#CCP4I VERSION CCP4Interface 1.4.4
#CCP4I SCRIPT LOG scala
#CCP4I DATE 13 Jul 2007 17:09:57
#CCP4I USER pjx
#CCP4I PROJECT PROJECT
#CCP4I JOB_ID 155
#CCP4I SCRATCH /tmp/pjx
#CCP4I HOSTNAME ccp4t.dl.ac.uk
#CCP4I PID 11168
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
Sorting input MTZ file /home/pjx/PROJECTS/myProject/aucn.mtz
***************************************************************************
SORTMTZ
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### CCP4 6.0: SORTMTZ version 6.0 : 06/09/05##
###############################################################
User: pjx Run date: 13/ 7/2007 Run time: 17:09:59
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.
Contents
Command Input
ASCEND/DESCEND
SORT KEYS
Data line--- ASCEND
Data line--- H K L M/ISYM BATCH
Input File Details
OPENED INPUT MTZ FILE
Logical Name: /home/pjx/PROJECTS/myProject/aucn.mtz Filename: /home/pjx/PROJECTS/myProject/aucn.mtz
* Title:
Processing data (images 4-13) collected on 9.6 with aucn soak...
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 DMSO
DMSO
red_aucn
88.9100 88.9100 229.2200 90.0000 90.0000 90.0000
0.00000
* Number of Columns = 16
* Number of Reflections = 9478
* Missing value set to NaN in input mtz file
* Number of Batches = 6
* Column Labels :
H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART
* Column Types :
H H H Y B J Q J Q R R R R R R R
* Associated datasets :
0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
88.9100 88.9100 229.2200 90.0000 90.0000 90.0000
* Resolution Range :
0.00080 0.11111 ( 35.267 - 3.000 A )
* Sort Order :
0 0 0 0 0
* Space group = 'P4122' (number 91)
5 sort keys, in columns 1 2 3 4 5
Output File Details
9478 records passed to sort
Header Information For Output MTZ File
WRITTEN OUTPUT MTZ FILE
Logical Name: /home/pjx/PROJECTS/myProject/aucn_sorted.mtz Filename: /home/pjx/PROJECTS/myProject/aucn_sorted.mtz
* Title:
Processing data (images 4-13) collected on 9.6 with aucn soak...
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 DMSO
DMSO
red_aucn
88.9100 88.9100 229.2200 90.0000 90.0000 90.0000
0.00000
* Number of Columns = 16
* Number of Reflections = 9478
* Missing value set to NaN in input mtz file
* Number of Batches = 6
* Column Labels :
H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART
* Column Types :
H H H Y B J Q J Q R R R R R R R
* Associated datasets :
0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
88.9100 88.9100 229.2200 90.0000 90.0000 90.0000
* Resolution Range :
0.00080 0.11111 ( 35.272 - 3.000 A )
* Sort Order :
1 2 3 4 5
* Space group = 'P4122' (number 91)
9478 records output
SORTMTZ: Normal termination
Times: User: 0.1s System: 0.0s Elapsed: 0:00
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### CCP4 6.0: Scala version 6.0 : ##
###############################################################
User: pjx Run date: 13/ 7/2007 Run time: 17:10:00
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: 3.2.32 *
* Date : 16/05/2007 *
* *
* Phil Evans, MRC LMB, Cambridge, UK *
* pre@mrc-lmb.cam.ac.uk *
* *
*******************************************
"Scala" P.R.Evans (1997), Joint CCP4 and ESF-EACBM Newsletter 33, 22-24
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: /home/pjx/PROJECTS/myProject/aucn_sorted.mtz
* Title:
Processing data (images 4-13) collected on 9.6 with aucn soak...
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 DMSO
DMSO
red_aucn
88.9100 88.9100 229.2200 90.0000 90.0000 90.0000
0.00000
* Number of Columns = 16
* Number of Reflections = 9478
* Missing value set to NaN in input mtz file
* Number of Batches = 6
* Column Labels :
H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART
* Column Types :
H H H Y B J Q J Q R R R R R R R
* Associated datasets :
0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
88.9100 88.9100 229.2200 90.0000 90.0000 90.0000
* Resolution Range :
0.00080 0.11111 ( 35.267 - 3.000 A )
* Sort Order :
1 2 3 4 5
* Space group = 'P4122' (number 91)
From ccp4_lrassn: expected type I does not match file type R for column MPART
(This may be intended for generic types R/I.)
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/pjx/CCP4I_uWORKSHOP/ccp4/lib/data/syminfo.lib
Reciprocal space symmetry:
Space group: "P 41 2 2" Point group: "PG422" Laue group: "4/mmm"
Reference asymmetric unit: "h>=k and k>=0 and l>=0"
(change of basis may be applied)
Spacegroup 91 "P 41 2 2"
Original indices for reflection hkl with symmetry number ISYM
Bijvoet positive
ISYM ISYM ISYM ISYM
ISYM 1 +h,+k,+l 3 -h,-k,+l 5 -k,+h,+l 7 +k,-h,+l
ISYM 9 -h,+k,-l 11 +h,-k,-l 13 +k,+h,-l 15 -k,-h,-l
Bijvoet negative
ISYM ISYM ISYM ISYM
ISYM 2 -h,-k,-l 4 +h,+k,-l 6 +k,-h,-l 8 -k,+h,-l
ISYM 10 +h,-k,+l 12 -h,+k,+l 14 -k,-h,+l 16 +k,+h,+l
Data line--- title Example run with aucn data
Data line--- name project DMSO crystal DMSO dataset red_aucn
Data line--- exclude EMAX 10.0
Data line--- partials check test 0.95 1.05 nogap
Data line--- intensities PROFILE PARTIALS
Data line--- final PARTIALS
Data line--- scales rotation SPACING 5 secondary 6 bfactor ON BROTATION SPACING 20
Data line--- UNFIX V
Data line--- FIX A0
Data line--- UNFIX A1
Data line--- initial MEAN
Data line--- tie surface 0.001
Data line--- tie bfactor 0.3
Data line--- cycles 10 converge 0.3 reject 2
Data line--- output AVERAGE
Data line--- print brief nooverlap
Data line--- RSIZE 80
Comment line--- ## This script run with the command ##########
>>>>>> CCP4 library signal ccp4_parser:Line is longer than allocated length, so truncated (Success)
raised in ccp4_parser <<<<<<
Comment line--- # scala HKLIN "/home/pjx/PROJECTS/myProject/aucn_sorted.mtz" HKLOUT "/tmp/pjx/PROJECT_155_2_mtz.tmp" SCALES "/home/pjx/PROJECTS/myProject/PROJECT_155.scala" ROGUES "/home/pjx/PROJECTS/myProject/PROJECT_155_rogues.log" NORMPLOT "/home/pjx/PROJECTS/myProject/PROJECT_155_normplot.xmgr" ANOMPLOT "/home/pjx/PROJECTS/myProject/PROJECT_155_anomplot.xmgr" PLOT "/home/pjx/PROJECTS/myProject/PROJECT_155_surface_plot.plt" CORRELPLOT "/home/pjx/PROJECTS/myProject/PROJECT_155_correlplot.xmgr" ROGUEPLOT "/hom
Comment line--- ################################################
Input keyworded commands (click for documentation):
TITLE
Example run with aucn data
NAME
project DMSO crystal DMSO dataset red_aucn
EXCLUDE
EMAX 10.0
PARTIALS
check test 0.95 1.05 nogap
INTENSITIES
PROFILE PARTIALS
FINAL
PARTIALS
SCALES
rotation SPACING 5 secondary 6 bfactor ON BROTATION SPACING 20
UNFIX
V
FIX
A0
UNFIX
A1
INITIAL
MEAN
TIE
surface 0.001
TIE
bfactor 0.3
CYCLES
10 converge 0.3 reject 2
OUTPUT
AVERAGE
PRINT
brief nooverlap
RSIZE
80
Contents
Run number 1 consists of batches :-
5 6 7 8 9 10
===== Dataset: DMSO/DMSO/red_aucn
Run(s): 1
* Wavelength and cell extracted from Batch headers, with rms variation:
