too large
Negative & 5sigma
BG gradient too large
Profile-fitted overloads
Spots on edge
Statistics below are accumulated from:-
46162 unique reflections,
158967 observations
0 are fully recorded,
158967 are summed partials,
0 are scaled partials)
this excludes
2235 good observations measured once only
Maximum number of parts in a partially recorded reflection:
partial sets with total fraction too small
partial sets with total fraction too large
partial sets with error flags (FLAG)
================================================================================
Analysis of applied scale factors (including input scale)
Mean scale factors analysed by Batch for each run and resolution
Analysis of TAILS correction (mean and range) by run and resolution
Spherical harmonic absorption correction(SECONDARY or ABSORPTION) for run
Minimum and maximum values:
Average values by polar coordinates Phi & Theta
&h3&Scale factors by batch
Scale factors analysed by Batch for each run
============================================
Note that 0k below is calculated for the centre of each rotation range,
at theta = 0 (for the B-factor) and at the centre of the detector:
This will be inappropriate if the detector is not centred on the beam, and the scale varies across the detector
Mn(k) is average applied scale, including any input scale
0k is the scale calculated from this scaling run
Bfactor and mean scale Mn(k) for each rotation range
$TABLE:&& Scales v rotation range, WAVE1 :
$GRAPHS:Mn(k) & 0k (at theta = 0) v range:N:1,6,7:
v range:A:1,5:
:Number rejected v range:N:1,9:
&&For inline graphs use a Java browser
&h3&Agreement by batch
Agreement between batches
-------------------------
RMS scatters are shown as SIGMA and SIGM0 for differences
from Mn(I+),Mn(I-) and Mn(Imean) respectively.
Rmerge in this table is the difference from Mn(Imean),
but in later tables Rmerge is the difference from Mn(I+),Mn(I-).
NFR,NPR count those (mixed & unmixed sets) included in SIGMA
those in SIGM0 and Rmerge
(mixed & unmixed FULLY/PARTIAL SETS)
number of reflections rejected for bad agreement
number of reflections rejected for M .gt. 1
(neither valid fully nor partial)
$TABLE : Analysis against all Batches for all runs , WAVE1 :
$GRAPHS :Rmerge v Batch for all runs :N:1,9:
:Imean & RMS Scatter:N:1,3,4,7: :Imean/RMS scatter:N:1,8:
:Number of rejections v Batch:N:1,11,12: $$
N_batch Batch_number Mn(Imean) Scatter_from_I+/-
Number_of_fulls Number_of_partials
Scatter_from_Imean Imean/Scatter_from_Imean Rmerge
Number_in_Rmerge
Number_rejected Number_invalid
Fraction_rejected $$
Imean/SIGM0
For inline graphs use a Java browser
SIGM0 Imean/SIGM0
================================================================================
:- R-merge up to this range,
:- Sum |Mn(I+) - Mn(I-)| / Sum (Mn(I+) + Mn(I-))
:- R-merge for fulls only,
:- number of independent hkl's
:- unmerged Ihl averaged in bin
:- rms scatter of observations
I/sigma :-
/ rms scatter
= AvI/SIGMA
:- average standard deviation derived from experimental SDs, after
:- application of SdFac SdB SdAdd
Mn(I/sd):- average & merged/sd() & ~= signal/noise
FRCBIAS :- Mean( Mn(If) - Ip )/Mean( Mn(I) )
for Nbias mixed sets only (If is a full if present, else the
partial with the smallest number of parts)
&h3&Agreement by resolution
4SINTH/LASQ bins (all statistics use Mn(I+),Mn(I-)etc)
______________________________________________________________
$TABLE: Analysis against resolution , WAVE1 :
$GRAPHS: I/sigma, Mean Mn(I)/sd(Mn(I)):N:2,11,13:
: Rmerge v Resolution:N:2,4,5,7:
: Average I,sd and Sigma :A:2,9,10,12: : Fractional bias :A:2,17: $$
N 1/resol^2 Dmin(A) Rmrg
SIGMA I/sigma
sd Mn(I/sd)
Ncent FRCBIAS
N 1/d^2 Dmin(A) Rmrg
SIGMA I/sigma
sd Mn(I/sd)
Ncent FRCBIAS
For inline graphs use a Java browser
