I am doing SAD phasing with the latest autoSHARP and CCP4 6.1.1 (SCALA version
3.3.9). The space
group is P21 with unit cell dimension 52.67, 28.61 and 105.16. If I give the
data as unmerged SHELX
file, it happens that the third cell dimension become identical to the first
when the data are
merged using SCALA. I put the whole log file as attachment. Is this a bug or am
I doing something wrong?
Michele
###############################################################
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### CCP4 6.1: SORTMTZ version 6.1 : 06/09/05##
###############################################################
User: unknown Run date: 17/11/2009 Run time: 17:01:10
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.
Data line--- H K L M/ISYM BATCH
Data line--- CONVERT/F2MTZCOMBAT_peak.mtz
OPENED INPUT MTZ FILE
Logical Name: CONVERT/F2MTZCOMBAT_peak.mtz Filename: CONVERT/F2MTZCOMBAT_peak.mtz
* Title:
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 ib18-sad
1
peak
52.6670 28.6140 105.1640 90.0000 95.9550 90.0000
0.00000
* Number of Columns = 13
* Number of Reflections = 47562
* Missing value set to NaN in input mtz file
* Number of Batches = 1
* Column Labels :
H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT
* Column Types :
H H H Y B J Q J Q R R R R
* Associated datasets :
0 0 0 1 1 1 1 1 1 1 1 1 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
52.6670 28.6140 105.1640 90.0000 95.9550 90.0000
* Resolution Range :
0.00065 0.18179 ( 39.094 - 2.345 A )
* Sort Order :
0 0 0 0 0
* Space group = 'P 1 21 1' (number 4)
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/michele/sharp/database/syminfo.lib
WRITTEN OUTPUT MTZ FILE
Logical Name: CONVERT/SCALAMERGE_peak.mtz Filename: CONVERT/SCALAMERGE_peak.mtz
* Title:
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 ib18-sad
1
peak
52.6670 28.6140 105.1640 90.0000 95.9550 90.0000
0.00000
* Number of Columns = 13
* Number of Reflections = 47562
* Missing value set to NaN in input mtz file
* Number of Batches = 1
* Column Labels :
H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT
* Column Types :
H H H Y B J Q J Q R R R R
* Associated datasets :
0 0 0 1 1 1 1 1 1 1 1 1 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
52.6670 28.6140 105.1640 90.0000 95.9550 90.0000
* Resolution Range :
0.00065 0.18179 ( 39.094 - 2.345 A )
* Sort Order :
1 2 3 4 5
* Space group = 'P 1 21 1' (number 4)
SORTMTZ
-------
Contents
--------
Command Input
Input File Details
Output File Details
Header Information for Output MTZ File
-------------------------------------------------------
Command Input
-------------
ASCEND/DESCEND
SORT KEYS
-------------------------------------------------------
Input File Details
------------------
5 sort keys, in columns 1 2 3 4 5
-------------------------------------------------------
Output File Details
-------------------
47562 records read from file 1
47562 records passed to sort
-------------------------------------------------------
Header Information For Output MTZ File
--------------------------------------
47562 records output
SORTMTZ: Normal termination
Times: User: 0.3s System: 0.0s Elapsed: 0:01
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###############################################################
### CCP4 6.1: Scala version 3.3.9 : 20/01/09##
###############################################################
User: unknown Run date: 17/11/2009 Run time: 17:01:11
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.