* Wavelength: 0.880000 Cell: 88.908 88.908 229.217 90.000 90.000 90.000
* rms 0.000000 rms 0.004 0.004 0.005 0.000 0.000 0.000
Wavelength: 0.880000 Cell: 88.908 88.908 229.217 90.000 90.000 90.000
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 0.950 and 1.050
Partials with missing parts in the middle will be rejected
Overall resolution limits: 35.2673 3.0001
In solving least-squares equations:-
Eigenvalue filter limit: 0.000001
No damping of shifts
At least TWO eigenvalues will be filtered
VARIANCE weights will be used in scaling
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 |--
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
*** WARNING: only one B-factor for sole run, B-factor refinement switched off ***
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 0.02000 1.00000 0.00000 0.02000
Layout of scale factors
=======================
Run number 1 Dataset: DMSO/DMSO/red_aucn
Relative B-factor: 0 factors at intervals of 1.00 on rotation
Scales:
Along rotation axis: 2 scales at intervals of 5.00
No variation of scale with detector coordinate
Spherical harmonic correction on SECONDARY beam direction in camera frame, l-order 6 non-centrosymmetric
===========================================
SURFACE parameters will be TIED to zero (ie restrained to a spherical correction)
with a standard deviation of 0.0010, number of ties = 48
Working array size = 53
--- WARNING ---: partials with different detector coordinates: batch = 8 1.4 0.2 | batch = 9 1.4 0.2
--- WARNING ---: partials with different detector coordinates: batch = 9 1.4 0.2 | batch = 10 1.4 0.2
--- WARNING ---: partials with different detector coordinates: batch = 5 1.4 0.3 | batch = 6 1.4 0.3
--- WARNING ---: partials with different detector coordinates: batch = 6 1.4 0.3 | batch = 7 1.4 0.3
--- WARNING ---: partials with different detector coordinates: batch = 5 1.7 0.3 | batch = 6 1.7 0.3
--- WARNING ---: partials with different detector coordinates: batch = 6 1.7 0.3 | batch = 7 1.7 0.3
--- WARNING ---: partials with different detector coordinates: batch = 8 1.4 0.2 | batch = 9 1.4 0.2
--- WARNING ---: partials with different detector coordinates: batch = 9 1.4 0.2 | batch = 10 1.4 0.2
--- WARNING ---: partials with different detector coordinates: batch = 8 1.3 0.2 | batch = 9 1.3 0.2
--- WARNING ---: partials with different detector coordinates: batch = 9 1.3 0.2 | batch = 10 1.3 0.2
--- WARNING ---: partials with different detector coordinates: batch = 6 1.7 0.2 | batch = 7 1.7 0.2
--- WARNING ---: partials with different detector coordinates: batch = 7 1.7 0.2 | batch = 8 1.7 0.2
--- WARNING ---: partials with different detector coordinates: batch = 9 1.7 0.2 | batch = 10 1.7 0.2
--- WARNING ---: partials with different detector coordinates: batch = 5 1.7 0.3 | batch = 6 1.7 0.3
--- WARNING ---: partials with different detector coordinates: batch = 5 1.4 0.3 | batch = 6 1.4 0.3
--- WARNING ---: partials with different detector coordinates: batch = 5 1.8 0.3 | batch = 6 1.8 0.3
--- WARNING ---: partials with different detector coordinates: batch = 6 1.8 0.3 | batch = 7 1.8 0.3
--- WARNING ---: partials with different detector coordinates: batch = 6 1.3 0.2 | batch = 7 1.3 0.2
--- WARNING ---: partials with different detector coordinates: batch = 7 1.3 0.2 | batch = 8 1.3 0.2
--- WARNING ---: partials with different detector coordinates: batch = 8 1.3 0.2 | batch = 9 1.3 0.2
--- WARNING ---: partials with different detector coordinates: batch = 7 1.3 0.2 | batch = 8 1.3 0.2
--- WARNING ---: partials with different detector coordinates: batch = 9 1.8 0.2 | batch = 10 1.8 0.2
--- WARNING ---: partials with different detector coordinates: batch = 7 1.8 0.2 | batch = 8 1.8 0.2
--- WARNING ---: partials with different detector coordinates: batch = 8 1.8 0.2 | batch = 9 1.8 0.2
--- WARNING ---: partials with different detector coordinates: batch = 9 1.8 0.2 | batch = 10 1.8 0.2
--- WARNING ---: partials with different detector coordinates: batch = 5 1.8 0.2 | batch = 6 1.8 0.2
--- WARNING ---: partials with different detector coordinates: batch = 6 1.8 0.2 | batch = 7 1.8 0.2
--- WARNING ---: partials with different detector coordinates: batch = 7 1.8 0.2 | batch = 8 1.8 0.2
--- WARNING ---: partials with different detector coordinates: batch = 5 1.3 0.3 | batch = 6 1.3 0.3
--- WARNING ---: partials with different detector coordinates: batch = 6 1.3 0.3 | batch = 7 1.3 0.3
--- WARNING ---: partials with different detector coordinates: batch = 6 1.3 0.2 | batch = 7 1.3 0.2
--- WARNING ---: partials with different detector coordinates: batch = 7 1.3 0.2 | batch = 8 1.3 0.2
--- WARNING ---: partials with different detector coordinates: batch = 7 1.3 0.2 | batch = 8 1.3 0.2
--- WARNING ---: partials with different detector coordinates: batch = 5 1.8 0.3 | batch = 6 1.8 0.2
--- WARNING ---: partials with different detector coordinates: batch = 6 1.8 0.2 | batch = 7 1.8 0.3
--- WARNING ---: partials with different detector coordinates: batch = 7 1.8 0.2 | batch = 8 1.8 0.2
--- WARNING ---: partials with different detector coordinates: batch = 8 1.8 0.2 | batch = 9 1.8 0.2
--- WARNING ---: partials with different detector coordinates: batch = 5 1.9 0.2 | batch = 6 1.9 0.2
--- WARNING ---: partials with different detector coordinates: batch = 6 1.9 0.2 | batch = 7 1.9 0.2
--- WARNING ---: partials with different detector coordinates: batch = 7 1.8 0.2 | batch = 8 1.8 0.2
--- WARNING ---: partials with different detector coordinates: batch = 6 1.8 0.2 | batch = 7 1.8 0.2
--- WARNING ---: partials with different detector coordinates: batch = 7 1.8 0.2 | batch = 8 1.8 0.2
Note that the number of ranges is one less than the number of scale factors
Initial scales for run 1
1.0000 1.0000
===== Cycle 1 =====
Residual Sum( w Del**2) = 0.408E+05, restraint residual = 0.00 , total residual = 0.597E+05
Sum( w Del**2) / (m-n) = 9.158
2 eigenvalues filtered out, smallest = -0.202E-09, largest filtered = 0.614 Damping factor = 0.000
4503 observations used from 2231 independent reflections
Whole reflections rejected (all observations):
289 too weak
0 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 2.629 46.506 (parameter 2 K1.2.1 )
FORMATTED UNKNOWN file opened on unit 1
Logical name: SCALES, Filename: /home/pjx/PROJECTS/myProject/PROJECT_155.scala
===== Cycle 2 =====
Residual Sum( w Del**2) = 0.718E+04, restraint residual = 0.232E+10, total residual = 0.233E+05
Sum( w Del**2) / (m-n) = 1.892
2 eigenvalues filtered out, smallest = 0.238E-02, largest filtered = 0.661 Damping factor = 0.000
3842 observations used from 1909 independent reflections
Whole reflections rejected (all observations):
289 too weak
