The logfile is composed of output from the following programs:
CCP4i: Sorting input MTZ file /home/pjx/PROJECTS/myProject/aucn.mtz
Current view: summary only [Show full logfile] [Hide logfile]
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############################################################### ############################################################### ############################################################### ### CCP4 5.99: SORTMTZ version 5.99 : 06/09/05## ############################################################### User: pjx Run date: 31/ 1/2006 Run time: 16:02:55 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 Input File Details Output File Details
Header Information for Output MTZ File
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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|
>>> Scales v rotation range, red_aucn Analysis against Batch, red_aucn Analysis against resolution , red_aucn Analysis against intensity, red_aucn Completeness, multiplicity, Rmeas v. resolution, red_aucn Correlations within dataset, red_aucn Run 1, standard deviation v. Intensity, red_aucn |
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Current view: full logfile [Show logfile summary] [Hide logfile]
############################################################### ############################################################### ############################################################### ### CCP4 5.99: Scala version 5.99 : ## ############################################################### User: pjx Run date: 31/ 1/2006 Run time: 16:02:56 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: 3.2.19 *
* Date : 22/12/2005 *
* *
* 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/CCP4_REMOTE/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 Bug 1070 Run scala on aucn data and generate file with free R flag column
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 ##########
Comment line--- # scala HKLIN /home/pjx/PROJECTS/myProject/aucn_sorted.mtz HKLOUT /tmp/pjx/PROJECT_22_2_mtz.tmp SCALES /home/pjx/PROJECTS/myProject/PROJECT_22.scala ROGUES /home/pjx/PROJECTS/myProject/PROJECT_22_rogues.log NORMPLOT /home/pjx/PROJECTS/myProject/PROJECT_22_normplot.xmgr ANOMPLOT /home/pjx/PROJECTS/myProject/PROJECT_22_anomplot.xmgr PLOT /home/pjx/PROJECTS/myProject/PROJECT_22_surface_plot.plt CORRELPLOT /home/pjx/PROJECTS/myProject/PROJECT_22_correlplot.xmgr
Comment line--- ################################################
Input keyworded commands (click for documentation):
TITLE
Bug 1070 Run scala on aucn data and generate file with free R flag column
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
Final scale factors
Scale factors by batch
Agreement by batch
Agreement by resolution
Agreement by intensity
Completeness & multiplicity
Axial reflections
Analysis of standard deviations
Run number 1 consists of batches :-
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 0.000 0.000 0.000 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 = -0.312E-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_22.scala
===== Cycle 2 =====
Residual Sum( w Del**2) = 0.796E+04, restraint residual = 0.232E+10, total residual = 0.245E+05
Sum( w Del**2) / (m-n) = 2.046
2 eigenvalues filtered out, smallest = 0.235E-02, largest filtered = 0.656 Damping factor = 0.000
3942 observations used from 1959 independent reflections
Whole reflections rejected (all observations):
289 too weak
272 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 1.177 9.634 (parameter 2 K1.2.1 )
===== Cycle 3 =====
Residual Sum( w Del**2) = 0.799E+04, restraint residual = 0.180E+10, total residual = 0.244E+05
Sum( w Del**2) / (m-n) = 2.066
2 eigenvalues filtered out, smallest = 0.191E-02, largest filtered = 0.646 Damping factor = 0.000
3918 observations used from 1947 independent reflections
Whole reflections rejected (all observations):
289 too weak
284 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 0.256 4.781 (parameter 2 K1.2.1 )
===== Cycle 4 =====
Residual Sum( w Del**2) = 0.812E+04, restraint residual = 0.164E+10, total residual = 0.245E+05
Sum( w Del**2) / (m-n) = 2.098
2 eigenvalues filtered out, smallest = 0.175E-02, largest filtered = 0.648 Damping factor = 0.000
3919 observations used from 1947 independent reflections
Whole reflections rejected (all observations):
289 too weak
284 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 0.109 2.166 (parameter 2 K1.2.1 )