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: CONVERT/SCALAMERGE_peak.mtz
* Title:
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 ib18-sad
1
peak
52.6670 28.6140 105.1640 90.0000 95.9550 90.0000
0.00000
* Number of Columns = 13
* Number of Reflections = 47562
* Missing value set to NaN in input mtz file
* Number of Batches = 1
* Column Labels :
H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT
* Column Types :
H H H Y B J Q J Q R R R R
* Associated datasets :
0 0 0 1 1 1 1 1 1 1 1 1 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
52.6670 28.6140 105.1640 90.0000 95.9550 90.0000
* Resolution Range :
0.00065 0.18179 ( 39.094 - 2.345 A )
* Sort Order :
1 2 3 4 5
* Space group = 'P 1 21 1' (number 4)
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/michele/sharp/database/syminfo.lib
Reciprocal space symmetry:
Space group: "P 1 21 1" Point group: "PG2" Laue group: "2/m"
Reference asymmetric unit: "k>=0 and (l>0 or (l=0 and h>=0))"
(change of basis may be applied)
Spacegroup 4 "P 1 21 1"
Original indices for reflection hkl with symmetry number ISYM
Bijvoet positive
ISYM ISYM ISYM ISYM
ISYM 1 +h,+k,+l 3 -h,+k,-l
Bijvoet negative
ISYM ISYM ISYM ISYM
ISYM 2 -h,-k,-l 4 +h,-k,+l
Data line--- ONLYMERGE
Data line--- SDCORR ADJUST FULLS 1.0 0.0 0.0 PARTIAL 1.0 0.0 0.0
Data line--- ANOMALOUS ON
Data line--- END
FORMATTED UNKNOWN file opened on unit 15
Logical name: ROGUES, Filename: CONVERT/SCALAMERGE_peak.rogues
FORMATTED UNKNOWN file opened on unit 9
Logical name: ANOMPLOT, Filename: CONVERT/SCALAMERGE_peak.ano.xmgr
FORMATTED UNKNOWN file opened on unit 8
Logical name: NORMPLOT, Filename: CONVERT/SCALAMERGE_peak.xmgr
FORMATTED UNKNOWN file opened on unit 10
Logical name: CORRELPLOT, Filename: CORRELPLOT
WRITTEN OUTPUT MTZ FILE
Logical Name: CONVERT/SCALAMERGE_peak.mtz1 Filename: CONVERT/SCALAMERGE_peak.mtz1
* Title:
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 ib18-sad
1
peak
52.6103 28.6140 52.6103 90.0000 95.9550 90.0000
0.00000
* Number of Columns = 9
* Number of Reflections = 13315
* 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)
52.6103 28.6140 52.6103 90.0000 95.9550 90.0000
* Resolution Range :
0.00146 0.71199 ( 26.163 - 1.185 A )
* Sort Order :
1 2 3 4 5
* Space group = 'P 1 21 1' (number 4)
*******************************************
* SCALA - continuous scaling program *
* *
* Version: 3.3.9 *
* Date : 2008/10/21 *
* *
* Phil Evans, MRC LMB, Cambridge, UK *
* [email protected] *
* *
*******************************************
$TEXT:Reference: $$ Please reference $$
P.R.Evans, "Scaling and assessment of data quality", Acta Cryst. D62, 72-82 (2005).
Note that definitions of Rmeas and Rpim in this paper are missing a square-root on the (n/n-1) factor
$$
Run number 1 consists of batches :-
1
===== Dataset: ib18-sad/1/peak
Run(s): 1
Wavelength: 0.000000 Cell: 52.610 28.614 52.610 90.000 95.955 90.000
PROFILE_FITTED intensities will be used
Fully-recorded and summed partial reflections will be used in scaling
Maximum number of parts in summed partials equivalent to 5.0 degrees
Summed partials accepted for scaling if total fraction lies between 0.950 and 1.050
Partials with missing parts in the middle will be rejected
Overall resolution limits: 39.0938 2.3454
Smoothing factors Maximum fractional distance
Time: 0.50 3.0000
Rotation: 1.00 3.0000
Detector: 1.00 3.0000
Reflections will be excluded from scaling in all runs if:
I .lt. sd(I) * 3.000
Reflections judged implausibly large will be rejected from scaling and merging
Maximum normalised F (ie E) for acentric reflection 10.000
Maximum normalised F (ie E) for centric reflection 12.000
Minimum probability before reflection is rejected 0.378E-43
Outlier rejection limits
========================
--| In scaling |--
==== For all observations including I+ & I- ====
Reflections measured 3 or more times: 6.000 maximum deviation from weighted mean of all other observations
Reflections measured twice: 6.000 maximum deviation from weighted mean
2 first refinement cycle to reject outliers
--| In merging |--
==== Within each I+ & I- set ====
Reflections measured 3 or more times: 6.000 maximum deviation from weighted mean of all other observations
Reflections measured twice: 6.000 maximum deviation from weighted mean
==== For all observations including I+ & I- ====
Maximum deviation will be determined from observed anomalous differences, see below
Run 1, no spindle axis defined
Standard deviations will be adjusted to SdFac * Sqrt[sd(I)**2 + SdB I + (SdAdd I)**2] as follows:-
Fulls Partials
Run SdFac SdB SdAdd SdFac SdB SdAdd
1 1.00000 0.00000 0.00000 1.00000 0.00000 0.00000
Layout of scale factors
=======================