322 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 1.241 9.436 (parameter 2 K1.2.1 )
===== Cycle 3 =====
Residual Sum( w Del**2) = 0.704E+04, restraint residual = 0.180E+10, total residual = 0.230E+05
Sum( w Del**2) / (m-n) = 1.879
2 eigenvalues filtered out, smallest = 0.183E-02, largest filtered = 0.651 Damping factor = 0.000
3796 observations used from 1886 independent reflections
Whole reflections rejected (all observations):
289 too weak
345 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 0.301 5.640 (parameter 2 K1.2.1 )
===== Cycle 4 =====
Residual Sum( w Del**2) = 0.716E+04, restraint residual = 0.163E+10, total residual = 0.231E+05
Sum( w Del**2) / (m-n) = 1.912
2 eigenvalues filtered out, smallest = 0.175E-02, largest filtered = 0.653 Damping factor = 0.000
3797 observations used from 1886 independent reflections
Whole reflections rejected (all observations):
289 too weak
345 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 0.115 2.205 (parameter 2 K1.2.1 )
===== Cycle 5 =====
Residual Sum( w Del**2) = 0.714E+04, restraint residual = 0.157E+10, total residual = 0.230E+05
Sum( w Del**2) / (m-n) = 1.911
2 eigenvalues filtered out, smallest = 0.170E-02, largest filtered = 0.656 Damping factor = 0.000
3789 observations used from 1882 independent reflections
Whole reflections rejected (all observations):
289 too weak
349 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 0.057 1.014 (parameter 2 K1.2.1 )
===== Cycle 6 =====
Residual Sum( w Del**2) = 0.710E+04, restraint residual = 0.153E+10, total residual = 0.230E+05
Sum( w Del**2) / (m-n) = 1.904
2 eigenvalues filtered out, smallest = 0.167E-02, largest filtered = 0.659 Damping factor = 0.000
3781 observations used from 1878 independent reflections
Whole reflections rejected (all observations):
289 too weak
353 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 0.050 0.769 (parameter 2 K1.2.1 )
===== Cycle 7 =====
Residual Sum( w Del**2) = 0.714E+04, restraint residual = 0.151E+10, total residual = 0.230E+05
Sum( w Del**2) / (m-n) = 1.913
2 eigenvalues filtered out, smallest = 0.159E-02, largest filtered = 0.659 Damping factor = 0.000
3783 observations used from 1879 independent reflections
Whole reflections rejected (all observations):
289 too weak
352 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 0.031 0.553 (parameter 2 K1.2.1 )
===== Cycle 8 =====
Residual Sum( w Del**2) = 0.712E+04, restraint residual = 0.149E+10, total residual = 0.230E+05
Sum( w Del**2) / (m-n) = 1.910
2 eigenvalues filtered out, smallest = 0.157E-02, largest filtered = 0.660 Damping factor = 0.000
3779 observations used from 1877 independent reflections
Whole reflections rejected (all observations):
289 too weak
354 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 0.021 0.333 (parameter 2 K1.2.1 )
===== Cycle 9 =====
Residual Sum( w Del**2) = 0.712E+04, restraint residual = 0.148E+10, total residual = 0.229E+05
Sum( w Del**2) / (m-n) = 1.909
2 eigenvalues filtered out, smallest = 0.155E-02, largest filtered = 0.661 Damping factor = 0.000
3777 observations used from 1876 independent reflections
Whole reflections rejected (all observations):
289 too weak
355 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 0.012 0.167 (parameter 2 K1.2.1 )
=== Shifts for cycle 9
Run number 1
Parameter: K1.1.1 K1.2.1 Y1.1 Y1.2 Y1.3 Y1.4 Y1.5 Y1.6 Y1.7 Y1.8
Old value: 1.000 1.430 -0.002 0.002 0.000 -0.004 0.003 0.001 -0.002 0.002
Shift : 0.000 -0.001 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
New value: 1.000 1.429 -0.002 0.002 0.000 -0.004 0.003 0.001 -0.002 0.002
Error : 0.002 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
Number : 3777 3777 3777 3777 3777 3777 3777 3777 3777 3777
Parameter: Y1.9 Y1.10 Y1.11 Y1.12 Y1.13 Y1.14 Y1.15 Y1.16 Y1.17 Y1.18
Old value: -0.006 0.004 0.003 -0.004 0.002 -0.001 -0.001 -0.009 0.004 0.006
Shift : 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
New value: -0.006 0.004 0.003 -0.004 0.002 -0.001 -0.001 -0.009 0.004 0.006
Error : 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
Number : 3777 3777 3777 3777 3777 3777 3777 3777 3777 3777
Parameter: Y1.19 Y1.20 Y1.21 Y1.22 Y1.23 Y1.24 Y1.25 Y1.26 Y1.27 Y1.28
Old value: -0.006 0.003 -0.003 -0.002 0.003 -0.001 -0.012 0.003 0.011 -0.007
Shift : 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
New value: -0.006 0.003 -0.003 -0.002 0.003 -0.001 -0.012 0.003 0.011 -0.007
Error : 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
Number : 3777 3777 3777 3777 3777 3777 3777 3777 3777 3777
Parameter: Y1.29 Y1.30 Y1.31 Y1.32 Y1.33 Y1.34 Y1.35 Y1.36 Y1.37 Y1.38
Old value: 0.004 -0.003 -0.005 0.006 -0.002 0.001 0.002 -0.014 0.001 0.016
Shift : 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
New value: 0.004 -0.003 -0.005 0.006 -0.002 0.001 0.002 -0.014 0.001 0.016
Error : 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
Number : 3777 3777 3777 3777 3777 3777 3777 3777 3777 3777
Parameter: Y1.39 Y1.40 Y1.41 Y1.42 Y1.43 Y1.44 Y1.45 Y1.46 Y1.47 Y1.48
Old value: -0.006 0.006 -0.003 -0.009 0.008 -0.002 0.002 0.004 -0.004 0.001
Shift : 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
New value: -0.006 0.006 -0.003 -0.009 0.008 -0.002 0.002 0.004 -0.004 0.001
Error : 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
Number : 3777 3777 3777 3777 3777 3777 3777 3777 3777 3777
Final scale factors
************************************************************************************************************************
Final scale factors:
====================
============ Run 1 =============
Relative B-factors:
Scales -- smoothed, individual, (sd):
1 2
1.088 1.281
1.000 1.429
(0.002) (0.005)
Rotation 343.00 348.00
Spherical harmonic expansion coefficients in SECONDARY beam frame
-0.002 0.002 0.000 -0.004 0.003 0.001 -0.002 0.002 -0.006 0.004
0.003 -0.004 0.002 -0.001 -0.001 -0.009 0.004 0.006 -0.006 0.003
-0.003 -0.002 0.003 -0.001 -0.012 0.003 0.011 -0.007 0.004 -0.003
-0.005 0.006 -0.002 0.001 0.002 -0.014 0.001 0.016 -0.006 0.006
-0.003 -0.009 0.008 -0.002 0.002 0.004 -0.004 0.001
END PLOT: Picture number 1
================================================================================
================================================================================
================================================================================
------ 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 5 parts
Summed partials accepted if total fraction lies between 0.950 and 1.050
Partials with missing parts in the middle will be rejected
Outliers will be omitted from output file
Reduced indices hkl will be output (ie reduced to asymmetric unit as in input file)
Intensity bins, WILSON mode, mid-bin intensity = 3092.