===== Cycle 5 =====
Residual Sum( w Del**2) = 0.813E+04, restraint residual = 0.158E+10, total residual = 0.245E+05
Sum( w Del**2) / (m-n) = 2.103
2 eigenvalues filtered out, smallest = 0.171E-02, largest filtered = 0.649 Damping factor = 0.000
3915 observations used from 1945 independent reflections
Whole reflections rejected (all observations):
289 too weak
286 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 0.031 0.485 (parameter 2 K1.2.1 )
===== Cycle 6 =====
Residual Sum( w Del**2) = 0.807E+04, restraint residual = 0.157E+10, total residual = 0.245E+05
Sum( w Del**2) / (m-n) = 2.093
2 eigenvalues filtered out, smallest = 0.169E-02, largest filtered = 0.650 Damping factor = 0.000
3907 observations used from 1941 independent reflections
Whole reflections rejected (all observations):
289 too weak
290 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 0.030 0.537 (parameter 2 K1.2.1 )
===== Cycle 7 =====
Residual Sum( w Del**2) = 0.807E+04, restraint residual = 0.155E+10, total residual = 0.244E+05
Sum( w Del**2) / (m-n) = 2.093
2 eigenvalues filtered out, smallest = 0.167E-02, largest filtered = 0.651 Damping factor = 0.000
3905 observations used from 1940 independent reflections
Whole reflections rejected (all observations):
289 too weak
291 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 0.018 0.303 (parameter 2 K1.2.1 )
===== Cycle 8 =====
Residual Sum( w Del**2) = 0.806E+04, restraint residual = 0.154E+10, total residual = 0.244E+05
Sum( w Del**2) / (m-n) = 2.093
2 eigenvalues filtered out, smallest = 0.165E-02, largest filtered = 0.651 Damping factor = 0.000
3903 observations used from 1939 independent reflections
Whole reflections rejected (all observations):
289 too weak
292 outliers
B-factors normalised on point 0 in run 1
Mean and maximum shift/sd : 0.002 0.023 (parameter 2 K1.2.1 )
=== Shifts for cycle 8
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 1.439 -0.002 0.002 0.000 -0.004 0.003 0.001 -0.002 0.002
Shift : 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
New value: 1.000 1.439 -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 : 3903 3903 3903 3903 3903 3903 3903 3903 3903 3903
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 : 3903 3903 3903 3903 3903 3903 3903 3903 3903 3903
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 : 3903 3903 3903 3903 3903 3903 3903 3903 3903 3903
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 0.017
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 0.017
Error : 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001
Number : 3903 3903 3903 3903 3903 3903 3903 3903 3903 3903
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 -0.010 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 -0.010 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 : 3903 3903 3903 3903 3903 3903 3903 3903 3903 3903
Final scale factors
************************************************************************************************************************
Final scale factors:
====================
============ Run 1 =============
Relative B-factors:
Scales -- smoothed, individual, (sd):
1 2
1.089 1.287
1.000 1.439
(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 0.017 -0.006 0.006
-0.003 -0.010 0.008 -0.002 0.002 0.004 -0.004 0.001
Number of out-of-bounds plot errors: 638
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 = 3091.
Outliers with two observations will be kept
===========================
Normal probability analysis
====== Run number: 1, Fulls ======
Number Slope Intercept
All data: 4652 3.100 0.020
Data within expected delta 0.90: 2940 2.630 0.013
====== Run number: 1, Partials ======
Number Slope Intercept
All data: 5089 3.064 0.020
Data within expected delta 0.90: 3215 2.588 0.006
Update of SDcorrection parameters:
Fulls Partials
initial values: 1.0000 0.0000 0.0200 1.0000 0.0000 0.0200
changed to: 2.6302 2.5878
==========================================
================================================================================
================================================================================
================================================================================
------ Final Pass for statistics of merging ------
================================================================================
================================================================================