Run number 1 Dataset: ib18-sad/1/peak
Scales:
Along rotation axis: 1 scales at intervals of 1.00
No variation of scale with detector coordinate
===========================================
Working array size = 1
================================================================================
================================================================================
================================================================================
------ Analysis Pass ------
================================================================================
================================================================================
================================================================================
Fully-recorded and summed partial reflections will be used in analysis
Summed partials must contain not more than 0 parts
Summed partials accepted if total fraction lies between 0.950 and 1.050
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, Fulls ======
Number Slope Intercept
All data: 43309 0.995 0.000
Data within expected delta 0.90: 27367 1.004 0.000
====== Run number: 1, Partials ======
Number Slope Intercept
All data: 43309 0.995 0.000
Data within expected delta 0.90: 27367 1.004 0.000
Update of SDcorrection parameters:
Fulls Partials
initial values: 1.0000 0.0000 0.0000 1.0000 0.0000 0.0000
changed to: 1.0043 1.0043
==========================================
===== Refinement of SD correction parameters
Intensity bins: mid-bin intensity = 9844. number of bins 21 10
Run 1 has fulls only,
>>>>> Pass 1 Initial residual: 0.00215 <<<<<<
Option: INDIVIDUAL SD parameters are different for fulls and partials
Best residual 0.00171 after 23 cycles
>>>>> Pass 2 Initial residual: 0.00171 <<<<<<
Option: INDIVIDUAL SD parameters are different for fulls and partials
Best residual 0.00170 after 10 cycles
===== Updated SDcorrection parameters:
Run Fulls Partials
1 1.024 3.01 -0.0152
================================================
Normal probability analysis of anomalous differences
====== Anomalous differences ======
Number Slope Intercept
All data: 11368 1.591 -0.741
Data within expected delta 0.90: 7184 1.260 -0.540
Outlier rejection limits limits for I+ v I- have been adjusted by a factor 3.700 * 1.260 (AnomProbSlope)
==== For all observations including I+ & I- ====
Reflections measured 3 or more times: 12.661 maximum deviation from weighted mean of all other observations
Reflections measured twice: 12.661 maximum deviation from weighted mean
================================================================================
================================================================================
================================================================================
------ Final Pass for statistics of merging ------
================================================================================
================================================================================
================================================================================
Intensity bins, WILSON mode, mid-bin intensity = 9844.
********************************************************************************
********************************************************************************
Statistics for all datasets
Number of observations read : 47562
Number of unique reflections read : 13315
Number of observations output : 13315
Number of outliers rejected : 6
Number of observations rejected on Emax limit : 0
Number of observations outside resolution limits : 0
Number of outliers rejected between I+ & I- : 6
(observations outside resolution limits are omitted from the output file)
Statistics below are accumulated from:- 13212 unique reflections, 47453 observations
(of which 47453 are fully recorded, 0 are summed partials, 0 are scaled partials)
this excludes 48 good observations measured once only
================================================================================
Analysis of applied scale factors (including input scale)
Mean scale factors analysed by Batch for each run and resolution
Rotation 1
dmax
7.42 1.00
5.24 1.00
4.28 1.00
3.71 1.00
3.32 1.00
3.03 1.00
2.80 1.00
2.62 1.00
2.47 1.00
2.35 1.00
Overall 1.00
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, peak :
$GRAPHS:Mn(k) & 0k (at theta = 0) v range:N:1,6,7:
:B v range:A:1,5:
:Number rejected v range:N:1,9: $$
N Run.Rot MidPhi Batch Bfactor Mn(k) 0k Number NumReject $$ $$
1 1.1 0.00 1 0.000 1.0000 1.0000 47556 6
$$
Total 0.000 1.0000 1.0000 47556 6
Bfactor Mn(k) 0k Number NumReject
Agreement between batches
-------------------------
RMS scatters are shown as SIGMA and SIGM0 for differences
from Mn(I+),Mn(I-) and Mn(Imean) respectively.