Outliers with two observations will be kept
===========================
Normal probability analysis
====== Run number: 1, Fulls ======
Number Slope Intercept
All data: 4652 3.114 0.020
Data within expected delta 0.90: 2940 2.640 0.013
====== Run number: 1, Partials ======
Number Slope Intercept
All data: 5089 3.077 0.020
Data within expected delta 0.90: 3215 2.598 0.006
Update of SDcorrection parameters:
Fulls Partials
initial values: 1.0000 0.0000 0.0200 1.0000 0.0000 0.0200
changed to: 2.6404 2.5977
==========================================
================================================================================
================================================================================
================================================================================
------ Final Pass for statistics of merging ------
================================================================================
================================================================================
================================================================================
FORMATTED UNKNOWN file opened on unit 15
Logical name: ROGUES, Filename: /home/pjx/PROJECTS/myProject/PROJECT_155_rogues.log
FORMATTED UNKNOWN file opened on unit 8
Logical name: NORMPLOT, Filename: /home/pjx/PROJECTS/myProject/PROJECT_155_normplot.xmgr
FORMATTED UNKNOWN file opened on unit 12
Logical name: ROGUEPLOT, Filename: /home/pjx/PROJECTS/myProject/PROJECT_155_rogueplot.xmgr
********************************************************************************
********************************************************************************
Statistics for all datasets
FORMATTED UNKNOWN file opened on unit 10
Logical name: CORRELPLOT, Filename: /home/pjx/PROJECTS/myProject/PROJECT_155_correlplot.xmgr
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /tmp/pjx/PROJECT_155_2_mtz.tmp
* Title:
Example run with aucn data
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 DMSO
DMSO
red_aucn
88.9083 88.9083 229.2167 90.0000 90.0000 90.0000
0.88000
* Number of Columns = 9
* Number of Reflections = 6645
* 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)
88.9083 88.9083 229.2167 90.0000 90.0000 90.0000
* Resolution Range :
0.00080 0.11111 ( 35.272 - 3.000 A )
* Sort Order :
1 2 3 4 5
* Space group = 'P4122' (number 91)
Number of observations read : 9478
Number of unique reflections read : 6775
Number of observations output : 6645
Number of outliers rejected : 10
Number of observations rejected on Emax limit : 0
Number of observations outside resolution limits : 0
(observations outside resolution limits are omitted from the output file)
Statistics below are accumulated from:- 2520 unique reflections, 5079 observations
(of which 4643 are fully recorded, 436 are summed partials, 0 are scaled partials)
this excludes 4125 good observations measured once only
Maximum number of parts in a partially recorded reflection: 4
3 partial sets with gaps
181 partial sets with total fraction too small
3 partial sets with total fraction too large
================================================================================
Analysis of applied scale factors (including input scale)
Mean scale factors analysed by Batch for each run and resolution
Rotation 5 6 7 8 9 10
dmax
9.49 1.11 1.15 1.20 1.27 1.31 1.36
6.71 1.11 1.16 1.21 1.26 1.32 1.36
5.48 1.13 1.15 1.21 1.26 1.32 1.36
4.74 1.11 1.17 1.20 1.26 1.31 1.36
4.24 1.12 1.16 1.21 1.26 1.31 1.36
3.87 1.13 1.16 1.20 1.27 1.31 1.36
3.59 1.12 1.16 1.21 1.25 1.31 1.35
3.35 1.13 1.16 1.21 1.27 1.30 1.37
3.16 1.12 1.17 1.20 1.26 1.31 1.35
3.00 1.13 1.16 1.22 1.25 1.32 1.34
Overall 1.12 1.16 1.21 1.26 1.31 1.36
Spherical harmonic absorption correction(SECONDARY or ABSORPTION) for run 1
Minimum and maximum values: 0.873 1.089
Average values by polar coordinates Phi & Theta
Theta 0.00 18.00 36.00 54.00 72.00 90.00 108.00 126.00 144.00 162.00 180.00
Phi
0.0 0.982 0.931 0.927
20.0 1.005 1.026 1.024
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
Total 0.000 1.2329 1.1994 9204 10
Bfactor Mn(k) 0k Number NumReject
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
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)
Overall 2849.4 286.6 4643 436 286.6 9.94 0.055 5079 10 0 0.002
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)
Agreement by resolution
By 4SINTH/LASQ bins (all statistics relative to Mn(I))
______________________________________________________________
Overall: 0.055 0.056 0.055 0.000 0 2849. 286.6 9.9 258. 10.9 5079 2520 7 0.008 355
Rmrg Rfull Rcum Ranom Nanom Av_I SIGMA I/sigma sd Mn(I)/sd Nmeas Nref Ncent FRCBIAS Nbias
Agreement by intensity
BY INTENSITY ranges (all statistics relative to Mn(I))
______________________________________________________________
Overall 0.055 0.056 0.000 0 2849. 286.6 9.9 257.6 5079 2520 7 0.008 355 25.4
Rmrg Rfull Ranom Nanom Av_I SIGMA I/Sigma sd Nmeas Nref Ncent FRCBIAS Nbias Abs.BIAS
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)
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)
Overall 9204 6645 363 36.8 36.8 1.4 0.0 0.0 0.0 0.077 0.077 0.055 0.054 0.054 0.079 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 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
Axial reflections
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.
Current values of SD corrections are:-SdFac * Sqrt[sd(I)**2 + SdB I + (SdAdd I)**2]
Fulls Partials
Run SdFac SdB SdAdd SdFac SdB SdAdd
1 2.64042 0.00000 0.02000 2.59771 0.00000 0.02000
TOTALS:
0 -280. 46127. 4694. 4643 0.01 1.20 5204. 436 -0.04 0.86
Range Imin Imax Irms Number MeanFull SigmaFull Irms Number MeanPart SigmaPartial
Fully_recordeds Partially_recordeds
Batches with differences in detector coordinates for partials:
8 9 10 5 6 7
================================================
Normal probability analysis, by run & partiality
====== Run number: 1, fulls ======
Number Slope Intercept
All data: 4652 1.160 0.000
Data within expected delta 0.90: 2940 0.996 0.003
====== Run number: 1, summed partials ======
Number Slope Intercept
All data: 437 0.939 -0.015
Data within expected delta 0.90: 277 0.844 -0.039
====== Run number: 1, fulls against fulls only ======
Number Slope Intercept
All data: 4310 1.194 0.000
Data within expected delta 0.90: 2724 1.011 0.000
==========================================
Final assessment of SDcorrection multipliers
Run Fulls Partials
SdFac_used _corrected _fullsonly SdFac_used _corrected
1 2.6404 2.6287 2.6690 2.5977 2.1930
================================================================================
Summary data for Project: DMSO Crystal: DMSO Dataset: red_aucn
Overall InnerShell OuterShell
Low resolution limit 35.27 35.27 3.16
High resolution limit 3.00 9.49 3.00
Rmerge 0.055 0.057 0.109
Rmeas (within I+/I-) 0.077 0.075 0.154
Rmeas (all I+ & I-) 0.077 0.075 0.154
Rpim (within I+/I-) 0.054 0.049 0.109
Rpim (all I+ & I-) 0.054 0.049 0.109
Fractional partial bias 0.008 0.034 -0.001
Total number of observations 9204 304 1347
Total number unique 6645 169 970
Mean((I)/sd(I)) 10.9 16.5 6.0
Completeness 36.8 29.3 36.7
Multiplicity 1.4 1.8 1.4
================================================================================
Scala: ** Normal termination **
Times: User: 1.5s System: 0.1s Elapsed: 0:04
TRUNCATE
###############################################################
###############################################################
###############################################################
### CCP4 6.0: TRUNCATE version 6.0 : 31/05/07##
###############################################################
User: pjx Run date: 13/ 7/2007 Run time: 17:10:44
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.