================================================================================
FORMATTED UNKNOWN file opened on unit 15
Logical name: ROGUES, Filename: /home/pjx/PROJECTS/myProject/PROJECT_22_rogues.log
FORMATTED UNKNOWN file opened on unit 8
Logical name: NORMPLOT, Filename: /home/pjx/PROJECTS/myProject/PROJECT_22_normplot.xmgr
******************************************************************************** ******************************************************************************** Statistics for all datasets FORMATTED UNKNOWN file opened on unit 10
Logical name: CORRELPLOT, Filename: /home/pjx/PROJECTS/myProject/PROJECT_22_correlplot.xmgr
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /tmp/pjx/PROJECT_22_2_mtz.tmp
* Title:
Bug 1070 Run scala on aucn data and generate file with free R flag col
* 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 1.16 1.21 1.27 1.32 1.37
6.71 1.11 1.16 1.21 1.26 1.32 1.36
5.48 1.13 1.15 1.21 1.27 1.32 1.36
4.74 1.11 1.17 1.21 1.27 1.32 1.37
4.24 1.12 1.16 1.21 1.26 1.32 1.37
3.87 1.13 1.16 1.20 1.27 1.31 1.36
3.59 1.12 1.16 1.22 1.26 1.32 1.36
3.35 1.13 1.16 1.21 1.27 1.31 1.37
3.16 1.12 1.17 1.20 1.27 1.32 1.36
3.00 1.13 1.16 1.22 1.25 1.33 1.35
Overall 1.12 1.16 1.21 1.26 1.32 1.36
Spherical harmonic absorption correction(SECONDARY or ABSORPTION) for run 1
Minimum and maximum values: 0.872 1.090
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 0.983 0.932 0.927
20.0 1.003 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
Bfactor and mean scale Mn(k) for each rotation range
$TABLE:>> Scales v rotation range, red_aucn :
$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: $$
N Run.Rot MidPhi Batch Bfactor Mn(k) 0k Number NumReject $$ $$
1 1.1 343.50 5 0.000 1.1230 1.1044 1613 2
2 1.2 344.50 6 0.000 1.1632 1.1395 1538 1
3 1.3 345.50 7 0.000 1.2099 1.1799 1544 1
4 1.4 346.50 8 0.000 1.2636 1.2234 1596 4
5 1.5 347.50 9 0.000 1.3180 1.2665 1533 1
6 1.6 348.50 10 0.000 1.3613 1.3061 1380 1
$$
">For inline graphs use a Java browser
Total 0.000 1.2369 1.2033 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)
$TABLE : Analysis against Batch, red_aucn :
$GRAPHS :Rmerge v Batch :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
$$
1 5 2832.4 234.6 778 80 234.6 12.07 0.050 858 2 0 0.002
2 6 3255.2 278.7 783 97 278.7 11.68 0.046 880 1 0 0.001
3 7 2913.5 248.9 806 93 248.9 11.70 0.051 899 1 0 0.001
4 8 2660.6 247.9 849 95 247.9 10.73 0.055 944 4 0 0.004
5 9 2670.8 331.6 759 60 331.6 8.05 0.064 819 1 0 0.001
6 10 2803.9 377.3 668 11 377.3 7.43 0.067 679 1 0 0.001
$$
For inline graphs use a Java browser
Overall 2858.2 286.2 4643 436 286.2 9.99 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))
______________________________________________________________
$TABLE: Analysis against resolution , red_aucn :
$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
$$
1 0.0111 9.49 0.057 0.061 0.057 0.000 0 7219 745.2 9.7 537 16.6 243 108 3 0.035 33
2 0.0222 6.71 0.038 0.037 0.048 0.000 0 4723 302.6 15.6 330 15.6 337 168 0 -0.024 24
3 0.0333 5.48 0.039 0.040 0.046 0.000 0 2503 153.2 16.3 188 13.5 339 168 1 0.016 22
4 0.0444 4.74 0.036 0.035 0.043 0.000 0 4094 219.7 18.6 288 14.0 418 209 0 0.025 23
5 0.0556 4.24 0.044 0.046 0.044 0.000 0 5270 365.7 14.4 364 14.2 466 233 1 0.017 28
6 0.0667 3.87 0.053 0.055 0.045 0.000 0 3383 322.0 10.5 270 12.7 565 281 0 0.012 37
7 0.0778 3.59 0.060 0.061 0.047 0.000 0 2448 258.4 9.5 237 11.0 632 316 2 -0.036 51
8 0.0889 3.35 0.069 0.075 0.049 0.000 0 1952 213.2 9.2 222 9.5 636 317 0 0.012 44
9 0.1000 3.16 0.094 0.096 0.052 0.000 0 1158 155.1 7.5 189 7.3 691 345 0 -0.018 45
10 0.1111 3.00 0.109 0.109 0.055 0.000 0 871 133.6 6.5 183 6.0 752 375 0 -0.001 48
$$
For inline graphs use a Java browser
Overall: 0.055 0.056 0.055 0.000 0 2858. 286.2 10.0 257. 11.0 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))
______________________________________________________________
$TABLE: Analysis against intensity, red_aucn :
$GRAPHS:Rmerge v Intensity :N:1,2,3,4:
$$
Imax Rmrg Rfull Ranom Nanom Av_I SIGMA I/Sigma sd Nmeas Nref Ncent FRCBIAS Nbias Abs.BIAS
$$ $$
400. 0.392 0.395 0.000 0 174. 205.1 0.8 139.9 910 453 1 0.024 57 3.8
834. 0.119 0.117 0.000 0 602. 93.8 6.4 143.7 749 374 1 -0.019 42 -11.3
1310. 0.091 0.089 0.000 0 1076. 186.7 5.8 156.7 631 314 1 -0.110 41 -117.6
1836. 0.065 0.062 0.000 0 1554. 135.6 11.5 168.5 524 261 0 0.041 34 63.0
