#CCP4I VERSION CCP4Interface 1.3.9
#CCP4I SCRIPT LOG scaleit
#CCP4I DATE 24 Jun 2003 13:24:24
#CCP4I USER mgwt
#CCP4I PROJECT 2003test
#CCP4I JOB_ID 32
#CCP4I SCRATCH /tmp/mgwt
#CCP4I HOSTNAME bragg3
#CCP4I PID 1940
SCALEIT
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### CCP4 4.2: SCALEIT version 4.2 : 07/08/02##
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User: mgwt Run date: 24/ 6/03 Run time:13:24:24
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 Scaling RNAse SA Derivatives (mir tutorial step 1)
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=FNAT SIGFP=SIGFNAT FPH1=FHG2 SIGFPH1=SIGFHG2 DPH1=DANOHG2 SIGDPH1=SIGDANOHG2 FPH2=FPTNCD25 SIGFPH2=
SIGFPTNCD25 DPH2=DANOPTNCD25 SIGDPH2=SIGDANOPTNCD25 FPH3=FIOD25 SIGFPH3=SIGFIOD25 DPH3=DANOIOD25 SIGDPH3=SIGDANOIOD25
FP=
FP= FNAT
FP= FNAT FPH= FHG2 SIGFHG2
FP=
FP= FNAT
FP= FNAT FPH= FPTNCD25 SIGFPTNCD25
FP=
FP= FNAT
FP= FNAT FPH= FIOD25 SIGFIOD25
Comment line--- ## This script run with the command ##########
Comment line--- # scaleit HKLIN /y/people/mgwt/CCP4/examples/tut2003/data/rnase25.mtz HKLOUT /y/people/mgwt/TEST/rnase25_scaleit1.m
tz
Comment line--- ################################################
Input MTZ File
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: HKLIN Filename: /y/people/mgwt/CCP4/examples/tut2003/data/rnase25.mtz
HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 1
* Title:
rename column labels for rnase25.mtz Scaleit tests........
* Number of Datasets = 4
* Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
1 RNASE /
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
1.54200
2 RNASE /
DERIV_HG
64.9000 78.3200 38.7900 90.0000 90.0000 90.0000
1.54200
3 RNASE /
DERIV_PT
64.8500 78.5600 39.5100 90.0000 90.0000 90.0000
1.54200
4 RNASE /
DERIV_I
65.0000 78.6600 38.8100 90.0000 90.0000 90.0000
1.54200
* Number of Columns = 18
* Number of Reflections = 7262
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Column Types :
H H H F Q F Q D Q F Q D Q F Q D Q I
* Associated datasets :
1 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 1
* Cell Dimensions :
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.16000 ( 50.000 - 2.500 A )
* Sort Order :
1 2 3 0 0
* Space group = P212121 (number 19)
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
* Input Program Labels :
H K L FP SIGFP FPH1 SIGFPH1 DPH1 SIGDPH1 FPH1(+) SIGFPH1(+) FPH1(-) SIGFPH1(-)
IMEAN1 SIGIMEAN1 I1(+) SIGI1(+) I1(-) SIGI1(-) FPH2 SIGFPH2 DPH2 SIGDPH2 FPH2(+)
SIGFPH2(+) FPH2(-) SIGFPH2(-) IMEAN2 SIGIMEAN2 I2(+) SIGI2(+) I2(-) SIGI2(-)
FPH3 SIGFPH3 DPH3 SIGDPH3 FPH3(+) SIGFPH3(+) FPH3(-) SIGFPH3(-) IMEAN3 SIGIMEAN3
I3(+) SIGI3(+) I3(-) SIGI3(-)
* Input File Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Lookup Table : the number indicates the input column no.