TRUNCATE INTENSITIES TO AMPLITUDES
==================================
Contents
Command Input
TITLE
TRUNCATE
NRESIDUE
LABOUT
ANOMALOUS
CELL
CONTENTS
HEADER
FALLOFF
HISTORY
LABIN
PLOT
RANGES
RESOLUTION
RSCALE
SCALE
SYMMETRY
VPAT
Data line--- title Example run with aucn data
Data line--- truncate YES
Data line--- anomalous YES
Data line--- nresidue 745
Data line--- plot OFF
Data line--- labout IMEAN=IMEAN_red_aucn SIGIMEAN=SIGIMEAN_red_aucn I(+)=I_red_aucn(+) SIGI(+)=SIGI_red_aucn(+) I(-)=I_red_aucn(-) SIGI(-)=SIGI_red_aucn(-) F=F_red_aucn SIGF=SIGF_red_aucn DANO=DANO_red_aucn SIGDANO=SIGDANO_red_aucn F(+)=F_red_aucn(+) SIGF(+)=SIGF_red_aucn(+) F(-)=F_red_aucn(-) SIGF(-)=SIGF_red_aucn(-) ISYM=ISYM_red_aucn
Data line--- falloff yes
Data line--- RSIZE 80
Data line--- end
Input MTZ File
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: /tmp/pjx/PROJECT_155_2_mtz.tmp
* Title:
Example run with aucn data
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 DMSO
DMSO
red_aucn
88.9083 88.9083 229.2167 90.0000 90.0000 90.0000
0.88000
* Number of Columns = 9
* Number of Reflections = 6645
* 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)
88.9083 88.9083 229.2167 90.0000 90.0000 90.0000
* Resolution Range :
0.00080 0.11111 ( 35.267 - 3.000 A )
* Sort Order :
1 2 3 4 5
* Space group = 'P4122' (number 91)
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/pjx/CCP4I_uWORKSHOP/ccp4/lib/data/syminfo.lib
Reciprocal space symmetry:
Space group: "P 41 2 2" Point group: "PG422" Laue group: "4/mmm"
Reference asymmetric unit: "h>=k and k>=0 and l>=0"
(change of basis may be applied)
Spacegroup 91 "P 41 2 2"
Original indices for reflection hkl with symmetry number ISYM
Bijvoet positive
ISYM ISYM ISYM ISYM
ISYM 1 +h,+k,+l 3 -h,-k,+l 5 -k,+h,+l 7 +k,-h,+l
ISYM 9 -h,+k,-l 11 +h,-k,-l 13 +k,+h,-l 15 -k,-h,-l
Bijvoet negative
ISYM ISYM ISYM ISYM
ISYM 2 -h,-k,-l 4 +h,+k,-l 6 +k,-h,-l 8 -k,+h,-l
ISYM 10 +h,-k,+l 12 -h,+k,+l 14 -k,-h,+l 16 +k,+h,+l
Cell Dimensions: 88.91 88.91 229.22 90.00 90.00 90.00
$TEXT:Warning: $$ comment $$
WARNING: **** Beware! - Cell dimensions could permit Twinning ****
$$
Output MTZ File
--- CIF Dictionary loaded ---
Logical name: "MMCIFDIC", full name "/home/pjx/CCP4I_uWORKSHOP/ccp4/lib/cif_mmdic.lib"
Information from DICTIONARY category:
Title: mmcif_std.dic Version: 2.0.09 Datablock id: mmcif_std.dic
--- Opening CIF ---
Logical name: "DEPOSITFILE", full name "/home/pjx/PROJECTS/myProject/DepositFiles/DMSO/red_aucn.truncate"
--- CIF opened for output ---
The file has been initialised with no data blocks.
New data block "data_DMSO[red_aucn]" created for logical unit "DEPOSITFILE"
Width of bin : 0.0018
Number of bins : 60
Limits on H,K,L.. 0 to 29 0 to 29 0 to 76
Resolution limits in As = 35.27 3.00
as 4sinsq/lsq = 0.00080 0.11111
Resolution limits used for scaling in As = 4.00 3.00
as 4sinsq/lsq = 0.06250 0.11111
FORMATTED OLD file opened on unit 45
Logical name: ATOMSF, Filename: /home/pjx/CCP4I_uWORKSHOP/ccp4/lib/data/atomsf.lib
Volume, Solvent Content etc
**** Volume solvent content etc ***
Asymmetric Unit Contents Scattering Factor Constants
Atom number in A.U. Atomic number (F = AA*EXP(-A*RHO) + BB*EXP(-B*RHO) + .. + CC)
C 3725 6 2.310 20.844 1.020 10.208 1.589 0.569 0.865 51.651 0.216
N 1006 7 12.213 0.006 3.132 9.893 2.013 28.997 1.166 0.583 -11.529
O 1118 8 3.049 13.277 2.287 5.701 1.546 0.324 0.867 32.909 0.251
H 5960 1 0.493 10.511 0.323 26.126 0.140 3.142 0.041 57.800 0.003
Volume per atom = 10.0 A**3
total number of atoms in unit cell = 94472
unit cell volume = 1811886.1
F000 = 354368.0
fraction of unit cell occupied by atoms = 0.521 =====
starting resolution = 35.27
finishing resolution = 3.00
resolution increment for plotting = 0.00
Scale from Wilson Plot
******* Wilson Plots *******
Nref is the number of observed reflections in a
hemisphere of reciprocal space.
N_unq is an estimate of the number of possible reflections
in an asymmetric unit of reciprocal space
( Nref should be approximately equal to Nsymp*N_unq)
Mn(ff) is the expected value of f**2
Mn(s - resln) is the average value of 4(sin theta/lambda)**2 and
the corresponding resolution limit.
Mn(fobssq) is the average value of Fobs**2
If the reflections which were not measured were all weak, then Mn(Fobs**2)
is better estimated using all possible reflections N_unq
(Option WILSON ALL). THIS SHOULD NOT NORMALLY BE USED
ln(Mn((Fo**2)1))/Mn(ff) uses the average derived from Nref,
ln(Mn((Fo**2)2))/Mn(ff) uses the average derived from N_unq.
A total of 6645 reflections were included in the Wilson plot
1
1 -54+
| *
|
|
| *
| *
-56+
| *
| * *
| * *
| * *
| *
-58+ *
| * *
| * * * *
| * *
| * *
| *
-60+ * *
| *
| *
|
l | * *
o | *
g -62+
( | * * *
F | * * * *
P | * **
s | *
q | *
/ -64+ *
M | * *
n | *
( | * *
f |
f -66+ *
) |
) |
| *
| * *
|
* -68+ *
1 |
0 | *
* | *
* | * *
1 |
-70+ *
| *
|
|
| *
|
-72+
+--+---------+---------+---------+---------+---------+----------+---------+---------+---------+---------+---------+------
0 1 2 3 4 5 6 7 8 9 10 11
4*sinsq/lambdasq *10**2
WILSON PLOT (observed reflections only)
WILSON PLOT for Ranges 35 - 60
Resolution range: 3.9459 3.0127
LSQ Line Gradient = -52.264618
Uncertainty in Gradient = 0.2309E+01
X Intercept = -0.4227E+01
Uncertainty in Intercept = 0.1019E+00
For a wilson plot B = - gradient
SCALE = exp( - intercept).