2424. 0.057 0.056 0.000 0 2130. 155.3 13.7 198.9 434 216 0 0.008 34 17.9
3091. 0.046 0.046 0.000 0 2716. 164.7 16.5 225.5 368 182 0 -0.009 28 -24.3
3860. 0.052 0.053 0.000 0 3448. 222.5 15.5 258.0 304 152 0 0.021 22 70.9
4771. 0.051 0.051 0.000 0 4309. 278.7 15.5 303.4 277 137 0 -0.003 16 -13.3
5885. 0.048 0.050 0.000 0 5332. 327.2 16.3 374.9 220 109 0 -0.004 26 -18.9
7321. 0.045 0.044 0.000 0 6612. 387.6 17.1 436.8 181 90 2 0.035 14 232.2
9346. 0.038 0.038 0.000 0 8291. 422.2 19.6 545.0 175 85 0 0.026 17 213.7
12807. 0.041 0.039 0.000 0 10648. 571.7 18.6 709.8 149 72 0 -0.007 12 -72.1
36840. 0.042 0.045 0.000 0 18097. 983.2 18.4 1214.1 157 75 2 0.020 12 420.3
$$
For inline graphs use a Java browser
Overall 0.055 0.056 0.000 0 2858. 286.2 10.0 257.4 5079 2520 7 0.008 355 25.1
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)
$TABLE: Completeness, multiplicity, Rmeas v. resolution, red_aucn :
$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: $$
N 1/resol^2 Dmin Nmeas Nref Ncent %poss C%poss Mlplct AnoCmp AnoFrc AnoMlt Rmeas Rmeas0 (Rsym) Rpim RpimO PCV PCV0
$$ $$
1 0.011 9.49 304 169 12 29.3 29.3 1.8 0.0 0.0 0.0 0.076 0.076 0.057 0.049 0.049 0.083 0.083
2 0.022 6.71 546 377 24 35.8 33.5 1.4 0.0 0.0 0.0 0.054 0.054 0.038 0.038 0.038 0.055 0.055
3 0.033 5.48 676 505 28 37.5 35.3 1.3 0.0 0.0 0.0 0.055 0.055 0.039 0.039 0.039 0.056 0.056
4 0.044 4.74 815 606 31 37.9 36.2 1.3 0.0 0.0 0.0 0.050 0.050 0.036 0.036 0.036 0.051 0.051
5 0.056 4.24 908 675 36 37.3 36.5 1.3 0.0 0.0 0.0 0.063 0.063 0.044 0.044 0.044 0.064 0.064
6 0.067 3.87 1030 746 39 37.0 36.6 1.4 0.0 0.0 0.0 0.075 0.075 0.053 0.053 0.053 0.076 0.076
7 0.078 3.59 1139 823 45 37.8 36.9 1.4 0.0 0.0 0.0 0.085 0.085 0.060 0.060 0.060 0.087 0.087
8 0.089 3.35 1174 855 46 36.3 36.8 1.4 0.0 0.0 0.0 0.098 0.098 0.069 0.069 0.069 0.100 0.100
9 0.100 3.16 1265 919 49 37.1 36.8 1.4 0.0 0.0 0.0 0.133 0.133 0.094 0.094 0.094 0.136 0.136
10 0.111 3.00 1347 970 53 36.7 36.8 1.4 0.0 0.0 0.0 0.154 0.154 0.109 0.108 0.108 0.159 0.159
$$
For inline graphs use a Java browser
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
$TABLE: Correlations within dataset, red_aucn :
$GRAPHS: Anom & Imean CCs v resolution - :A:2,4,6,12:
:RMS correlation ratio:A:2,8,10:$$
N 1/resol^2 dmax CC_anom N_anom CC_cen N_cen RCR_anom N_anom RCR_cen N_cen CC_Imean N_Imean $$
$$
1 0.0111 9.49 0.227 7 0.000 0 0.682 6 0.000 0 0.986 7
2 0.0222 6.71 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0
3 0.0333 5.48 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0
4 0.0444 4.74 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0
5 0.0556 4.24 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0
6 0.0667 3.87 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0
7 0.0778 3.59 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0
8 0.0889 3.35 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0
9 0.1000 3.16 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0
10 0.1111 3.00 0.000 0 0.000 0 0.000 0 0.000 0 0.000 0
$$
Overall 0.227 7 0.000 0 0.682 6 0.000 0 0.986 7
For inline graphs use a Java browser
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 2.63020 0.00000 0.02000 2.58776 0.00000 0.02000
$TABLE: Run 1, standard deviation v. Intensity, red_aucn :
$GRAPHS: Sigma(scatter/SD) Run 1:N:4,7,11: : Mean(scatter/SD) Run 1:A:4,6,10: $$
Range Imin Imax Irms Number MeanFull SigmaFull Irms Number MeanPart SigmaPartial $$
Fully_recordeds Partially_recordeds
$$
1 -281. 400. 305. 847 0.00 1.28 241. 63 0.02 0.66
2 400. 834. 621. 701 0.00 0.91 629. 48 -0.06 0.77
3 834. 1310. 1093. 580 -0.03 1.49 1179. 51 0.31 0.95
4 1310. 1836. 1569. 483 0.02 1.12 1540. 41 -0.22 0.98
5 1836. 2424. 2141. 392 0.02 1.13 2142. 42 -0.15 0.94
6 2424. 3091. 2729. 329 0.00 1.04 2721. 39 0.01 0.71
7 3091. 3860. 3462. 273 0.02 1.25 3466. 31 -0.15 0.88
8 3860. 4771. 4332. 255 0.00 1.31 4262. 22 0.01 0.95
9 4771. 5885. 5340. 186 0.00 1.29 5418. 34 -0.01 0.86
10 5885. 7321. 6647. 164 0.04 1.25 6526. 17 -0.36 0.93
11 7321. 9346. 8340. 157 0.03 1.07 8170. 18 -0.21 0.87
12 9346. 12807. 10736. 131 0.01 1.11 10455. 18 -0.01 0.93
13 12807. 46253. 18539. 145 0.02 1.18 21497. 12 -0.20 0.60
$$
For inline graphs use a Java browser
TOTALS:
0 -281. 46253. 4709. 4643 0.01 1.20 5220. 436 -0.04 0.87
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 1.159 0.000
Data within expected delta 0.90: 2940 0.996 0.003
====== Run number: 1, summed partials ======
Number Slope Intercept
