#CCP4I VERSION CCP4Interface 1.4.4
#CCP4I SCRIPT LOG scaleit
#CCP4I DATE 28 Jun 2006 11:30:15
#CCP4I USER mpr
#CCP4I PROJECT PROJECT
#CCP4I JOB_ID 220
#CCP4I SCRATCH /tmp/mpr
#CCP4I HOSTNAME william-scotts-computer-2.local
#CCP4I PID 775
SCALEIT
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### CCP4 6.0: SCALEIT version 6.0 : 06/09/05##
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User: mpr Run date: 28/ 6/2006 Run time: 11:30:15
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
TITLE
ANALYSE
CONVERGE
LABIN
EXCLUDE
GRAPH
RESOLUTION
WEIGHT
NOWT
REFINE
SCALE
SCATTER
SYMMETRY
END
Data line--- title [No title given]
Data line--- NOWT
Calculate scales WITHOUT any sigma weighting.
Data line--- converge NCYC 4
Maximum number of cycles 4
Data line--- converge ABS 0.001
Absolute convergence limit 0.0010
Data line--- converge TOLR -7
Tolerance -7.00000
Data line--- REFINE ANISOTROPIC
Data line--- auto
Automatic scaling of all columns in given datasets
Data line--- LABIN FP=F_nat SIGFP=SIGF_nat FPH1=F_mal SIGFPH1=SIGF_mal
FP=
FP= F_nat
FP= F_nat FPH= F_mal SIGF_mal
Comment line--- ## This script run with the command ##########
Comment line--- # scaleit HKLIN /Users/mpr/xtal/ssrl_061406/mpr78/merge/cad.mtz HKLOUT /Users/mpr/xtal/ssrl_061406/mpr78/merge/cad_scaleit1.mtz
Comment line--- ################################################
Input MTZ File
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: /Users/mpr/xtal/ssrl_061406/mpr78/merge/cad.mtz
* Title:
[No title given] mpr1_p21_13 dataset
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 2
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 Unspecified
mpr1_4
Unspecified
44.8295 99.4813 73.1151 90.0000 103.3539 90.0000
0.97945
2 Unspecified
mpr78_1
Unspecified
45.2896 100.0178 71.9303 90.0000 104.4158 90.0000
0.97946
* Number of Columns = 7
* Number of Reflections = 19176
* Missing value set to NaN in input mtz file
* Column Labels :
H K L F_nat SIGF_nat F_mal SIGF_mal
* Column Types :
H H H F Q F Q
* Associated datasets :
0 0 0 1 1 2 2
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
44.8295 99.4813 73.1151 90.0000 103.3539 90.0000
* Resolution Range :
0.00020 0.15090 ( 71.067 - 2.574 A )
* Sort Order :
1 2 3 0 0
* Space group = 'P21' (number 4)
AUTOMATIC COLUMN SELECTION
==========================
The program will use DATASET information from the MTZ file
to identify all scalable columns for each specified
derivative i.e. FPH, DPH, IMEAN etc and apply the scale
factor to all these columns.