SIGMA I/sigma
sd Mn(I/sd)
Ncent FRCBIAS
&h3&Agreement by intensity
INTENSITY ranges (all statistics use Mn(I+),Mn(I-)etc)
______________________________________________________________
$TABLE: Analysis against intensity, WAVE1 :
$GRAPHS:Rmerge v Intensity :N:1,2,3,4:
For inline graphs use a Java browser
&h3&Completeness & multiplicity
Completeness and multiplicity, including reflections measured only once
=======================================================================
%poss is completeness in the shell, Cm%poss in cumulative to that resolution
The anomalous completeness values (AnomCmpl) are the percentage of possible anomalous differences measured
AnomFrc is the % of measured acentric reflections for which an anomalous difference has been measured
Rmeas: redundancy-independent (multiplicity-weighted) Rmerge
or R(r.i.m.) (Rmeas is relative to I+ or I-, RmeasO is relative to overall mean)
pooled coefficient of variation (PCV is relative to I+ or I-, PCV0 is relative to overall mean)
PCV is a multiplicity-weighted RMS Rmerge
Rpim: precision-indicating (multiplicity-weighted) Rmerge
(Rpim is relative to I+ or I-, RpimO is relative to overall mean)
See:- &Improved R-factors for diffraction data analysis in macromolecular crystallography&
Kay Diederichs & P. Andrew Karplus, Nature Structural Biology, 4, 269-275 (1997)
&On the use of the merging R factor as a qualityindicator for X-ray data&
Manfred Weiss & Rolf Hilgenfeld, J.Appl.Cryst. 30, 203-205 (1997)
&Global Indicators of X-ray data quality&
Manfred Weiss, J.Appl.Cryst. 34, 130-135 (2001)
$TABLE: Completeness, multiplicity, Rmeas v. resolution, WAVE1 :
$GRAPHS:Completeness v Resolution :N:2,7,8,10,11:
:Multiplicity v Resolution :N:2,9,12:
:Rpim (precision R) v Resolution :N:2,16,17:
:Rmeas, Rsym & PCV v Resolution :N:2,13,14,15,18,19:
N 1/resol^2 Dmin
%poss C%poss Mlplct AnoCmp AnoFrc AnoMlt Rmeas Rmeas0
For inline graphs use a Java browser
%poss C%poss Mlplct AnoCmp AnoFrc AnoMlt Rmeas Rmeas0
Correlation coefficients for anomalous differences & Imean between random subsets within dataset
===============================================================================================
The RMS Correlation Ratio (RCR) is calculated from a scatter plot of pairs of DeltaI(anom) from the two subsets
by comparing the RMS value (excluding extremes) projected on the line with slope = 1 (&correlation&) with the
RMS value perpendicular to this (&error&). This ratio will be & 1 if there is an anomalous signal
$TABLE: Correlations within dataset, WAVE1 :
$GRAPHS: Anom & Imean CCs v resolution - :A:2,4,6,12:
:RMS correlation ratio:A:2,8,10:$$
N 1/resol^2 dmax CC_anom
N_cen RCR_anom
N_cen CC_Imean
For inline graphs use a Java browser
&h3&Axial reflections
$TABLE: Axial reflections, axis h, WAVE1 :
$GRAPHS: I/sigI vs. h:0|
33.99:1,4:
: I vs. h:0|
For inline graphs use a Java browser
$TABLE: Axial reflections, axis k, WAVE1 :
$GRAPHS: I/sigI vs. k:0|
25.11:1,4:
: I vs. k:0|
For inline graphs use a Java browser
$TABLE: Axial reflections, axis l, WAVE1 :
$GRAPHS: I/sigI vs. l:0|
18.21:1,4:
: I vs. l:0|
For inline graphs use a Java browser
&h3&Analysis of standard deviations
ANALYSIS OF STANDARD DEVIATIONS
===============================
This plots the distribution of the number of observations
with Chi = (Ihl - Mn(Iothers) )/sqrt[sd(Ihl)**2 + sd(Mn(I))**2] in ranges from -5 to +5 .
If the SD is a true estimate of the error, this distribution should have Mean=0.0 and Sigma=1.0
for all ranges of intensity.
The analysis is repeated for ranges of increasing Imean. The Mean is expected to increase with Imean
since the latter is a weighted mean and sd(Ihl) & Ihl are correlated.
If the Sigma increases with Imean, increase the value of SdAdd.