All data: 437 0.940 -0.014
Data within expected delta 0.90: 277 0.846 -0.038
====== Run number: 1, fulls against fulls only ======
Number Slope Intercept
All data: 4310 1.193 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 2.6302 2.6185 2.6589 2.5878 2.1881
================================================================================
Summary data for Project: DMSO Crystal: DMSO Dataset: red_aucn
Overall OuterShell
Low resolution limit 35.27 3.16
High resolution limit 3.00 3.00
Rmerge 0.055 0.109
Rmeas (within I+/I-) 0.077 0.154
Rmeas (all I+ & I-) 0.077 0.154
Rpim (within I+/I-) 0.054 0.108
Rpim (all I+ & I-) 0.054 0.108
Fractional partial bias 0.008 -0.001
Total number of observations 9204 1347
Total number unique 6645 970
Mean((I)/sd(I)) 11.0 6.0
Completeness 36.8 36.7
Multiplicity 1.4 1.4
================================================================================
Scala: ** Normal termination ** Times: User: 2.2s System: 0.1s Elapsed: 0:03
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
############################################################### ############################################################### ############################################################### ### CCP4 5.99: MTZDUMP version 5.99 : 06/09/05## ############################################################### User: pjx Run date: 31/ 1/2006 Run time: 16:03:01 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.
List reflection: 0
Symmetry to be listed
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: /tmp/pjx/PROJECT_22_2_mtz.tmp
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/pjx/CCP4_REMOTE/ccp4/lib/data/syminfo.lib
* Title:
Bug 1070 Run scala on aucn data and generate file with free R flag col
* 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
* Number of Symmetry Operations = 8
* Number of Primitive Operations = 8
* Space Group = 91 'P4122'
* Lattice Type = P
* Point Group Name = PG422
* Symmetry Operations :
Symmetry 1 X, Y, Z
1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 1.00 0.00
0.00 0.00 0.00 1.00
Symmetry 2 -X, -Y, Z+1/2
-1.00 0.00 0.00 0.00
0.00 -1.00 0.00 0.00
0.00 0.00 1.00 0.50
0.00 0.00 0.00 1.00
Symmetry 3 -Y, X, Z+1/4
0.00 -1.00 0.00 0.00
1.00 0.00 0.00 0.00
0.00 0.00 1.00 0.25
0.00 0.00 0.00 1.00
Symmetry 4 Y, -X, Z+3/4
0.00 1.00 0.00 0.00
-1.00 0.00 0.00 0.00
0.00 0.00 1.00 0.75
0.00 0.00 0.00 1.00
Symmetry 5 -X, Y, -Z
-1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.00
0.00 0.00 -1.00 0.00
0.00 0.00 0.00 1.00
Symmetry 6 X, -Y, -Z+1/2
1.00 0.00 0.00 0.00
0.00 -1.00 0.00 0.00
0.00 0.00 -1.00 0.50
0.00 0.00 0.00 1.00
Symmetry 7 Y, X, -Z+3/4
0.00 1.00 0.00 0.00
1.00 0.00 0.00 0.00
0.00 0.00 -1.00 0.75
0.00 0.00 0.00 1.00
Symmetry 8 -Y, -X, -Z+1/4
0.00 -1.00 0.00 0.00
-1.00 0.00 0.00 0.00
0.00 0.00 -1.00 0.25
0.00 0.00 0.00 1.00
****** EPSILON ZONES - Reflection Classes and their multiplicity ******
EPSILON Zone 1
Reflections of type h00
Multiplicity 2
EPSILON Zone 2
Reflections of type 0k0
Multiplicity 2
EPSILON Zone 3
Reflections of type 00l
Multiplicity 4
EPSILON Zone 4
Reflections of type hh0
Multiplicity 2
EPSILON Zone 5
Reflections of type h -h0
Multiplicity 2
EPSILON Zone 6
Reflections of type hkl
Multiplicity 1
****** CENTRIC ZONES ******
CENTRIC Zone 1
Reflections of type 0kl
CENTRIC Zone 2
Reflections of type h0l
CENTRIC Zone 3
Reflections of type hk0
CENTRIC Zone 4
Reflections of type hhl
CENTRIC Zone 5
Reflections of type h -hl
OVERALL FILE STATISTICS for resolution range 0.001 - 0.111
=======================
Col Sort Min Max Num % Mean Mean Resolution Type Column
num order Missing complete abs. Low High label
1 ASC 1 28 0 100.00 14.9 14.9 35.27 3.00 H H
2 NONE 0 18 0 100.00 7.5 7.5 35.27 3.00 H K
3 NONE 0 75 0 100.00 31.3 31.3 35.27 3.00 H L
4 NONE -280.5 46252.6 0 100.00 2954.78 2956.91 35.27 3.00 J IMEAN
5 NONE 2.9 2910.0 0 100.00 224.66 224.66 35.27 3.00 Q SIGIMEAN
6 NONE -272.5 30271.1 0 100.00 1816.98 1819.05 35.27 3.00 K I(+)
7 NONE 0.0 2619.7 0 100.00 160.35 160.35 35.27 3.00 M SIGI(+)
8 NONE -280.5 46252.6 0 100.00 2097.19 2099.10 35.27 3.00 K I(-)
9 NONE 0.0 3108.6 0 100.00 178.33 178.33 35.27 3.00 M SIGI(-)
No. of reflections used in FILE STATISTICS 6645
MTZDUMP: NO REFLECTIONS LISTED Times: User: 0.2s System: 0.0s Elapsed: 0:00