This is a new feature and there may be problems -
check the information below for warnings or errors
and report any problems to ccp4@dl.ac.uk
* Automatic column selection completed *
* You should check the above output for errors
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /sw/share/xtal/ccp4-6.0/lib/data/syminfo.lib
****** CENTRIC ZONES ******
CENTRIC Zone 1
Reflections of type h0l
Output File
SPACE GROUP NUMBER 4
SPACE GROUP NAME P21
POINT GROUP NAME PG2
NUMBER OF SYMMETRY OPERATORS 2
NUMBER OF PRIMITIVE SYMMETRY OPERATORS 2
ANISOTROPIC DERIVATIVE TO NATIVE SCALING
========================================
Position of Native F 4
Position of Derivative F 6
Number of Cycles 4
Convergence Limit 0.001000
Derivative: FP= F_nat FPH= F_mal SIGF_mal
Initial derivative scale factor (for F) = 0.7506 from 15165 reflections
The anisotropic scale is applied to the derivative F as
(derivative scale)* exp( - (B11*H**2 + B22*K**2 + B33*L**2 + 2*(B12*H*K + B13*H*L + B23*K*L) ) )
CORRELATION MATRIX ELEMENTS > 0.7
CORRELATION MATRIX ELEMENTS > 0.7
CORRELATION MATRIX ELEMENTS > 0.7
CORRELATION MATRIX ELEMENTS > 0.7
-- Cycle Number: 4
MEAN RESIDUAL W D**2/( M - N) : 3636969.08711 FOR 15165 REFLECTIONS
SCALES (for F)
NATIVE DERIVATIVE B11 B22 B33 B12 B13 B23
SHIFTS 0.0000 -0.0002 -0.000026 -0.000001 0.000000 0.000000 -0.000001 0.000000
SD 'S 0.0015 0.0014 0.000076 0.000016 0.000013 0.000026 0.000022 0.000010
RMS isomorphous difference for derivative 1 is 19.83
Number of observations: 15165
*****************************************************
*** ANALYSIS OF TEMPERATURE FACTORS ***
*****************************************************
Remember: the scale is applied to the derivative F as
(derivative scale)* exp( - (B11*H**2 + B22*K**2 + B33*L**2 + 2*(B12*H*K + B13*H*L + B23*K*L) ) )
An equivalent form of the anisotropic temperature factor is
exp(-0.25( h**2 * (a*)**2 * beta11 + k**2 * (b*)**2 * beta22 + l**2 * (c*)**2 * beta33
+ 2*k*l*(b*)*(c*)*beta23 + 2*l*h*(c*)*(a*) *beta31 + 2*h*k*(a*)*(b*) *beta12))
(This means the Uij terms of an anisotropic temperature factor is equal to betaij/(8*pi**2.)
Note: REFMAC5 outputs betaij/4
The isotropic equivalent is ::
exp(-B (sin**2(theta)/lamda**2) ) =
exp(-0.25( h**2 * (a*)**2 * B + k**2 * (b*)**2 * B + l**2 * (c*)**2 * B
+ 2*k*l*(b*)*(c*)*cosAS*B + 2*l*h*(c*)*(a*)*cosBS*B + 2*h*k*(a*)*(b*)*cosGS*B))
For derivative : 1
beta matrix - array elements beta11 beta12 beta13
beta21 beta22 beta23,
beta31 beta32 beta33
29.9610 0.0000 -5.1972
0.0000 15.6911 0.0000
-5.1972 0.0000 7.0888
Latent roots and vectors of "BETA" -
Vectors are relative to orthogonal axial system parallel to a* cXa* c
LAMBDA 1 7.77164602
0.977
0.000
-0.212 length 1.0000
LAMBDA 2 1.49080801
0.212
0.000
0.977 length 1.0000
LAMBDA 3 3.92277575
0.000
1.000
0.000 length 1.0000
The equivalent isotropic temperature factor is 3.5682
This gives a spherical temperature "volume" equal to the ellipsoidal "volume",
APPLICATION OF SCALES AND ANALYSIS OF DIFFERENCES
Both forms for Anisotropic scales listed
SCALE (F) B11 B22 B33 B12 B13 B23
Derivative 1 0.937 0.01388 0.00159 0.00140 0.00000 -0.00110 0.00000
Derivative 1 0.937 6.60127 3.92278 1.77220 0.00000 -0.85486 0.00000
----------------------------------------------------------
----------------------------------------------------------
Isomorphous Differences
Derivative title: FP= F_nat FPH= F_mal SIGF_mal