In the table, Cmin, Cmax & Cmean are respectively the minimum, maximum and mean
of the applied SD correction, ie SDcorrected/SDoriginal
Current values of SD corrections are:-SdFac * Sqrt[sd(I)**2 + SdB I + (SdAdd I)**2]
========= Run
1 =========
$TABLE: Run
1, standard deviation v. Intensity, WAVE1 :
$GRAPHS: Sigma(scatter/SD) Run
1:N:11,7,14:
: Mean(scatter/SD) Run
1:A:11,6,13:
: MeanCorrection Run
1:N:11,10,17: $$
Range Imin Imax Irms Number MeanFull SigmaFull MinCorFull MaxCorFull MeanCorFull Irms
Number MeanPart SigmaPartial MinCorPartial MaxCorPartial MeanCorPartial
Fully_recordeds
Partially_recordeds
Mean Sigma
Mean Sigma
For inline graphs use a Java browser
Mean Sigma
Mean Sigma
Fully_recordeds
Partially_recordeds
In the following analyses,
Chi = (Ihl - Mn(Iothers) )/sqrt[sd(Ihl)**2 + sd(Mn(I))**2]
Chi**2 analysis by position of detector (Xdet, Ydet)
Each entry is 10 * Chi**2
(ie relative discrepancy **2)
921 28 36 43 1945
Chi analysis by position of detector (Xdet, Ydet)
Each entry is
10 * Mn(Chi) (ie signed relative discrepancy)
921 28 36 43 1945
Number of outlier rejections in each area
921 28 36 43 1945
Number of observations in each area
921 28 36 43 1945
================================================
Normal probability analysis of anomalous differences
====== Anomalous differences ======
Slope Intercept
Data within expected delta 0.90:
================================================
Normal probability analysis, by run & partiality
====== Run number:
1, Run 1: summed partials ======
Slope Intercept
Data within expected delta 0.90:
==========================================
Final assessment of SDcorrection multipliers
SdFac_used
_corrected
_fullsonly
SdFac_used
_corrected
================================================================================
Summary data for
Project: AUTOMATIC Crystal: DEFAULT Dataset: WAVE1
InnerShell
OuterShell
Low resolution limit
High resolution limit
Rmerge in top intensity bin
Rmeas (within I+/I-)
Rmeas (all I+ & I-)
Rpim (within I+/I-)
Rpim (all I+ & I-)
Fractional partial bias
Total number of observations
Total number unique
Mean((I)/sd(I))
Completeness
Multiplicity
Anomalous completeness
Anomalous multiplicity
DelAnom correlation between half-sets
Mid-Slope of Anom Normal Probability
Outlier rejection and statistics assume that there is anomalous scattering, ie I+ differs from I-
Average unit cell:
Space group: P 21 21 21
Average mosaicity:
Minimum and maximum SD correction factors: Partials
================================================================================
OPENED INPUT MTZ FILE
Logical Name: HKLIN
Filename: /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_sorted.mtz
********************************************************************************
********************************************************************************
Statistics for dataset
AUTOMATIC/DEFAULT/WAVE2
UNKNOWN file opened on unit
Logical name: CORRELPLOT_WAVE2, Filename: CORRELPLOT_WAVE2
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
WRITTEN OUTPUT MTZ FILE
Logical Name: /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled_WAVE2.mtz
Filename: /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled_WAVE2.mtz
* Base dataset:
0 HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 AUTOMATIC
* Number of Columns = 9
* Number of Reflections = 49857
* Missing value set to NaN in input mtz file
* Column Labels :
H K L IMEAN SIGIMEAN I(+) SIGI(+) I(-) SIGI(-)
* Column Types :
H H H J Q K M K M
* Associated datasets :
0 0 0 1 1 1 1 1 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
Resolution Range :
* Sort Order :
* Space group = 'P 21 21 21' (number
Number of observations read
Number of unique reflections read
Number of observations output
Number of outliers rejected
Number of observations rejected on Emax limit
Number of observations outside resolution limits :
(observations outside resolution limits are omitted from the output file)
Numbers of observations (including parts of reflections) marked in the FLAG column
By default all flagged observations are rejected
Observations may be counted in more than one category
MaxAccepted
BGratio too large
PKratio too large
Negative & 5sigma
BG gradient too large
Profile-fitted overloads
Spots on edge
Statistics below are accumulated from:-
44457 unique reflections,
151635 observations
0 are fully recorded,
151635 are summed partials,
0 are scaled partials)
this excludes
2395 good observations measured once only
Maximum number of parts in a partially recorded reflection:
partial sets with total fraction too small
partial sets with total fraction too large
partial sets with error flags (FLAG)
================================================================================
Analysis of applied scale factors (including input scale)
Mean scale factors analysed by Batch for each run and resolution
Analysis of TAILS correction (mean and range) by run and resolution
Spherical harmonic absorption correction(SECONDARY or ABSORPTION) for run
Minimum and maximum values:
Average values by polar coordinates Phi & Theta
&h3&Scale factors by batch
Scale factors analysed by Batch for each run
============================================
Note that 0k below is calculated for the centre of each rotation range,
at theta = 0 (for the B-factor) and at the centre of the detector:
This will be inappropriate if the detector is not centred on the beam, and the scale varies across the detector
Mn(k) is average applied scale, including any input scale
0k is the scale calculated from this scaling run
Bfactor and mean scale Mn(k) for each rotation range
$TABLE:&& Scales v rotation range, WAVE2 :
$GRAPHS:Mn(k) & 0k (at theta = 0) v range:N:1,6,7:
v range:A:1,5:
:Number rejected v range:N:1,9:
&&For inline graphs use a Java browser
&h3&Agreement by batch
Agreement between batches
-------------------------
RMS scatters are shown as SIGMA and SIGM0 for differences
from Mn(I+),Mn(I-) and Mn(Imean) respectively.