Least squares straight line gives: B = 52.265 SCALE = 68.52428
where F(absolute)**2 = SCALE*F(observed)**2*EXP(-B*2*SINTH**2/L**2)
Analysis of Mean Intensity
Range Min. S Max. S Dmax(A) Mn(I)/w Mn(SD) Nref Nposs
1 0.00080 0.00264 19.45 3114.3 158.5 11 83
2 0.00264 0.00448 14.94 3807.9 249.7 25 102
3 0.00448 0.00632 12.58 7657.7 471.5 37 118
4 0.00632 0.00816 11.07 6813.0 408.0 32 141
5 0.00816 0.01000 10.00 8519.4 439.3 35 150
6 0.01000 0.01183 9.19 6159.1 322.1 50 171
7 0.01183 0.01367 8.55 5416.4 335.8 55 178
8 0.01367 0.01551 8.03 6212.9 366.5 50 178
9 0.01551 0.01735 7.59 5302.3 309.3 61 198
10 0.01735 0.01919 7.22 4756.1 309.7 72 211
11 0.01919 0.02103 6.90 3463.5 218.3 64 202
12 0.02103 0.02287 6.61 2855.2 201.0 77 229
13 0.02287 0.02470 6.36 3291.2 216.5 68 223
14 0.02470 0.02654 6.14 3023.7 201.1 90 251
15 0.02654 0.02838 5.94 2725.2 190.1 86 232
16 0.02838 0.03022 5.75 3125.5 207.6 92 253
17 0.03022 0.03206 5.59 2796.3 196.1 77 250
18 0.03206 0.03390 5.43 3187.4 215.4 96 280
19 0.03390 0.03573 5.29 3554.0 237.6 107 272
20 0.03573 0.03757 5.16 4539.6 272.8 92 276
21 0.03757 0.03941 5.04 3886.5 244.8 95 283
22 0.03941 0.04125 4.92 5019.8 318.3 97 283
23 0.04125 0.04309 4.82 3907.4 243.1 113 306
24 0.04309 0.04493 4.72 4522.4 308.6 101 303
25 0.04493 0.04676 4.62 5158.6 311.6 104 309
26 0.04676 0.04860 4.54 5459.7 330.5 106 306
27 0.04860 0.05044 4.45 5106.5 314.8 122 313
28 0.05044 0.05228 4.37 5917.9 390.4 110 335
29 0.05228 0.05412 4.30 3977.7 257.3 126 339
30 0.05412 0.05596 4.23 4194.0 274.0 105 311
31 0.05596 0.05780 4.16 4406.0 289.0 126 351
32 0.05780 0.05963 4.09 3902.9 252.2 119 344
33 0.05963 0.06147 4.03 3968.0 273.1 114 341
34 0.06147 0.06331 3.97 3154.3 233.5 130 368
35 0.06331 0.06515 3.92 3592.4 252.8 126 360
36 0.06515 0.06699 3.86 4018.5 296.6 122 347
37 0.06699 0.06883 3.81 3388.8 243.2 144 388
38 0.06883 0.07066 3.76 3195.1 236.7 140 368
39 0.07066 0.07250 3.71 2812.8 222.1 135 368
40 0.07250 0.07434 3.67 2428.3 198.2 135 404
41 0.07434 0.07618 3.62 2702.1 228.2 128 370
42 0.07618 0.07802 3.58 2500.4 207.1 143 389
43 0.07802 0.07986 3.54 2317.6 198.0 138 400
44 0.07986 0.08170 3.50 2237.0 201.2 149 401
45 0.08170 0.08353 3.46 2087.7 193.0 136 414
46 0.08353 0.08537 3.42 2274.4 194.3 139 388
47 0.08537 0.08721 3.39 1808.0 179.8 146 429
48 0.08721 0.08905 3.35 1676.1 174.1 139 413
49 0.08905 0.09089 3.32 1768.7 185.6 154 401
50 0.09089 0.09273 3.28 1423.1 164.6 151 441
51 0.09273 0.09456 3.25 1428.4 166.9 155 446
52 0.09456 0.09640 3.22 1222.6 153.3 152 414
53 0.09640 0.09824 3.19 1387.3 161.4 150 428
54 0.09824 0.10008 3.16 1104.9 154.5 154 434
55 0.10008 0.10192 3.13 1019.6 150.7 161 462
56 0.10192 0.10376 3.10 1233.9 164.6 163 445
57 0.10376 0.10559 3.08 1090.0 160.8 159 454
58 0.10559 0.10743 3.05 1099.3 154.0 157 448
59 0.10743 0.10927 3.03 945.8 144.0 159 462
60 0.10927 0.11111 3.00 858.8 146.6 165 449
Analysis of mean intensity by parity for reflection classes
For each class, Mn(I/sig(I)) is given for even and odd parity with respect to the condition,
eg group 1: h even & odd; group 7 h+k+l even & odd; group 8 h+k=2n & h+l=2n & k+l=2n or not
Range Min_S Dmax Nref 1 2 3 4 5 6 7 8
h k l h+k h+l k+l h+k+l h+k,h+l,k+l
1 0.00080 19.45 11 6.3 0.0 22.7 0.1 7.3 5.0 22.7 0.1 7.3 5.0 7.2 5.1 7.2 5.1 21.6 2.8
2 0.00264 14.94 25 14.5 14.3 16.2 11.8 14.4 14.4 17.8 10.1 14.8 14.0 14.6 14.2 14.2 14.6 18.3 12.9
3 0.00448 12.58 37 20.1 14.6 13.5 18.4 17.2 15.9 14.6 18.3 16.2 16.9 17.6 15.5 17.0 15.9 15.3 16.9
4 0.00632 11.07 32 18.8 15.5 15.9 17.0 17.1 16.2 16.8 16.5 17.7 15.7 15.9 17.4 14.9 18.2 17.1 16.5
5 0.00816 10.00 35 18.8 19.5 18.3 20.4 18.8 19.7 20.3 18.6 19.4 19.1 19.4 19.1 19.2 19.3 20.5 18.9
6 0.01000 9.19 50 18.4 19.2 18.8 18.4 19.0 18.2 19.1 18.1 18.9 18.3 18.4 18.8 18.9 18.3 19.1 18.4
7 0.01183 8.55 55 14.9 17.4 15.8 15.9 15.5 16.3 15.3 16.4 17.1 14.8 15.4 16.3 15.4 16.3 16.0 15.8
8 0.01367 8.03 50 16.7 18.8 17.2 17.8 17.6 17.4 17.0 18.2 18.0 16.8 18.0 17.1 17.4 17.6 17.8 17.3
9 0.01551 7.59 61 16.6 14.5 17.2 14.3 15.0 16.3 17.5 14.2 16.0 15.4 15.1 16.2 15.6 15.7 17.3 15.2
10 0.01735 7.22 72 15.3 14.7 15.3 14.6 15.4 14.6 15.3 14.7 15.0 15.0 15.0 15.0 16.4 13.5 15.3 14.9
11 0.01919 6.90 64 15.7 15.0 15.0 15.5 14.6 15.9 15.7 14.8 14.9 15.5 15.7 14.7 14.6 15.8 15.8 15.0
12 0.02103 6.61 77 14.7 12.6 11.4 14.6 13.0 13.7 14.8 12.1 15.2 11.6 14.0 12.8 12.6 14.0 17.9 12.2
13 0.02287 6.36 68 16.1 12.4 12.6 14.4 12.8 14.7 13.5 13.9 14.0 13.4 13.5 14.0 14.5 12.9 13.5 13.8