* Array element n corresponds to the nth program label
1 2 3 4 5 6 7 8 9 0 0 0 0 0 0
0 0 0 0 10 11 12 13 0 0 0 0 0 0 0
0 0 0 14 15 16 17 0 0 0 0 0 0 0 0
0 0
Centric Zone 1 Reflections of Type 0kl
Centric Zone 2 Reflections of Type h0l
Centric Zone 3 Reflections of Type hk0
Output File
(Q)QOPEN: file opened on unit 2 Status: UNKNOWN
Logical Name: HKLOUT Filename: /y/people/mgwt/TEST/rnase25_scaleit1.mtz
SPACE GROUP NUMBER 19
SPACE GROUP NAME P212121
POINT GROUP NAME PG222
NUMBER OF SYMMETRY OPERATORS 4
NUMBER OF PRIMITIVE SYMMETRY OPERATORS 4
ANISOTROPIC DERIVATIVE TO NATIVE SCALING
========================================
Position of Native F 4
Position of Derivative F 6
Number of Cycles 4
Convergence Limit 0.001000
Derivative has Anomalous Difference to be Scaled
Derivative: FP= FNAT FPH= FHG2 SIGFHG2 DANOHG2 SIGDANOHG2
Initial derivative scale factor (for F) = 0.9182 from 3701 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) : 443520985.97495 FOR 3701 REFLECTIONS
SCALES (for F)
NATIVE DERIVATIVE B11 B22 B33 B12 B13 B23
SHIFTS 0.0000 0.0000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
SD 'S 0.0009 0.0007 0.000014 0.000010 0.000040 0.000008 0.000016 0.000015
RMS isomorphous difference for derivative 1 is 71.37
Number of observations: 3701
RMS anomalous difference for derivative 1 is 63.71
Number of observations: 3405
ANISOTROPIC DERIVATIVE TO NATIVE SCALING
========================================
Position of Native F 4
Position of Derivative F 10
Number of Cycles 4
Convergence Limit 0.001000
Derivative has Anomalous Difference to be Scaled
Derivative: FP= FNAT FPH= FPTNCD25 SIGFPTNCD25 DANOPTNCD25 SIGDANOPTNCD25
Initial derivative scale factor (for F) = 0.9928 from 6919 reflections
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) : 469935050.46256 FOR 6919 REFLECTIONS
SCALES (for F)
NATIVE DERIVATIVE B11 B22 B33 B12 B13 B23
SHIFTS 0.0000 0.0000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
SD 'S 0.0011 0.0012 0.000012 0.000009 0.000036 0.000007 0.000014 0.000013
RMS isomorphous difference for derivative 2 is 80.80
Number of observations: 6919
RMS anomalous difference for derivative 2 is 21.05
Number of observations: 5746
ANISOTROPIC DERIVATIVE TO NATIVE SCALING
========================================
Position of Native F 4
Position of Derivative F 14
Number of Cycles 4
Convergence Limit 0.001000
Derivative has Anomalous Difference to be Scaled
Derivative: FP= FNAT FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
Initial derivative scale factor (for F) = 1.0291 from 6894 reflections
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) : 538774649.41532 FOR 6894 REFLECTIONS
SCALES (for F)