Rmerge in this table is the difference from Mn(Imean),
but in later tables Rmerge is the difference from Mn(I+),Mn(I-).
NFR,NPR count those (mixed & unmixed sets) included in SIGMA
those in SIGM0 and Rmerge
(mixed & unmixed FULLY/PARTIAL SETS)
number of reflections rejected for bad agreement
number of reflections rejected for M .gt. 1
(neither valid fully nor partial)
$TABLE : Analysis against all Batches for all runs , WAVE2 :
$GRAPHS :Rmerge v Batch for all runs :N:1,9:
:Imean & RMS Scatter:N:1,3,4,7: :Imean/RMS scatter:N:1,8:
:Number of rejections v Batch:N:1,11,12: $$
N_batch Batch_number Mn(Imean) Scatter_from_I+/-
Number_of_fulls Number_of_partials
Scatter_from_Imean Imean/Scatter_from_Imean Rmerge
Number_in_Rmerge
Number_rejected Number_invalid
Fraction_rejected $$
Imean/SIGM0
For inline graphs use a Java browser
SIGM0 Imean/SIGM0
================================================================================
:- R-merge up to this range,
:- Sum |Mn(I+) - Mn(I-)| / Sum (Mn(I+) + Mn(I-))
:- R-merge for fulls only,
:- number of independent hkl's
:- unmerged Ihl averaged in bin
:- rms scatter of observations
I/sigma :-
/ rms scatter
= AvI/SIGMA
:- average standard deviation derived from experimental SDs, after
:- application of SdFac SdB SdAdd
Mn(I/sd):- average & merged/sd() & ~= signal/noise
FRCBIAS :- Mean( Mn(If) - Ip )/Mean( Mn(I) )
for Nbias mixed sets only (If is a full if present, else the
partial with the smallest number of parts)
&h3&Agreement by resolution
4SINTH/LASQ bins (all statistics use Mn(I+),Mn(I-)etc)
______________________________________________________________
$TABLE: Analysis against resolution , WAVE2 :
$GRAPHS: I/sigma, Mean Mn(I)/sd(Mn(I)):N:2,11,13:
: Rmerge v Resolution:N:2,4,5,7:
: Average I,sd and Sigma :A:2,9,10,12: : Fractional bias :A:2,17: $$
N 1/resol^2 Dmin(A) Rmrg
SIGMA I/sigma
sd Mn(I/sd)
Ncent FRCBIAS
N 1/d^2 Dmin(A) Rmrg
SIGMA I/sigma
sd Mn(I/sd)
Ncent FRCBIAS
For inline graphs use a Java browser
SIGMA I/sigma
sd Mn(I/sd)
Ncent FRCBIAS
&h3&Agreement by intensity
INTENSITY ranges (all statistics use Mn(I+),Mn(I-)etc)
______________________________________________________________
$TABLE: Analysis against intensity, WAVE2 :
$GRAPHS:Rmerge v Intensity :N:1,2,3,4:
For inline graphs use a Java browser
&h3&Completeness & multiplicity
Completeness and multiplicity, including reflections measured only once
=======================================================================
%poss is completeness in the shell, Cm%poss in cumulative to that resolution
The anomalous completeness values (AnomCmpl) are the percentage of possible anomalous differences measured
AnomFrc is the % of measured acentric reflections for which an anomalous difference has been measured
Rmeas: redundancy-independent (multiplicity-weighted) Rmerge
or R(r.i.m.) (Rmeas is relative to I+ or I-, RmeasO is relative to overall mean)
pooled coefficient of variation (PCV is relative to I+ or I-, PCV0 is relative to overall mean)
PCV is a multiplicity-weighted RMS Rmerge
Rpim: precision-indicating (multiplicity-weighted) Rmerge
(Rpim is relative to I+ or I-, RpimO is relative to overall mean)
See:- &Improved R-factors for diffraction data analysis in macromolecular crystallography&
Kay Diederichs & P. Andrew Karplus, Nature Structural Biology, 4, 269-275 (1997)
&On the use of the merging R factor as a qualityindicator for X-ray data&
Manfred Weiss & Rolf Hilgenfeld, J.Appl.Cryst. 30, 203-205 (1997)
&Global Indicators of X-ray data quality&
Manfred Weiss, J.Appl.Cryst. 34, 130-135 (2001)
$TABLE: Completeness, multiplicity, Rmeas v. resolution, WAVE2 :
$GRAPHS:Completeness v Resolution :N:2,7,8,10,11:
:Multiplicity v Resolution :N:2,9,12:
:Rpim (precision R) v Resolution :N:2,16,17:
:Rmeas, Rsym & PCV v Resolution :N:2,13,14,15,18,19:
N 1/resol^2 Dmin
%poss C%poss Mlplct AnoCmp AnoFrc AnoMlt Rmeas Rmeas0
For inline graphs use a Java browser
%poss C%poss Mlplct AnoCmp AnoFrc AnoMlt Rmeas Rmeas0