Rmerge in this table is the difference from Mn(Imean),
but in later tables Rmerge is the difference from Mn(I+),Mn(I-).
NFR,NPR count those (mixed & unmixed sets) included in SIGMA
NR those in SIGM0 and Rmerge
(mixed & unmixed FULLY/PARTIAL SETS)
NBREJ number of reflections rejected for bad agreement
NBRJM number of reflections rejected for M .gt. 1
(neither valid fully nor partial)
$TABLE : Analysis against all Batches for all runs , peak :
$GRAPHS :Rmerge v Batch for all runs :N:1,9: :Imean & RMS Scatter:N:1,3,4,7: :Imean/RMS scatter:N:1,8:
:Number of rejections v Batch:N:1,11,12: $$
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 $$
N BATCH Mn(Imean) SIGMA NFR NPR SIGM0 Imean/SIGM0 Rmerge NR NBREJ NBRJM FracRejtd
$$
1 1 9188.0 926.3 43307 0 1433.4 6.41 0.061 47453 6 0 0.000
$$
Overall 9188.0 926.3 43307 0 1433.4 6.41 0.061 47453 6 0 0.000
Mn(Imean) SIGMA NFR NPR SIGM0 Imean/SIGM0 Rmerge NR NBREJ NBRJM FracRejtd
================================================================================
Rcum :- R-merge up to this range,
Ranom :- Sum |Mn(I+) - Mn(I-)| / Sum (Mn(I+) + Mn(I-))
Rfull :- R-merge for fulls only,
Nref :- number of independent hkl's
SIGMA :- rms scatter of observations
sd :- average standard deviation derived from experimental SDs, after
:- application of SDFAC SDADD
FRCBIAS :- Mean( Mn(If) - Ip )/Mean( Mn(I) )
for Nbias mixed sets only (If is a full if present, else the partial with the smallest number of parts)
By 4SINTH/LASQ bins (all statistics use Mn(I+),Mn(I-)etc)
______________________________________________________________
$TABLE: Analysis against resolution , peak :
$GRAPHS: I/sigma, Mean Mn(I)/sd(Mn(I)):N:2,11,13:
: Rmerge v Resolution:N:2,4,5,7:
: Average I,sd and Sigma :A:2,9,10,12: : Fractional bias :A:2,17: $$
N 1/resol^2 Dmin(A) Rmrg Rfull Rcum Ranom Nanom Av_I SIGMA I/sigma sd Mn(I/sd) Nmeas Nref Ncent FRCBIAS Nbias $$
N 1/d^2 Dmin(A) Rmrg Rfull Rcum Ranom Nanom Av_I SIGMA I/sigma sd Mn(I/sd) Nmeas Nref Ncent FRCBIAS Nbias
$$
1 0.0182 7.42 0.020 0.020 0.020 0.041 277 51528 2375 21.7 2173 34.4 1304 424 142 - 0
2 0.0364 5.24 0.025 0.025 0.021 0.078 601 14433 797 18.1 691 30.0 2557 772 147 - 0
3 0.0545 4.28 0.025 0.025 0.023 0.038 805 35643 2426 14.7 1568 33.6 3296 999 157 - 0
4 0.0727 3.71 0.029 0.029 0.025 0.042 954 19185 1019 18.8 943 30.4 3796 1125 144 - 0
5 0.0909 3.32 0.036 0.036 0.026 0.050 1129 10413 583 17.9 660 23.0 4356 1284 141 - 0
6 0.1091 3.03 0.056 0.056 0.028 0.060 1316 5006 421 11.9 487 14.8 4959 1438 154 - 0
7 0.1273 2.80 0.080 0.080 0.031 0.072 1411 3244 383 8.5 438 10.1 5326 1530 148 - 0
8 0.1454 2.62 0.135 0.135 0.033 0.109 1520 1703 319 5.3 409 6.2 5641 1626 150 - 0
9 0.1636 2.47 0.211 0.211 0.036 0.179 1685 1067 306 3.5 397 4.2 6157 1757 159 - 0
10 0.1818 2.35 0.327 0.327 0.039 0.273 1665 703 303 2.3 414 2.7 5915 1695 141 - 0