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############################################################### ############################################################### ############################################################### ### CCP4 5.99: UNIQUE version 5.99 : 06/09/05## ############################################################### User: pjx Run date: 31/ 1/2006 Run time: 16:03:03 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--- CELL 88.9083 88.9083 229.2167 90.0000 90.0000 90.0000
Data line--- SYMMETRY 'P4122'
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/pjx/CCP4_REMOTE/ccp4/lib/data/syminfo.lib
Data line--- LABOUT F=FUNI SIGF=SIGFUNI
Data line--- RESOLUTION 3.000
Comment line--- ## This script run with the command ##########
Comment line--- # unique HKLOUT /tmp/pjx/PROJECT_22_4_mtz.tmp
Comment line--- ################################################
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 -k,+h,+l 5 -h,-k,+l 7 +k,-h,+l
ISYM 9 +h,-k,-l 11 +k,+h,-l 13 -h,+k,-l 15 -k,-h,-l
Bijvoet negative
ISYM ISYM ISYM ISYM
ISYM 2 -h,-k,-l 4 +k,-h,-l 6 +h,+k,-l 8 -k,+h,-l
ISYM 10 -h,+k,+l 12 -k,-h,+l 14 +h,-k,+l 16 +k,+h,+l
Maximum and minimum Bragg spacings 3.000 10000.000 Angstroms
Limits on H,K,L.. 0 to 29 0 to 29 0 to 76
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /tmp/pjx/PROJECT_22_4_mtz.tmp
* Title:
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 0
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
* Number of Columns = 5
* Number of Reflections = 19235
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FUNI SIGFUNI
* Column Types :
H H H F Q
* Associated datasets :
0 0 0 0 0
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
88.9083 88.9083 229.2167 90.0000 90.0000 90.0000
* Resolution Range :
0.00013 0.11111 ( 88.908 - 3.000 A )
* Sort Order :
1 2 3 0 0
* Space group = 'P 41 2 2' (number 91)
69300 reflections tested
19235 reflections within resolution limits written to output file
UNIQUE: Normal Termination Times: User: 0.5s System: 0.0s Elapsed: 0:00
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############################################################### ############################################################### ############################################################### ### CCP4 5.99: FREERFLAG version 5.99 : 06/09/05## ############################################################### User: pjx Run date: 31/ 1/2006 Run time: 16:03:04 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--- FREERFRAC 0.05
Data line--- END
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: /tmp/pjx/PROJECT_22_4_mtz.tmp
* Title:
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 0
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
* Number of Columns = 5
* Number of Reflections = 19235
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FUNI SIGFUNI
* Column Types :
H H H F Q
* Associated datasets :
0 0 0 0 0
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
88.9083 88.9083 229.2167 90.0000 90.0000 90.0000
* Resolution Range :
0.00013 0.11111 ( 88.736 - 3.000 A )
* Sort Order :
1 2 3 0 0
* Space group = 'P 41 2 2' (number 91)
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/pjx/CCP4_REMOTE/ccp4/lib/data/syminfo.lib
****** EPSILON ZONES - Reflection Classes and their multiplicity ******
EPSILON Zone 1
Reflections of type h00
Multiplicity 2
EPSILON Zone 2
Reflections of type 0k0
Multiplicity 2
EPSILON Zone 3
Reflections of type 00l
Multiplicity 4
EPSILON Zone 4
Reflections of type hh0
Multiplicity 2
EPSILON Zone 5
Reflections of type h -h0
Multiplicity 2
EPSILON Zone 6
Reflections of type hkl
Multiplicity 1
***** All Reflections binned into 20 segments
*** labelled 0 through to 19 *****
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /tmp/pjx/PROJECT_22_5_mtz.tmp
* Title:
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 0
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
* Number of Columns = 6
* Number of Reflections = 19235
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FUNI SIGFUNI FreeR_flag
* Column Types :
H H H F Q I
* Associated datasets :
0 0 0 0 0 0
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
88.9083 88.9083 229.2167 90.0000 90.0000 90.0000
* Resolution Range :
0.00013 0.11111 ( 88.908 - 3.000 A )
* Sort Order :
1 2 3 0 0
* Space group = 'P 41 2 2' (number 91)
Number of reflections: 19235
Number for flagged reflection for each bin:
Reflection flag =: Number:
0 988 0
1 978 0
2 966 0
3 914 0
4 988 0
5 945 0
6 981 0
7 970 0
8 980 0
9 966 0
10 996 0