Correlation coefficients for anomalous differences & Imean between random subsets within dataset
===============================================================================================
The RMS Correlation Ratio (RCR) is calculated from a scatter plot of pairs of DeltaI(anom) from the two subsets
by comparing the RMS value (excluding extremes) projected on the line with slope = 1 (&correlation&) with the
RMS value perpendicular to this (&error&). This ratio will be & 1 if there is an anomalous signal
$TABLE: Correlations within dataset, WAVE2 :
$GRAPHS: Anom & Imean CCs v resolution - :A:2,4,6,12:
:RMS correlation ratio:A:2,8,10:$$
N 1/resol^2 dmax CC_anom
N_cen RCR_anom
N_cen CC_Imean
For inline graphs use a Java browser
&h3&Axial reflections
$TABLE: Axial reflections, axis h, WAVE2 :
$GRAPHS: I/sigI vs. h:0|
37.64:1,4:
: I vs. h:0|
For inline graphs use a Java browser
$TABLE: Axial reflections, axis k, WAVE2 :
$GRAPHS: I/sigI vs. k:0|
27.50:1,4:
: I vs. k:0|
For inline graphs use a Java browser
$TABLE: Axial reflections, axis l, WAVE2 :
$GRAPHS: I/sigI vs. l:0|
19.18:1,4:
: I vs. l:0|
For inline graphs use a Java browser
&h3&Analysis of standard deviations
ANALYSIS OF STANDARD DEVIATIONS
===============================
This plots the distribution of the number of observations
with Chi = (Ihl - Mn(Iothers) )/sqrt[sd(Ihl)**2 + sd(Mn(I))**2] in ranges from -5 to +5 .
If the SD is a true estimate of the error, this distribution should have Mean=0.0 and Sigma=1.0
for all ranges of intensity.
The analysis is repeated for ranges of increasing Imean. The Mean is expected to increase with Imean
since the latter is a weighted mean and sd(Ihl) & Ihl are correlated.
If the Sigma increases with Imean, increase the value of SdAdd.
In the table, Cmin, Cmax & Cmean are respectively the minimum, maximum and mean
of the applied SD correction, ie SDcorrected/SDoriginal
Current values of SD corrections are:-SdFac * Sqrt[sd(I)**2 + SdB I + (SdAdd I)**2]
========= Run
2 =========
$TABLE: Run
2, standard deviation v. Intensity, WAVE2 :
$GRAPHS: Sigma(scatter/SD) Run
2:N:11,7,14:
: Mean(scatter/SD) Run
2:A:11,6,13:
: MeanCorrection Run
2:N:11,10,17: $$
Range Imin Imax Irms Number MeanFull SigmaFull MinCorFull MaxCorFull MeanCorFull Irms
Number MeanPart SigmaPartial MinCorPartial MaxCorPartial MeanCorPartial
Fully_recordeds
Partially_recordeds
Mean Sigma
Mean Sigma
For inline graphs use a Java browser
Mean Sigma
Mean Sigma
Fully_recordeds
Partially_recordeds
In the following analyses,
Chi = (Ihl - Mn(Iothers) )/sqrt[sd(Ihl)**2 + sd(Mn(I))**2]
Chi**2 analysis by position of detector (Xdet, Ydet)
Each entry is 10 * Chi**2
(ie relative discrepancy **2)
921 28 36 43 1945
Chi analysis by position of detector (Xdet, Ydet)
Each entry is
10 * Mn(Chi) (ie signed relative discrepancy)
921 28 36 43 1945
Number of outlier rejections in each area
921 28 36 43 1945
Number of observations in each area
921 28 36 43 1945
================================================
Normal probability analysis of anomalous differences
====== Anomalous differences ======
Slope Intercept
Data within expected delta 0.90:
================================================
Normal probability analysis, by run & partiality
====== Run number:
2, Run 2: summed partials ======
Slope Intercept
Data within expected delta 0.90:
==========================================
Final assessment of SDcorrection multipliers
SdFac_used
_corrected
_fullsonly
SdFac_used
_corrected
================================================================================
Summary data for
Project: AUTOMATIC Crystal: DEFAULT Dataset: WAVE2
InnerShell
OuterShell
Low resolution limit
High resolution limit
Rmerge in top intensity bin
Rmeas (within I+/I-)
Rmeas (all I+ & I-)
Rpim (within I+/I-)
Rpim (all I+ & I-)
Fractional partial bias
Total number of observations
Total number unique
Mean((I)/sd(I))
Completeness
Multiplicity
Anomalous completeness
Anomalous multiplicity