$$
Overall: 0.039 0.039 0.039 0.053 11363 9287 926 10.0 651 15.1 43307 12650 1483 0.000 0
Rmrg Rfull Rcum Ranom Nanom Av_I SIGMA I/sigma sd Mn(I/sd) Nmeas Nref Ncent FRCBIAS Nbias
BY INTENSITY ranges (all statistics use Mn(I+),Mn(I-)etc)
______________________________________________________________
$TABLE: Analysis against intensity, peak :
$GRAPHS:Rmerge v Intensity :N:1,2,3,4:
$$
Imax Rmrg Rfull Ranom Nanom Av_I SIGMA I/Sigma sd Nmeas Nref Ncent FRCBIAS Nbias Abs.BIAS
$$ $$
1080. 0.565 0.565 0.426 5152 356. 270.0 1.3 359.6 18651 5322 511 0.000 0 0.0
2241. 0.141 0.141 0.120 1471 1608. 304.9 5.3 382.5 5690 1657 186 0.000 0 0.0
3495. 0.084 0.084 0.084 782 2837. 316.7 9.0 397.7 3068 904 105 0.000 0 0.0
4857. 0.058 0.058 0.069 621 4173. 325.0 12.8 418.4 2465 718 79 0.000 0 0.0
6350. 0.048 0.048 0.067 463 5633. 361.2 15.6 457.1 1818 539 65 0.000 0 0.0
8000. 0.038 0.038 0.061 405 7214. 355.3 20.3 492.2 1626 491 65 0.000 0 0.0
9844. 0.035 0.035 0.058 340 8941. 405.5 22.1 544.5 1358 408 51 0.000 0 0.0
11936. 0.032 0.032 0.061 301 10967. 451.7 24.3 617.3 1201 357 46 0.000 0 0.0
14350. 0.031 0.031 0.056 256 13239. 519.6 25.5 693.9 1022 310 42 0.000 0 0.0
17205. 0.027 0.027 0.062 212 15895. 557.2 28.5 790.0 867 265 47 0.000 0 0.0
20700. 0.026 0.026 0.054 231 19075. 642.4 29.7 912.6 910 277 36 0.000 0 0.0
25205. 0.025 0.025 0.049 236 22926. 741.2 30.9 1055.1 970 288 41 0.000 0 0.0
31555. 0.025 0.025 0.046 214 28373. 905.2 31.3 1271.4 866 255 37 0.000 0 0.0
42410. 0.025 0.025 0.048 203 36882. 1167.1 31.6 1604.7 844 258 55 0.000 0 0.0
999999. 0.022 0.022 0.033 476 101243. 3952.4 25.6 4217.3 1951 601 117 0.000 0 0.0
$$
Overall 0.039 0.039 0.053 11363 9287. 926.3 10.0 650.6 43307 12650 1483 0.000 0 0.0
Rmrg Rfull Ranom Nanom Av_I SIGMA I/Sigma sd Nmeas Nref Ncent FRCBIAS Nbias Abs.BIAS
Completeness and multiplicity, including reflections measured only once
=======================================================================
%poss is completeness in the shell, Cm%poss in cumulative to that resolution
The anomalous completeness values (AnomCmpl) are the percentage of possible anomalous differences measured
AnomFrc is the % of measured acentric reflections for which an anomalous difference has been measured
Rmeas: redundancy-independent (multiplicity-weighted) Rmerge or R(r.i.m.) (Rmeas is relative to I+ or I-, RmeasO is relative to overall mean)
PCV: pooled coefficient of variation (PCV is relative to I+ or I-, PCV0 is relative to overall mean)
PCV is a multiplicity-weighted RMS Rmerge
Rpim: precision-indicating (multiplicity-weighted) Rmerge (Rpim is relative to I+ or I-, RpimO is relative to overall mean)
See:- "Improved R-factors for diffraction data analysis in macromolecular crystallography"