Differences greater than 4.1630 * RMSDIF are unlikely,
ie acceptable differences are less than 82.56
Maximum difference 162.00
Difference interval for Histogram 10
1 sort keys, in columns 8
************************************************************************************************************************
Large differences (isomorphous & anomalous)
H K L RES FP SIGP FPH1 SIGF1
-6 0 1 0.018 103 2 15 1
=========
-5 17 4 0.043 14 1 105 2
=========
-4 0 22 0.091 57 1 181 2
=========
-3 0 6 0.009 144 3 49 1
=========
-3 0 22 0.091 31 1 161 2
=========
-3 4 18 0.062 30 1 114 1
=========
-2 0 7 0.010 105 2 9 1
=========
-2 0 13 0.032 7 2 93 1
=========
-2 1 5 0.006 28 0 115 1
=========
-2 2 20 0.076 90 2 177 2
=========
-2 3 8 0.013 96 2 210 2
=========
-1 0 5 0.005 97 2 4 1
=========
-1 0 22 0.093 133 3 27 2
=========
-1 2 6 0.007 232 5 140 1
=========
-1 4 5 0.006 230 7 121 1
=========
-1 4 6 0.008 217 6 102 1
=========
-1 4 17 0.057 25 1 109 2
=========
-1 6 17 0.059 19 1 102 1
=========
-1 7 19 0.074 63 1 160 2
=========
0 0 18 0.064 9 3 105 2
=========
0 0 19 0.071 40 1 143 2
=========
0 2 18 0.064 152 3 60 1
=========
0 5 4 0.006 155 3 43 1
=========
0 7 19 0.076 16 1 123 2
=========
1 0 17 0.060 109 3 202 3
=========
1 3 16 0.054 53 1 172 2
=========
1 3 17 0.061 52 1 144 1
=========
1 5 2 0.004 241 7 157 2
=========
1 10 15 0.057 51 1 136 1
=========
1 16 7 0.037 36 1 130 1
=========
2 0 8 0.017 102 4 13 1
=========
2 0 17 0.064 111 3 231 3
=========
2 0 18 0.071 92 2 196 3
=========
2 0 19 0.079 16 3 117 2
=========
2 0 20 0.087 117 3 23 2
=========
2 1 17 0.064 150 2 41 1
=========
2 1 18 0.072 141 2 44 1
=========
2 3 18 0.072 105 2 22 1
=========
2 4 19 0.081 13 1 98 1
=========
3 0 16 0.062 126 3 8 3
=========
3 3 13 0.045 35 1 122 1
=========
4 0 16 0.069 11 3 109 1
=========
4 0 17 0.076 205 5 42 1
=========
4 0 18 0.083 132 5 19 2
=========
4 1 17 0.076 58 1 188 2
=========
4 1 18 0.083 66 1 177 2
=========
4 2 17 0.076 122 2 31 1
=========
4 3 16 0.069 138 3 36 1
=========
5 0 13 0.056 26 1 165 2
=========
5 0 14 0.062 117 3 22 2
=========
5 1 17 0.083 9 2 163 1
=========
5 2 2 0.016 86 2 177 2
=========
5 3 17 0.084 10 2 98 1
=========
5 5 15 0.071 151 3 49 1
=========
5 8 16 0.082 93 2 10 2
=========
6 2 16 0.084 50 1 136 1
=========
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /Users/mpr/xtal/ssrl_061406/mpr78/merge/cad_scaleit1.mtz
* Title:
[No title given]
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 2
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 Unspecified
mpr1_4
Unspecified
44.8295 99.4813 73.1151 90.0000 103.3539 90.0000
0.97945
2 Unspecified
mpr78_1
Unspecified
45.2896 100.0178 71.9303 90.0000 104.4158 90.0000
0.97946
* Number of Columns = 7
* Number of Reflections = 19176
* Missing value set to NaN in input mtz file
* Column Labels :
H K L F_nat SIGF_nat F_mal SIGF_mal
* Column Types :
H H H F Q F Q
* Associated datasets :
0 0 0 1 1 2 2
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
44.8295 99.4813 73.1151 90.0000 103.3539 90.0000
* Resolution Range :
0.00020 0.15090 ( 71.138 - 2.574 A )
* Sort Order :
1 2 3 0 0
* Space group = 'P21' (number 4)
19053 STRUCTURE FACTORS SCALED AND WRITTEN TO OUTPUT FILE
ANALYSES OF SCALE FACTOR ON INTENSITIESAFTER CORRECTION
========================================================
15165 records passed to sort
14594 acentric, 571 centric.