DelAnom correlation between half-sets
Mid-Slope of Anom Normal Probability
Outlier rejection and statistics assume that there is anomalous scattering, ie I+ differs from I-
Average unit cell:
Space group: P 21 21 21
Average mosaicity:
Minimum and maximum SD correction factors: Partials
================================================================================
OPENED INPUT MTZ FILE
Logical Name: HKLIN
Filename: /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_sorted.mtz
********************************************************************************
********************************************************************************
Statistics for dataset
AUTOMATIC/DEFAULT/WAVE3
UNKNOWN file opened on unit
Logical name: CORRELPLOT_WAVE3, Filename: CORRELPLOT_WAVE3
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
Observation rejected by Emax test: h,k,l, Batch, E:
WRITTEN OUTPUT MTZ FILE
Logical Name: /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled_WAVE3.mtz
Filename: /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled_WAVE3.mtz
* Base dataset:
0 HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 AUTOMATIC
* Number of Columns = 9
* Number of Reflections = 52695
* Missing value set to NaN in input mtz file
* Column Labels :
H K L IMEAN SIGIMEAN I(+) SIGI(+) I(-) SIGI(-)
* Column Types :
H H H J Q K M K M
* Associated datasets :
0 0 0 1 1 1 1 1 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
Resolution Range :
* Sort Order :
* Space group = 'P 21 21 21' (number
Number of observations read
Number of unique reflections read
Number of observations output
Number of outliers rejected
Number of observations rejected on Emax limit
Number of observations outside resolution limits :
(observations outside resolution limits are omitted from the output file)
Numbers of observations (including parts of reflections) marked in the FLAG column
By default all flagged observations are rejected
Observations may be counted in more than one category
MaxAccepted
BGratio too large
PKratio too large
Negative & 5sigma
BG gradient too large
Profile-fitted overloads
Spots on edge
Statistics below are accumulated from:-
51787 unique reflections,
210026 observations
0 are fully recorded,
210026 are summed partials,
0 are scaled partials)
this excludes
772 good observations measured once only
Maximum number of parts in a partially recorded reflection:
partial sets with total fraction too small
partial sets with total fraction too large
partial sets with error flags (FLAG)
================================================================================
Analysis of applied scale factors (including input scale)
Mean scale factors analysed by Batch for each run and resolution
Analysis of TAILS correction (mean and range) by run and resolution
Spherical harmonic absorption correction(SECONDARY or ABSORPTION) for run
Minimum and maximum values:
Average values by polar coordinates Phi & Theta
&h3&Scale factors by batch
Scale factors analysed by Batch for each run
============================================
Note that 0k below is calculated for the centre of each rotation range,
at theta = 0 (for the B-factor) and at the centre of the detector:
This will be inappropriate if the detector is not centred on the beam, and the scale varies across the detector
Mn(k) is average applied scale, including any input scale
0k is the scale calculated from this scaling run
Bfactor and mean scale Mn(k) for each rotation range
$TABLE:&& Scales v rotation range, WAVE3 :
$GRAPHS:Mn(k) & 0k (at theta = 0) v range:N:1,6,7:
v range:A:1,5:
:Number rejected v range:N:1,9:
&&For inline graphs use a Java browser
&h3&Agreement by batch
Agreement between batches
-------------------------
RMS scatters are shown as SIGMA and SIGM0 for differences
from Mn(I+),Mn(I-) and Mn(Imean) respectively.
Rmerge in this table is the difference from Mn(Imean),
but in later tables Rmerge is the difference from Mn(I+),Mn(I-).