Kay Diederichs & P. Andrew Karplus, Nature Structural Biology, 4, 269-275 (1997)
"On the use of the merging R factor as a qualityindicator for X-ray data"
Manfred Weiss & Rolf Hilgenfeld, J.Appl.Cryst. 30, 203-205 (1997)
"Global Indicators of X-ray data quality"
Manfred Weiss, J.Appl.Cryst. 34, 130-135 (2001)
$TABLE: Completeness, multiplicity, Rmeas v. resolution, peak :
$GRAPHS:Completeness v Resolution :N:2,7,8,10,11:
:Multiplicity v Resolution :N:2,9,12:
:Rpim (precision R) v Resolution :N:2,16,17:
:Rmeas, Rsym & PCV v Resolution :N:2,13,14,15,18,19: $$
N 1/resol^2 Dmin Nmeas Nref Ncent %poss C%poss Mlplct AnoCmp AnoFrc AnoMlt Rmeas Rmeas0 (Rsym) Rpim RpimO PCV PCV0
$$ $$
1 0.018 7.42 1384 446 144 93.3 93.3 3.1 86.0 91.7 1.9 0.027 0.050 0.020 0.019 0.027 0.028 0.052
2 0.036 5.24 2707 797 148 97.6 96.1 3.4 90.6 92.6 1.9 0.035 0.084 0.025 0.024 0.044 0.035 0.089
3 0.055 4.28 3537 1030 157 99.0 97.4 3.4 91.2 92.2 1.9 0.034 0.048 0.025 0.023 0.026 0.035 0.053
4 0.073 3.71 4080 1157 145 109.1 101.2 3.5 101.5 94.3 1.9 0.040 0.054 0.029 0.028 0.029 0.041 0.060
5 0.091 3.32 4738 1333 143 124.7 106.9 3.6 116.5 94.9 1.9 0.049 0.067 0.036 0.034 0.035 0.050 0.075
6 0.109 3.03 5439 1500 155 139.6 113.4 3.6 134.6 97.8 1.9 0.077 0.089 0.056 0.053 0.047 0.081 0.101
7 0.127 2.80 5838 1592 149 153.4 119.9 3.7 147.6 97.8 1.9 0.109 0.117 0.080 0.074 0.061 0.115 0.130
8 0.145 2.62 6261 1717 151 164.8 126.2 3.6 157.8 97.1 1.8 0.185 0.192 0.135 0.126 0.100 0.198 0.221
9 0.164 2.47 6851 1863 160 175.1 132.3 3.7 170.8 98.9 1.8 0.288 0.301 0.211 0.196 0.157 0.306 0.336
10 0.182 2.35 6721 1880 144 179.1 137.5 3.6 169.8 95.9 1.8 0.447 0.467 0.327 0.304 0.243 0.470 0.531
$$
Overall 47556 13315 1496 137.5 137.5 3.6 131.5 96.1 1.9 0.054 0.072 0.039 0.037 0.038 0.055 0.079
Nmeas Nref Ncent %poss C%poss Mlplct AnoCmp AnoFrc AnoMlt Rmeas Rmeas0 (Rsym) Rpim RpimO PCV PCV0
Correlation coefficients for anomalous differences & Imean between random subsets within dataset
===============================================================================================
The RMS Correlation Ratio (RCR) is calculated from a scatter plot of pairs of DeltaI(anom) from the two subsets
by comparing the RMS value (excluding extremes) projected on the line with slope = 1 ("correlation") with the
RMS value perpendicular to this ("error"). This ratio will be > 1 if there is an anomalous signal
$TABLE: Correlations within dataset, peak :
$GRAPHS: Anom & Imean CCs v resolution - :A:2,4,6,12:
:RMS correlation ratio:A:2,8,10:$$
N 1/resol^2 dmax CC_anom N_anom CC_cen N_cen RCR_anom N_anom RCR_cen N_cen CC_Imean N_Imean $$
$$
1 0.0182 7.42 0.630 215 - 0 2.430 215 - 0 0.998 267
2 0.0364 5.24 0.790 472 - 0 3.624 472 - 0 0.998 584
3 0.0545 4.28 0.555 589 - 0 2.111 589 - 0 0.998 779
4 0.0727 3.71 0.467 694 - 0 1.979 694 - 0 0.998 927