Least squares line : Gradient - intercept SUMDEL Npoints
Gradient should be 1 for 2 equivalent data sets
Gradient should be >> 1 for derivative v native data sets
$TEXT:reference:
$$ Normal probability $$
Dave Smith and Lynne Howell ( J.Appl. Cryst 1992 25 81-86) $$
Total (cent) 571 14.842 2.261 6961.2 361 9.865 0.690 267.4
Total (acen) 14594 12.822 1.714 159301.8 9222 8.006 0.700 4790.9
------------------------------------------------------------------------------------------------------------------------
Scaling for derivative no. 1 Derivative title: FP= F_nat FPH= F_mal SIGF_mal
Histogram showing distribution of differences
Table shows the number of reflections in bins of difference, for each resolution shell
Bins are headed by the difference corresponding to the mid-point of each bin
Isomorphous Differences
-----------------------
Derivative title: FP= F_nat FPH= F_mal SIGF_mal
d -80 -70 -60 -50 -40 -30 -20 -10 0 10 20 30 40 50 60 70 80
16.28 0 0 0 0 3 1 3 2 8 3 3 5 2 2 0 3 0
9.40 4 3 11 16 16 23 29 43 29 38 42 24 16 15 4 3 8
7.28 2 2 13 16 32 47 64 58 64 57 41 25 22 9 10 2 5
6.15 4 5 7 25 32 65 69 84 96 60 53 23 17 9 3 2 0
5.43 2 2 12 21 33 51 78 104 116 87 70 37 28 11 7 0 0
4.91 5 5 5 21 39 76 99 120 124 91 61 40 20 9 7 2 1
4.52 3 6 15 21 32 61 106 139 143 117 82 47 30 5 4 1 0
4.20 5 3 11 18 34 62 116 138 173 130 97 60 28 10 2 5 0
3.95 11 6 8 10 37 61 104 173 186 144 86 45 29 12 2 2 3
3.74 6 4 12 17 24 51 126 190 217 173 84 41 22 9 4 3 6
3.55 6 2 4 8 15 66 97 168 266 226 106 51 22 10 4 2 5
3.39 5 1 5 10 24 41 94 214 308 238 74 29 19 7 6 2 3
3.26 3 2 4 6 10 39 95 232 394 226 85 26 9 4 5 1 3
3.13 0 1 2 1 7 25 86 258 441 247 73 30 12 4 0 1 0
3.02 0 0 1 0 5 9 62 245 581 248 48 14 6 3 2 0 0
2.92 0 0 0 1 1 9 37 214 762 205 30 13 2 1 0 0 0
2.83 0 0 0 0 0 4 28 172 919 169 18 2 0 0 0 0 0
2.75 0 0 0 0 0 1 10 62 376 52 5 0 0 0 0 0 0
2.68 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.61 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Total 56 42 110 191 344 692 1303 2616 5203 2511 1058 512 284 120 60 29 34
THE TOTALS 15165. 2365. 1.143 0.959 0.374 0.601 0.323 13.5 162.
1
SCALEIT: Normal termination of SCALEIT
Times: User: 0.8s System: 0.1s Elapsed: 0:02
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
Automatic column selection has been switched off for all subsquent runs of Scaleit
***************************************************************************
#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 28 Jun 2006 11:30:17
#CCP4I TERMINATION OUTPUT_FILES /Users/mpr/CCP4/PROJECT_220_scaleit.summary PROJECT
#CCP4I MESSAGE Task completed successfully