NFR,NPR count those (mixed & unmixed sets) included in SIGMA
those in SIGM0 and Rmerge
(mixed & unmixed FULLY/PARTIAL SETS)
number of reflections rejected for bad agreement
number of reflections rejected for M .gt. 1
(neither valid fully nor partial)
$TABLE : Analysis against all Batches for all runs , WAVE3 :
$GRAPHS :Rmerge v Batch for all runs :N:1,9:
:Imean & RMS Scatter:N:1,3,4,7: :Imean/RMS scatter:N:1,8:
:Number of rejections v Batch:N:1,11,12: $$
N_batch Batch_number Mn(Imean) Scatter_from_I+/-
Number_of_fulls Number_of_partials
Scatter_from_Imean Imean/Scatter_from_Imean Rmerge
Number_in_Rmerge
Number_rejected Number_invalid
Fraction_rejected $$
Imean/SIGM0
For inline graphs use a Java browser
SIGM0 Imean/SIGM0
================================================================================
:- R-merge up to this range,
:- Sum |Mn(I+) - Mn(I-)| / Sum (Mn(I+) + Mn(I-))
:- R-merge for fulls only,
:- number of independent hkl's
:- unmerged Ihl averaged in bin
:- rms scatter of observations
I/sigma :-
/ rms scatter
= AvI/SIGMA
:- average standard deviation derived from experimental SDs, after
:- application of SdFac SdB SdAdd
Mn(I/sd):- average & merged/sd() & ~= signal/noise
FRCBIAS :- Mean( Mn(If) - Ip )/Mean( Mn(I) )
for Nbias mixed sets only (If is a full if present, else the
partial with the smallest number of parts)
&h3&Agreement by resolution
4SINTH/LASQ bins (all statistics use Mn(I+),Mn(I-)etc)
______________________________________________________________
$TABLE: Analysis against resolution , WAVE3 :
$GRAPHS: I/sigma, Mean Mn(I)/sd(Mn(I)):N:2,11,13:
: Rmerge v Resolution:N:2,4,5,7:
: Average I,sd and Sigma :A:2,9,10,12: : Fractional bias :A:2,17: $$
N 1/resol^2 Dmin(A) Rmrg
SIGMA I/sigma
sd Mn(I/sd)
Ncent FRCBIAS
N 1/d^2 Dmin(A) Rmrg
SIGMA I/sigma
sd Mn(I/sd)
Ncent FRCBIAS
For inline graphs use a Java browser
SIGMA I/sigma
sd Mn(I/sd)
Ncent FRCBIAS
&h3&Agreement by intensity
INTENSITY ranges (all statistics use Mn(I+),Mn(I-)etc)
______________________________________________________________
$TABLE: Analysis against intensity, WAVE3 :
$GRAPHS:Rmerge v Intensity :N:1,2,3,4:
For inline graphs use a Java browser
&h3&Completeness & multiplicity
Completeness and multiplicity, including reflections measured only once
=======================================================================
%poss is completeness in the shell, Cm%poss in cumulative to that resolution
The anomalous completeness values (AnomCmpl) are the percentage of possible anomalous differences measured
AnomFrc is the % of measured acentric reflections for which an anomalous difference has been measured
Rmeas: redundancy-independent (multiplicity-weighted) Rmerge
or R(r.i.m.) (Rmeas is relative to I+ or I-, RmeasO is relative to overall mean)
pooled coefficient of variation (PCV is relative to I+ or I-, PCV0 is relative to overall mean)
PCV is a multiplicity-weighted RMS Rmerge
Rpim: precision-indicating (multiplicity-weighted) Rmerge
(Rpim is relative to I+ or I-, RpimO is relative to overall mean)
See:- &Improved R-factors for diffraction data analysis in macromolecular crystallography&
Kay Diederichs & P. Andrew Karplus, Nature Structural Biology, 4, 269-275 (1997)
&On the use of the merging R factor as a qualityindicator for X-ray data&
Manfred Weiss & Rolf Hilgenfeld, J.Appl.Cryst. 30, 203-205 (1997)
&Global Indicators of X-ray data quality&
Manfred Weiss, J.Appl.Cryst. 34, 130-135 (2001)
$TABLE: Completeness, multiplicity, Rmeas v. resolution, WAVE3 :
$GRAPHS:Completeness v Resolution :N:2,7,8,10,11:
:Multiplicity v Resolution :N:2,9,12:
:Rpim (precision R) v Resolution :N:2,16,17:
:Rmeas, Rsym & PCV v Resolution :N:2,13,14,15,18,19:
N 1/resol^2 Dmin
%poss C%poss Mlplct AnoCmp AnoFrc AnoMlt Rmeas Rmeas0
For inline graphs use a Java browser
%poss C%poss Mlplct AnoCmp AnoFrc AnoMlt Rmeas Rmeas0
Correlation coefficients for anomalous differences & Imean between random subsets within dataset
===============================================================================================
The RMS Correlation Ratio (RCR) is calculated from a scatter plot of pairs of DeltaI(anom) from the two subsets
by comparing the RMS value (excluding extremes) projected on the line with slope = 1 (&correlation&) with the
RMS value perpendicular to this (&error&). This ratio will be & 1 if there is an anomalous signal
$TABLE: Correlations within dataset, WAVE3 :
$GRAPHS: Anom & Imean CCs v resolution - :A:2,4,6,12:
:RMS correlation ratio:A:2,8,10:$$
N 1/resol^2 dmax CC_anom
N_cen RCR_anom
N_cen CC_Imean
For inline graphs use a Java browser
&h3&Axial reflections
$TABLE: Axial reflections, axis h, WAVE3 :
$GRAPHS: I/sigI vs. h:0|
29.13:1,4:
: I vs. h:0|
For inline graphs use a Java browser
$TABLE: Axial reflections, axis k, WAVE3 :
$GRAPHS: I/sigI vs. k:0|
24.64:1,4:
: I vs. k:0|
For inline graphs use a Java browser
$TABLE: Axial reflections, axis l, WAVE3 :
$GRAPHS: I/sigI vs. l:0|
19.17:1,4:
: I vs. l:0|
For inline graphs use a Java browser
&h3&Analysis of standard deviations
ANALYSIS OF STANDARD DEVIATIONS
===============================
This plots the distribution of the number of observations
with Chi = (Ihl - Mn(Iothers) )/sqrt[sd(Ihl)**2 + sd(Mn(I))**2] in ranges from -5 to +5 .