5 0.0909 3.32 0.510 793 - 0 2.002 793 - 0 0.997 1085
6 0.1091 3.03 0.244 889 - 0 1.376 889 - 0 0.996 1258
7 0.1273 2.80 0.137 952 - 0 1.205 952 - 0 0.996 1351
8 0.1454 2.62 0.084 982 - 0 1.104 982 - 0 0.990 1433
9 0.1636 2.47 0.032 1091 - 0 1.060 1091 - 0 0.975 1580
10 0.1818 2.35 0.017 1041 - 0 1.024 1041 - 0 0.934 1537
$$
Overall 0.635 7718 0.000 0 2.222 7718 0.000 0 0.998 10801
$TABLE: Axial reflections, axis h, peak :
$GRAPHS: I/sigI vs. h:0| 22x0| 37.31:1,4:
: I vs. h:0| 22x0| 68278.09:1,2:$$
h I sigI I/sigI $$ $$
2 883. 59. 15.018
3 7713. 258. 29.890
4 320. 74. 4.304
5 62071. 1830. 33.917
6 4070. 179. 22.692
7 2181. 149. 14.666
8 2455. 146. 16.843
9 26. 130. 0.200
10 41109. 1239. 33.178
11 1913. 173. 11.034
12 59296. 1774. 33.419
13 138. 218. 0.634
14 9114. 417. 21.843
15 522. 304. 1.714
16 6253. 336. 18.589
17 1917. 297. 6.460
18 2294. 322. 7.128
19 -179. 216. -0.832
20 -23. 280. -0.081
21 575. 269. 2.137
22 41. 226. 0.180
$$
$TABLE: Axial reflections, axis k, peak :
$GRAPHS: I/sigI vs. k:0| 12x0| 37.56:1,4:
: I vs. k:0| 12x0| 97500.31:1,2:$$
k I sigI I/sigI $$ $$
2 88637. 2596. 34.143
4 20292. 621. 32.687
6 37022. 1129. 32.780
8 2309. 172. 13.438
10 677. 167. 4.058
12 19. 166. 0.116
$$
$TABLE: Axial reflections, axis l, peak :
$GRAPHS: I/sigI vs. l:0| 44x0| 37.99:1,4:
: I vs. l:0| 44x0| 641698.06:1,2:$$
l I sigI I/sigI $$ $$
3 572. 44. 12.864
4 13349. 417. 32.018
5 6096. 211. 28.947
6 5429. 194. 27.965
7 10769. 349. 30.813
8 1054. 86. 12.219
9 429. 80. 5.370
10 38990. 1165. 33.460
11 2748. 147. 18.699
12 30212. 917. 32.931
13 4446. 197. 22.554
14 9648. 342. 28.226
15 2116. 146. 14.445
16 3429. 181. 18.986
17 35641. 1079. 33.028
18 1151. 151. 7.641
19 1577. 162. 9.729
20 7769. 314. 24.723
22 583362. 16890. 34.538
23 68402. 2033. 33.648
24 295660. 8585. 34.440
25 50041. 1511. 33.124
26 105818. 3115. 33.968
27 9007. 385. 23.411
28 3610. 270. 13.397
29 40566. 1252. 32.400
30 452. 262. 1.728
31 43974. 1353. 32.500
32 18946. 661. 28.650
33 16309. 592. 27.546
34 14463. 551. 26.258
35 37426. 1174. 31.883
36 1153. 262. 4.397
37 811. 283. 2.865
38 12296. 496. 24.802
39 1923. 276. 6.977
40 -64. 278. -0.231
41 664. 275. 2.413
42 6098. 379. 16.094
43 6897. 399. 17.278
44 772. 341. 2.268
$$
ANALYSIS OF STANDARD DEVIATIONS
===============================
This plots the distribution of the number of observations
with Chi = (Ihl - Mn(Iothers) )/sqrt[sd(Ihl)**2 + sd(Mn(I))**2] in ranges from -5 to +5 .
If the SD is a true estimate of the error, this distribution should have Mean=0.0 and Sigma=1.0
for all ranges of intensity.
The analysis is repeated for ranges of increasing Imean. The Mean is expected to increase with Imean
since the latter is a weighted mean and sd(Ihl) & Ihl are correlated.
If the Sigma increases with Imean, increase the value of SdAdd.