11 916 0
12 970 0
13 932 0
14 909 0
15 968 0
16 959 0
17 953 0
18 1003 0
19 953 0
FREERFLAG: Normal termination Times: User: 0.3s System: 0.0s Elapsed: 0:00
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############################################################### ############################################################### ############################################################### ### CCP4 5.99: CAD version 5.99 : 18/11/05## ############################################################### User: pjx Run date: 31/ 1/2006 Run time: 16:03:05 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--- LABI FILE 2 E1=FreeR_flag
Data line--- LABI FILE 1 ALLIN
Data line--- END
No CTYP lines input for file: 1
No CTYP lines input for file: 2
Indices output even if all data items flagged "missing"
Warning, NOT all LABOUT data lines given
Warning, NOT all LABOUT data lines given
OPENED INPUT MTZ FILE
Logical Name: HKLIN1 Filename: /tmp/pjx/PROJECT_22_2_mtz.tmp
* Title:
Bug 1070 Run scala on aucn data and generate file with free R flag col
* 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/CCP4_REMOTE/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
Chosen Asymmetric unit of reciprocal space:
[4/mmm] hkl:h>=0, k>=0, l>=0 and h>=k
** "Missing" flag set in HKLIN1 to Nan:
** "Missing" entries LISTED as -999.000
Data line--- LABIN E1=IMEAN E2=SIGIMEAN E3=I(+) E4=SIGI(+) E5=I(-) E6=SIGI(-)
After Processing File_Number: 1
Number of columns so far : 9
Accummulated Out_Put_MTZ_labels are:
E11=IMEAN E21=SIGIMEAN E31=I(+) E41=SIGI(+)
E51=I(-) E61=SIGI(-)
MTZOUT_LABELS are H K L and -
IMEAN SIGIMEAN I(+) SIGI(+)
I(-) SIGI(-)
OPENED INPUT MTZ FILE
Logical Name: HKLIN2 Filename: /tmp/pjx/PROJECT_22_5_mtz.tmp
* Title:
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 0
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
* Number of Columns = 6
* Number of Reflections = 19235
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FUNI SIGFUNI FreeR_flag
* Column Types :
H H H F Q I
* Associated datasets :
0 0 0 0 0 0
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
88.9083 88.9083 229.2167 90.0000 90.0000 90.0000
* Resolution Range :
0.00013 0.11111 ( 88.736 - 3.000 A )
* Sort Order :
1 2 3 0 0
* Space group = 'P 41 2 2' (number 91)
Data line--- LABIN E1=FreeR_flag
After Processing File_Number: 2
Number of columns so far : 10
Accummulated Out_Put_MTZ_labels are:
E11=IMEAN E21=SIGIMEAN E31=I(+) E41=SIGI(+)
E51=I(-) E61=SIGI(-) E12=FreeR_flag
MTZOUT_LABELS are H K L and -
IMEAN SIGIMEAN I(+) SIGI(+)
I(-) SIGI(-) FreeR_flag
3 sort keys, in columns 1 2 3
Data line--- LABIN E1=IMEAN E2=SIGIMEAN E3=I(+) E4=SIGI(+) E5=I(-) E6=SIGI(-)
OPENED INPUT MTZ FILE
Logical Name: HKLIN1 Filename: /tmp/pjx/PROJECT_22_2_mtz.tmp
* Title:
Bug 1070 Run scala on aucn data and generate file with free R flag col
* 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)
Column pairs - SIGs: 7 9
Column pairs - SIGs: 9 7
Column pairs - I+ I-: 6 8
Column pairs - I+ I-: 8 6
Reading from HKLIN mtz file_Number = :1
This file written with MTZLIB Version Number : MTZ:V1.1
File HKLIN1 contains a total of 9 Columns
and a total of 6645 Reflections
****** EPSILON ZONES - Reflection Classes and their multiplicity ******
EPSILON Zone 1
Reflections of type h00
Multiplicity 2
EPSILON Zone 2
Reflections of type 0k0
Multiplicity 2
EPSILON Zone 3
Reflections of type 00l
Multiplicity 4
EPSILON Zone 4
Reflections of type hh0
Multiplicity 2
EPSILON Zone 5
Reflections of type h -h0
Multiplicity 2
EPSILON Zone 6
Reflections of type hkl
Multiplicity 1
****** CENTRIC ZONES ******
CENTRIC Zone 1
Reflections of type 0kl
CENTRIC Zone 2
Reflections of type h0l
CENTRIC Zone 3
Reflections of type hk0
CENTRIC Zone 4
Reflections of type hhl
CENTRIC Zone 5
Reflections of type h -hl
For file HKLIN1
Total Number of HKL read = 6645
Total Number of HKL systematic absent = 0
Total Number of HKL reject for resolution limits = 0
Total Number of HKL passed to sort for this file = 7008
Data line--- LABIN E1=FreeR_flag
OPENED INPUT MTZ FILE
Logical Name: HKLIN2 Filename: /tmp/pjx/PROJECT_22_5_mtz.tmp
* Title:
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 0
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
* Number of Columns = 6
* Number of Reflections = 19235
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FUNI SIGFUNI FreeR_flag
* Column Types :
H H H F Q I
* Associated datasets :
0 0 0 0 0 0
