On Tue, Nov 17, 2009 at 05:48:31PM +0100, Michele Lunelli wrote:
> 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?
SCALA (as far as I know) gets its cell dimensions from the so-called
batch header (since each image could have a different cell it averages
those). So the problem isn't yet visible in your output - just do
% mtzdmp CONVERT/F2MTZCOMBAT_peak.mtz -b
and look at the batch header. Most likely COMBAT (if that is what you
used guessing from the name) wrote a wrong batch header - it seems to
leave it at some default or undefined state which can be fatal further
down the line.
POINTLESS is very good in converting other reflection file formats
into correct multi-record MTZ files (at least I see that for
XDS_ASCII.HKL files).
Cheers
Clemens
PS: unless you processed your data natively into SHELX format - if you
have the data in MTZ or *.sca format you can give those directly
to autoSHARP ... jumping between different formats should in
theory preserve all information correctly, but it's an error prone
path.
>
>
> Michele
>
> ###############################################################
> ###############################################################
> ###############################################################
> ### 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
>
> ###############################################################
> ###############################################################
> ###############################################################
> ### 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
--
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************