14 0.02470 6.14 90 15.8 13.6 14.2 14.9 14.3 14.8 14.6 14.5 14.4 14.7 14.5 14.6 13.9 15.1 14.4 14.6
15 0.02654 5.94 86 12.5 13.6 13.7 12.5 12.9 13.3 13.0 13.3 13.8 12.4 13.5 12.6 12.0 14.1 14.0 12.8
16 0.02838 5.75 92 11.9 14.0 12.8 13.0 11.6 14.1 12.9 12.9 12.1 13.6 12.4 13.4 13.5 12.2 11.6 13.3
17 0.03022 5.59 77 14.8 12.4 13.3 13.9 13.0 14.2 14.5 12.8 13.4 13.8 14.1 13.3 13.3 13.9 15.0 13.3
18 0.03206 5.43 96 12.2 13.9 14.2 11.8 13.1 13.1 13.3 12.9 12.7 13.5 12.8 13.4 12.7 13.5 12.6 13.3
19 0.03390 5.29 107 14.6 13.4 14.5 13.3 13.9 13.9 13.9 14.0 14.2 13.6 14.3 13.5 13.9 14.0 14.5 13.7
20 0.03573 5.16 92 15.2 14.0 16.4 12.9 13.7 15.4 14.0 15.2 14.9 14.3 14.4 14.7 14.6 14.5 14.2 14.7
21 0.03757 5.04 95 13.9 14.4 13.8 14.4 13.2 15.1 14.3 14.0 14.6 13.7 13.5 14.6 14.2 14.0 14.2 14.1
22 0.03941 4.92 97 15.1 13.0 13.3 14.7 13.8 14.3 13.6 14.5 14.0 14.1 14.8 13.2 14.5 13.6 14.3 13.9
23 0.04125 4.82 113 13.1 14.2 13.2 14.2 13.3 14.0 13.4 13.9 13.8 13.6 14.1 13.2 13.4 13.9 14.0 13.6
24 0.04309 4.72 101 13.0 14.6 14.0 13.5 13.7 13.8 13.8 13.7 13.9 13.5 13.6 13.9 13.9 13.6 13.8 13.7
25 0.04493 4.62 104 14.6 14.9 15.2 14.1 14.5 15.0 14.8 14.7 14.9 14.5 14.1 15.3 15.0 14.3 14.4 14.8
26 0.04676 4.54 106 14.3 14.2 13.2 15.2 14.1 14.3 13.8 14.7 14.1 14.4 13.9 14.6 14.2 14.2 13.4 14.5
27 0.04860 4.45 122 14.4 14.6 14.7 14.2 15.0 14.0 14.2 14.8 14.9 14.2 14.8 14.2 13.6 15.5 14.9 14.4
28 0.05044 4.37 110 13.8 14.7 14.2 14.3 13.7 14.9 14.4 14.1 14.6 13.9 14.0 14.5 13.9 14.6 14.5 14.2
29 0.05228 4.30 126 13.0 13.6 13.4 13.3 14.0 12.7 13.4 13.2 13.6 13.1 13.9 12.8 13.2 13.5 14.3 13.0
30 0.05412 4.23 105 12.9 14.3 13.7 13.8 14.3 13.3 13.0 14.4 13.0 14.6 13.4 14.0 14.4 13.2 11.6 14.3
31 0.05596 4.16 126 13.3 13.8 13.1 13.9 13.0 14.1 13.8 13.3 13.4 13.7 13.5 13.5 14.0 13.1 13.6 13.5
32 0.05780 4.09 119 13.3 13.6 13.1 13.8 13.6 13.2 12.9 13.9 13.5 13.4 14.1 13.0 14.0 12.8 13.5 13.4
33 0.05963 4.03 114 12.9 12.7 13.2 12.3 13.2 12.3 12.6 12.9 13.4 12.1 12.7 12.8 12.7 12.9 13.1 12.6
34 0.06147 3.97 130 11.5 11.4 11.3 11.6 10.6 12.3 10.7 12.3 10.8 12.1 12.0 11.1 11.7 11.2 10.3 11.8
35 0.06331 3.92 126 13.1 11.8 12.4 12.2 12.1 12.6 12.7 12.0 11.9 12.8 12.8 11.7 11.7 13.0 12.7 12.2
36 0.06515 3.86 122 13.1 11.3 11.9 12.3 12.2 12.0 12.4 11.7 10.9 13.2 11.6 12.5 11.5 12.5 10.8 12.5
37 0.06699 3.81 144 12.1 12.2 12.1 12.2 11.9 12.4 12.4 11.9 12.6 11.7 11.5 12.9 11.9 12.4 12.2 12.1
38 0.06883 3.76 140 11.8 10.8 10.9 11.8 10.9 11.7 11.0 11.8 10.5 12.1 10.7 11.9 11.1 11.5 9.6 11.9
39 0.07066 3.71 135 11.2 10.6 10.3 11.4 9.7 12.4 11.1 10.8 10.3 11.4 10.9 10.9 11.8 9.9 10.4 11.0
40 0.07250 3.67 135 10.5 11.4 9.9 11.9 10.8 11.0 11.3 10.6 11.7 10.1 9.7 12.0 10.9 10.9 10.9 10.9
41 0.07434 3.62 128 9.9 10.2 10.4 9.6 10.4 9.7 10.7 9.3 10.6 9.5 10.3 9.7 10.7 9.5 11.5 9.5
42 0.07618 3.58 143 11.1 10.3 10.8 10.6 11.0 10.4 10.8 10.6 10.3 11.1 11.5 9.9 10.1 11.3 11.1 10.5
43 0.07802 3.54 138 10.0 10.2 10.5 9.7 10.0 10.2 10.5 9.7 10.0 10.2 10.2 10.0 9.3 10.8 10.6 9.9
44 0.07986 3.50 149 9.9 9.6 9.9 9.6 9.1 10.5 8.9 10.7 10.2 9.3 9.5 10.1 10.1 9.4 9.1 10.0
45 0.08170 3.46 136 8.9 9.6 10.2 8.2 8.9 9.5 9.5 8.9 9.7 8.7 9.3 9.0 9.1 9.3 10.1 8.9
46 0.08353 3.42 139 9.8 10.5 10.7 9.6 10.3 10.0 10.1 10.2 9.7 10.7 9.1 10.8 10.3 10.0 8.6 10.6
47 0.08537 3.39 146 8.1 9.5 8.4 9.2 8.0 9.6 8.0 9.7 8.9 8.6 8.2 9.4 8.5 9.0 7.6 9.2
48 0.08721 3.35 139 9.3 8.0 8.2 9.1 9.0 8.2 8.9 8.4 8.2 9.0 8.4 8.8 9.0 8.2 8.2 8.7
49 0.08905 3.32 154 8.2 7.5 8.2 7.4 8.1 7.5 8.0 7.6 7.8 7.8 7.6 8.0 8.3 7.1 7.8 7.8
50 0.09089 3.28 151 7.4 7.6 7.5 7.6 7.2 7.8 8.0 7.1 8.0 7.1 7.8 7.3 7.1 7.8 8.9 7.1
51 0.09273 3.25 155 7.7 7.1 7.0 7.9 6.8 8.1 7.5 7.3 6.9 7.9 7.2 7.6 7.0 7.8 6.9 7.7
52 0.09456 3.22 152 6.9 7.1 6.5 7.5 7.5 6.6 7.4 6.5 7.1 6.9 6.9 7.1 6.6 7.5 7.5 6.9
53 0.09640 3.19 150 6.6 8.0 7.0 7.6 7.7 6.9 7.1 7.5 7.5 7.1 6.7 7.9 7.4 7.2 6.8 7.5
54 0.09824 3.16 154 6.5 6.3 6.1 6.8 5.8 7.0 6.9 6.0 5.5 7.2 6.4 6.4 6.2 6.7 6.0 6.5
55 0.10008 3.13 161 5.2 6.3 5.4 6.2 5.5 6.0 6.4 5.2 5.9 5.7 5.6 5.9 6.3 5.2 6.5 5.6
56 0.10192 3.10 163 6.7 6.5 5.8 7.2 6.5 6.7 6.9 6.2 7.2 5.9 6.5 6.7 6.3 6.8 7.4 6.2
57 0.10376 3.08 159 5.5 6.4 5.9 6.1 5.7 6.3 5.7 6.2 5.1 6.8 5.7 6.3 6.4 5.6 4.4 6.4
58 0.10559 3.05 157 6.9 5.9 6.3 6.5 6.1 6.7 6.4 6.4 7.1 5.5 6.6 6.2 5.9 6.9 7.2 6.1
59 0.10743 3.03 159 5.9 6.0 5.9 6.1 6.6 5.4 6.0 6.0 5.4 6.6 5.9 6.1 6.9 5.2 5.3 6.2
60 0.10927 3.00 165 5.0 5.9 5.5 5.4 5.7 5.2 5.2 5.6 5.6 5.2 5.3 5.6 5.2 5.7 5.2 5.5
Totals: 6645 10.9 10.9 10.8 11.0 10.8 11.1 11.0 10.8 10.9 10.9 10.8 11.0 10.9 11.0 10.9 10.9