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
88.9083 88.9083 229.2167 90.0000 90.0000 90.0000
* Resolution Range :
0.00013 0.11111 ( 88.736 - 3.000 A )
* Sort Order :
1 2 3 0 0
* Space group = 'P 41 2 2' (number 91)
Reading from HKLIN mtz file_Number = :2
This file written with MTZLIB Version Number : MTZ:V1.1
File HKLIN2 contains a total of 6 Columns
and a total of 19235 Reflections
For file HKLIN2
Total Number of HKL read = 19235
Total Number of HKL systematic absent = 0
Total Number of HKL reject for resolution limits = 0
Total Number of HKL passed to sort for this file = 22768
Total number read for all files = 25880
Total passed to sort for all files = 29776
Total number systematic absent = 0
Total number rejected outside resol= 0
Number of columns per file:
File_Number = 1 Number_Columns_Selected = 6
File_Number = 2 Number_Columns_Selected = 1
Data line--- LABOUT E11=IMEAN E21=SIGIMEAN E31=I(+) E41=SIGI(+) E51=I(-) E61=SIGI(-) E12=FreeR_flag
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /tmp/pjx/PROJECT_22_6_mtz.tmp
* Title:
Bug 1070 Run scala on aucn data and generate file with free R flag col
* 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 = 10
* Number of Reflections = 19235
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FreeR_flag IMEAN SIGIMEAN I(+) SIGI(+) I(-) SIGI(-)
* Column Types :
H H H I J Q K M K M
* Associated datasets :
0 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 :
0.00013 0.11111 ( 88.908 - 3.000 A )
* Sort Order :
1 2 3 0 0
* Space group = 'P4122' (number 91)
Total number from Sorting Routine = 29776
Final Total of Unique records to HKLOUT = 19235
Final Total of Missing records to HKLOUT = 0
CAD: *** Normal Termination of CAD *** Times: User: 0.8s System: 0.0s Elapsed: 0:01
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############################################################### ############################################################### ############################################################### ### CCP4 5.99: FREERFLAG version 5.99 : 06/09/05## ############################################################### User: pjx Run date: 31/ 1/2006 Run time: 16:03:07 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--- COMPLETE FREE=FreeR_flag
Data line--- END
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: /tmp/pjx/PROJECT_22_6_mtz.tmp
* Title:
Bug 1070 Run scala on aucn data and generate file with free R flag col
* 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 = 10
* Number of Reflections = 19235
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FreeR_flag IMEAN SIGIMEAN I(+) SIGI(+) I(-) SIGI(-)
* Column Types :
H H H I J Q K M K M
* Associated datasets :
0 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 :
0.00013 0.11111 ( 88.736 - 3.000 A )
* Sort Order :
1 2 3 0 0
* Space group = 'P4122' (number 91)
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/pjx/CCP4_REMOTE/ccp4/lib/data/syminfo.lib
****** EPSILON ZONES - Reflection Classes and their multiplicity ******
EPSILON Zone 1
Reflections of type h00
Multiplicity 2
EPSILON Zone 2
Reflections of type 0k0
Multiplicity 2
EPSILON Zone 3
Reflections of type 00l
Multiplicity 4
EPSILON Zone 4
Reflections of type hh0
Multiplicity 2
EPSILON Zone 5
Reflections of type h -h0
Multiplicity 2
EPSILON Zone 6
Reflections of type hkl
Multiplicity 1
***** All Reflections binned into 20 segments
*** labelled 0 through to 19 *****
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /home/pjx/PROJECTS/myProject/aucn_scala1.mtz
* Title:
Bug 1070 Run scala on aucn data and generate file with free R flag col
* 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 = 10
* Number of Reflections = 19235
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FreeR_flag IMEAN SIGIMEAN I(+) SIGI(+) I(-) SIGI(-)
* Column Types :
H H H I J Q K M K M
* Associated datasets :
0 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 :
0.00013 0.11111 ( 88.908 - 3.000 A )
* Sort Order :
1 2 3 0 0
* Space group = 'P4122' (number 91)
Number of reflections: 19235
Number for flagged reflection for each bin:
Reflection flag =: Number:
0 988 0
1 978 0
2 966 0
3 914 0
4 988 0
5 945 0
6 981 0
7 970 0
8 980 0
9 966 0
10 996 0
11 916 0
12 970 0
13 932 0
14 909 0
15 968 0
16 959 0
17 953 0
18 1003 0
19 953 0
FREERFLAG: Normal termination Times: User: 0.3s System: 0.0s Elapsed: 0:01
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