In the table, Cmin, Cmax & Cmean are respectively the minimum, maximum and mean
of the applied SD correction, ie SDcorrected/SDoriginal
Current values of SD corrections are:-SdFac * Sqrt[sd(I)**2 + SdB LP I + (SdAdd I)**2]
Fulls Partials
Run SdFac SdB SdAdd SdFac SdB SdAdd
1 1.02415 3.01264 -0.01516 1.02415 3.01264 -0.01516
$TABLE:Run 1, standard deviation v. Intensity, peak :
$GRAPHS: Sigma(scatter/SD) Run 1:N:4,7: : Mean(scatter/SD) Run 1:A:4,6:
: MeanCorrection Run 1:N:4,10: $$
Range Imin Imax Irms Number MeanFull SigmaFull MinCorFull MaxCorFull MeanCorFull $$
Fully_recordeds
Range Imin Imax Irms N Mean Sigma Cmin Cmax Cmean
$$
1 -685 1080 541 18651 0.00 0.94 0.99 1.44 1.03
2 1080 2241 1682 5690 0.00 0.99 1.03 1.31 1.05
3 2241 3495 2888 3068 0.00 1.02 1.03 1.21 1.06
4 3495 4857 4219 2465 0.00 0.99 1.03 1.21 1.06
5 4857 6350 5678 1818 0.00 1.00 1.03 1.14 1.06
6 6350 8000 7256 1626 0.00 0.94 1.03 1.09 1.05
7 8000 9844 8988 1358 0.00 0.98 1.03 1.08 1.04
8 9844 11936 11018 1201 0.00 0.98 1.03 1.05 1.03
9 11936 14350 13295 1022 0.00 1.01 1.01 1.03 1.02
10 14350 17205 15970 867 0.00 0.94 0.99 1.02 1.02
11 17205 20700 19141 910 0.00 0.94 0.97 1.02 1.01
12 20700 25205 23004 970 0.00 0.96 0.97 1.01 1.00
13 25205 31555 28485 866 0.00 0.96 0.96 1.01 0.99
14 31555 42410 37082 844 0.00 0.98 0.89 1.00 0.98
15 42410 999999 139823 1951 0.00 0.95 0.94 0.99 0.97
$$
TOTALS:
0 -685 999999 31047 43307 0.00 0.96 0.89 1.44 1.03
Range Imin Imax Irms N Mean Sigma Cmin Cmax Cmean
Fully_recordeds
================================================
Normal probability analysis of anomalous differences
====== Anomalous differences ======
Number Slope Intercept
All data: 11363 1.573 -0.738
Data within expected delta 0.90: 7181 1.259 -0.540
================================================
Normal probability analysis, by run & partiality
====== Run number: 1, fulls ======
Number Slope Intercept
All data: 43313 0.971 0.002
Data within expected delta 0.90: 27369 0.974 0.000
==========================================
Final assessment of SDcorrection multipliers
Run Fulls Partials
SdFac_used _corrected _fullsonly SdFac_used _corrected
1 1.0242 0.9976 0.0000 1.0242 0.0000
Harvest: No HARVESTHOME or HOME environment variable found - no deposit file created
================================================================================
$TEXT:Result: $$ $$
Summary data for Project: ib18-sad Crystal: 1 Dataset: peak
Overall InnerShell OuterShell
Low resolution limit 39.09 39.09 2.47
High resolution limit 2.35 7.42 2.35
Rmerge 0.039 0.020 0.327
Rmerge in top intensity bin 0.022 - -
Rmeas (within I+/I-) 0.054 0.027 0.447
Rmeas (all I+ & I-) 0.072 0.050 0.467
Rpim (within I+/I-) 0.037 0.019 0.304
Rpim (all I+ & I-) 0.038 0.027 0.243
Fractional partial bias 0.000 0.000 0.000
Total number of observations 47556 1384 6721
Total number unique 13315 446 1880
Mean((I)/sd(I)) 15.1 34.4 2.7
Completeness 137.5 93.3 179.1
Multiplicity 3.6 3.1 3.6
Anomalous completeness 131.5 86.0 169.8
Anomalous multiplicity 1.9 1.9 1.8
DelAnom correlation between half-sets 0.635 0.630 0.017
Mid-Slope of Anom Normal Probability 1.259 - -
Average unit cell: 52.61 28.61 52.61 90.00 95.96 90.00
Space group: P 1 21 1
Average mosaicity: 0.00
Minimum and maximum SD correction factors: Fulls 0.89 1.44
Dataset: ib18-sad/1/peak
written as averaged data to output file CONVERT/SCALAMERGE_peak.mtz1
Maximum resolution: 2.35A
$$
================================================================================
Scala: ** Normal termination **
Times: User: 2.3s System: 0.3s Elapsed: 0:02