Amplitudes will be scaled by 8.278 from sqrt(I)
Header Information to Output MTZ File
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /tmp/pjx/PROJECT_155_4_mtz_red_aucn.tmp
* Title:
Example run with aucn data
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 DMSO
DMSO
red_aucn
88.9083 88.9083 229.2167 90.0000 90.0000 90.0000
0.88000
* Number of Columns = 18
* Number of Reflections = 6645
* Missing value set to NaN in input mtz file
* Column Labels :
H K L F_red_aucn SIGF_red_aucn DANO_red_aucn SIGDANO_red_aucn F_red_aucn(+) SIGF_red_aucn(+) F_red_aucn(-) SIGF_red_aucn(-) IMEAN_red_aucn SIGIMEAN_red_aucn I_red_aucn(+) SIGI_red_aucn(+) I_red_aucn(-) SIGI_red_aucn(-) ISYM_red_aucn
* Column Types :
H H H F Q D Q G L G L J Q K M K M Y
* 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)
88.9083 88.9083 229.2167 90.0000 90.0000 90.0000
* Resolution Range :
0.00080 0.11111 ( 35.271 - 3.000 A )
* Sort Order :
1 2 3 4 5
* Space group = 'P4122' (number 91)
Number of reflections input = 6645
Number of terms output = 6645
Number of terms rejected = 0
( having EITHER Iobs .LT. -3.7*SDobs OR Iobs .LT. (SDobs)**2/MeanI - 4.0*SDobs )
Distributions of Observed Intensity
Distributions of Observed Intensity Magnitudes
----------------------------------------------
Tables below give percentage of terms for which I.le.Z
where Z is defined as I/Mn(I) for the range of 4*((Sintheta/Lambda)**2)
Also the 2nd, 3rd & 4th moments of I, Mn(I**k)/Mn(I)**k for k = 2,3,4 (labelled Moment2, Moment3, Moment4))
Z values in tables :
0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
Acentric Moments of Intensity
ACENTRIC MOMENTS OF INTENSITY
------------------------------
THEORETICAL Distribution
Nref Nz(0.1 - 0.2 - 0.3 - 0.4 - 0.5 - 0.6 - 0.7 - 0.8 - 0.9 -1.0) Moment(Z2 Z3 Z4 E1 E3)
9.5 18.1 25.9 33.0 39.3 45.1 50.3 55.1 59.3 63.2 2.00 6.00 24.00
Observed distribution in ranges of 4*((Sintheta/Lambda)**2)
Totals of Observed Distributions (averages) :
6282 10.1 19.4 27.1 34.2 40.6 46.3 51.3 56.4 60.3 64.5 2.09 6.76 29.68 0.46 0.00
Centric Moments of Intensity
CENTRIC MOMENTS OF INTENSITY: 1Bar N(Z)
-----------------------------
THEORETICAL Distribution
Nref Nz(0.1 - 0.2 - 0.3 - 0.4 - 0.5 - 0.6 - 0.7 - 0.8 - 0.9 -1.0) Moment(Z2 Z3 Z4 E1 E3)
24.8 34.5 41.6 47.3 52.1 56.1 59.7 62.9 65.7 68.3 3.00 15.00 105.00
Observed distribution in ranges of 4*((Sintheta/Lambda)**2)
Totals of Observed Distributions (averages) :
363 20.9 31.4 38.3 43.5 47.4 51.8 57.0 61.4 63.4 64.7 2.46 8.45 34.60 9.94 0.02
Cumulative Intensity Distribution
Mean Amplitude vs. Resolution
TOTALS 6645 2945.45 224.82 13.10 10.92 378.91 20.01 18.93 21.78
Minimum F = 8.609
with SD = 4.133
Maximum F = 1759.353
with SD = 56.865
Anisotropic Analysis: FALLOFF
ANALYSIS OF THE ANISOTROPY OF THE DATA ACCORDING TO THE FALLOFF PROCEDURE.
--------------------------------------------------------------------------
Direction 1 is perpendicular to b* and Direction 3
Direction 2 is along b*
Direction 3 is perpendicular to a* and b*
Average F (d1 d2 d3) + overall average: 345.14 345.14 0.00 379.04
$TEXT:Warning: $$ comment $$
WARNING: ***Beware-serious ANISOTROPY; data analyses may be invalid ***
$$
number A-AX reflections less than 30.0 degrees from dir1 8544
number B-AX reflections less than 30.0 degrees from dir2 8544
number C-AX reflections less than 30.0 degrees from dir3 15856
number overall reflections 106304
TRUNCATE: Normal termination
Times: User: 0.3s System: 0.0s Elapsed: 0:01
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
Renaming file /tmp/pjx/PROJECT_155_4_mtz_red_aucn.tmp to
/home/pjx/PROJECTS/myProject/aucn_scala4.mtz
***************************************************************************
#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 13 Jul 2007 17:10:45
#CCP4I TERMINATION OUTPUT_FILES /home/pjx/PROJECTS/myProject/aucn_sorted.mtz PROJECT /home/pjx/PROJECTS/myProject/PROJECT_155.scala PROJECT /home/pjx/PROJECTS/myProject/PROJECT_155_rogues.log PROJECT /home/pjx/PROJECTS/myProject/PROJECT_155_normplot.xmgr PROJECT /home/pjx/PROJECTS/myProject/PROJECT_155_anomplot.xmgr PROJECT /home/pjx/PROJECTS/myProject/PROJECT_155_surface_plot.plt PROJECT /home/pjx/PROJECTS/myProject/PROJECT_155_rogueplot.xmgr PROJECT /home/pjx/PROJECTS/myProject/PROJECT_155_correlplot.xmgr PROJECT /home/pjx/PROJECTS/myProject/PROJECT_155_red_aucn.scala.cif PROJECT /home/pjx/PROJECTS/myProject/PROJECT_155_red_aucn.truncate.cif PROJECT
#CCP4I MESSAGE Task completed successfully