If the SD is a true estimate of the error, this distribution should have Mean=0.0 and Sigma=1.0
for all ranges of intensity.
The analysis is repeated for ranges of increasing Imean. The Mean is expected to increase with Imean
since the latter is a weighted mean and sd(Ihl) & Ihl are correlated.
If the Sigma increases with Imean, increase the value of SdAdd.
In the table, Cmin, Cmax & Cmean are respectively the minimum, maximum and mean
of the applied SD correction, ie SDcorrected/SDoriginal
Current values of SD corrections are:-SdFac * Sqrt[sd(I)**2 + SdB I + (SdAdd I)**2]
========= Run
3 =========
$TABLE: Run
3, standard deviation v. Intensity, WAVE3 :
$GRAPHS: Sigma(scatter/SD) Run
3:N:11,7,14:
: Mean(scatter/SD) Run
3:A:11,6,13:
: MeanCorrection Run
3:N:11,10,17: $$
Range Imin Imax Irms Number MeanFull SigmaFull MinCorFull MaxCorFull MeanCorFull Irms
Number MeanPart SigmaPartial MinCorPartial MaxCorPartial MeanCorPartial
Fully_recordeds
Partially_recordeds
Mean Sigma
Mean Sigma
For inline graphs use a Java browser
Mean Sigma
Mean Sigma
Fully_recordeds
Partially_recordeds
In the following analyses,
Chi = (Ihl - Mn(Iothers) )/sqrt[sd(Ihl)**2 + sd(Mn(I))**2]
Chi**2 analysis by position of detector (Xdet, Ydet)
Each entry is 10 * Chi**2
(ie relative discrepancy **2)
921 28 36 43 1945
Chi analysis by position of detector (Xdet, Ydet)
Each entry is
10 * Mn(Chi) (ie signed relative discrepancy)
921 28 36 43 1945
Number of outlier rejections in each area
921 28 36 43 1945
Number of observations in each area
921 28 36 43 1945
851 82 70 1977
================================================
Normal probability analysis of anomalous differences
====== Anomalous differences ======
Slope Intercept
Data within expected delta 0.90:
================================================
Normal probability analysis, by run & partiality
====== Run number:
3, Run 3: summed partials ======
Slope Intercept
Data within expected delta 0.90:
==========================================
Final assessment of SDcorrection multipliers
SdFac_used
_corrected
_fullsonly
SdFac_used
_corrected
================================================================================
Summary data for
Project: AUTOMATIC Crystal: DEFAULT Dataset: WAVE3
InnerShell
OuterShell
Low resolution limit
High resolution limit
Rmerge in top intensity bin
Rmeas (within I+/I-)
Rmeas (all I+ & I-)
Rpim (within I+/I-)
Rpim (all I+ & I-)
Fractional partial bias
Total number of observations
Total number unique
Mean((I)/sd(I))
Completeness
Multiplicity
Anomalous completeness
Anomalous multiplicity
DelAnom correlation between half-sets
Mid-Slope of Anom Normal Probability
Outlier rejection and statistics assume that there is anomalous scattering, ie I+ differs from I-
Average unit cell:
Space group: P 21 21 21
Average mosaicity:
Minimum and maximum SD correction factors: Partials
================================================================================
$TEXT:Result: $$ $$
datasets processed
Dataset: AUTOMATIC/DEFAULT/WAVE1
written as averaged data to output file /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled_WAVE1.mtz
Maximum resolution:
Dataset: AUTOMATIC/DEFAULT/WAVE2
written as averaged data to output file /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled_WAVE2.mtz
Maximum resolution:
Dataset: AUTOMATIC/DEFAULT/WAVE3
written as averaged data to output file /home/pjb/Diamond/xia2_runs/TM-images/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled_WAVE3.mtz
Maximum resolution:
See Summary Tables in logfile for details
** Normal termination **
Times: User:
927.4s System:
21.8s Elapsed:
Current view: summary only
Current view: full logfile
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