NATIVE DERIVATIVE B11 B22 B33 B12 B13 B23
SHIFTS 0.0000 -0.0001 -0.000001 0.000000 0.000001 0.000000 0.000000 0.000000
SD 'S 0.0014 0.0015 0.000013 0.000011 0.000043 0.000007 0.000014 0.000015
RMS isomorphous difference for derivative 3 is 92.62
Number of observations: 6894
RMS anomalous difference for derivative 3 is 24.60
Number of observations: 5652
*****************************************************
*** 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.)
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
-15.6146 0.0000 0.0000
0.0000 -6.1605 0.0000
0.0000 0.0000 -14.9181
Latent roots and vectors of "BETA" -
Vectors are relative to orthogonal axial system parallel to a* cXa* c
LAMBDA 1 -3.90365887
1.000
0.000
0.000 length 1.0000
LAMBDA 2 -3.72952914
0.000
0.000
-1.000 length 1.0000
LAMBDA 3 -1.54011869
0.000
-1.000
0.000 length 1.0000
The equivalent isotropic temperature factor is -2.8196
This gives a spherical temperature "volume" equal to the ellipsoidal "volume",
For derivative : 2
beta matrix - array elements beta11 beta12 beta13
beta21 beta22 beta23,
beta31 beta32 beta33
-1.5381 0.0000 0.0000
0.0000 6.5757 0.0000
0.0000 0.0000 1.8895
Latent roots and vectors of "BETA" -
Vectors are relative to orthogonal axial system parallel to a* cXa* c
LAMBDA 1 -0.38452160
1.000
0.000
0.000 length 1.0000
LAMBDA 2 1.64391494
0.000
-1.000
0.000 length 1.0000
LAMBDA 3 0.47236428
0.000
0.000
1.000 length 1.0000
The equivalent isotropic temperature factor is -0.6684
This gives a spherical temperature "volume" equal to the ellipsoidal "volume",
For derivative : 3
beta matrix - array elements beta11 beta12 beta13
beta21 beta22 beta23,
beta31 beta32 beta33
4.3392 0.0000 0.0000
0.0000 3.0815 0.0000
0.0000 0.0000 -0.9292
Latent roots and vectors of "BETA" -
Vectors are relative to orthogonal axial system parallel to a* cXa* c
LAMBDA 1 1.08479500
1.000
0.000
0.000 length 1.0000
LAMBDA 2 0.77036947
0.000
-1.000
0.000 length 1.0000
LAMBDA 3 -0.23229219
0.000
0.000
1.000 length 1.0000
The equivalent isotropic temperature factor is -0.5791
This gives a spherical temperature "volume" equal to the ellipsoidal "volume",
APPLICATION OF SCALES AND ANALYSIS OF DIFFERENCES
SCALE (F) B11 B22 B33 B12 B13 B23
Derivative 1 0.795 -0.00371 -0.00100 -0.00991 0.00000 0.00000 0.00000
Derivative 2 1.039 -0.00037 0.00107 0.00126 0.00000 0.00000 0.00000
Derivative 3 1.064 0.00103 0.00050 -0.00062 0.00000 0.00000 0.00000
----------------------------------------------------------
----------------------------------------------------------
Isomorphous Differences
Derivative title: FP= FNAT FPH= FHG2 SIGFHG2 DANOHG2 SIGDANOHG2
Differences greater than 3.8323 * RMSDIF are unlikely,
ie acceptable differences are less than 273.50
Maximum difference 307.00
Difference interval for Histogram 36
----------------------------------------------------------
Anomalous Differences
Differences greater than 3.8120 * RMSDIF are unlikely,
ie acceptable differences are less than 242.85
Maximum difference 293.00
Difference interval for Histogram 32
----------------------------------------------------------
----------------------------------------------------------
Isomorphous Differences
Derivative title: FP= FNAT FPH= FPTNCD25 SIGFPTNCD25 DANOPTNCD25 SIGDANOPTNCD25
Differences greater than 3.9807 * RMSDIF are unlikely,
ie acceptable differences are less than 321.65
Maximum difference 468.00
Difference interval for Histogram 40
----------------------------------------------------------
Anomalous Differences
Differences greater than 3.9380 * RMSDIF are unlikely,
ie acceptable differences are less than 82.88
Maximum difference 144.00
Difference interval for Histogram 11
----------------------------------------------------------
----------------------------------------------------------
Isomorphous Differences
Derivative title: FP= FNAT FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
Differences greater than 3.9798 * RMSDIF are unlikely,
ie acceptable differences are less than 368.63
Maximum difference 627.00
Difference interval for Histogram 46
----------------------------------------------------------
Anomalous Differences
Differences greater than 3.9341 * RMSDIF are unlikely,
ie acceptable differences are less than 96.78
Maximum difference 171.00
Difference interval for Histogram 12
************************************************************************************************************************
Large differences (isomorphous & anomalous)
H K L RES FP SIGP FPH1 SIGF1 DPH1 SIGD1 FPH2 SIGF2 DPH2 SIGD2 FPH3 SIGF3 DPH3 SIGD3
0 0 2 0.003 29 88 104 17 -49 41 63 8 0 0 622 9 0 0
=========
0 2 0 0.001 1486 17 1748 11 -104 20 1023 11 0 0 0 0 0 0
=========
0 2 1 0.001 1139 9 978 9 90 17 772 8 0 0 0 0 0 0
=========
0 2 9 0.054 367 7 193 41 0 0 486 3 0 0 887 11 0 0
=========
0 3 8 0.044 13 14 120 58 0 0 362 3 0 0 68 29 0 0
=========
0 5 3 0.010 112 2 225 17 64 34 529 7 0 0 20 18 0 0
=========
0 6 0 0.006 1391 12 1132 11 -15 20 1197 13 0 0 763 9 0 0
=========
0 7 1 0.009 625 12 483 11 -9 23 631 8 0 0 180 3 0 0
=========
0 8 2 0.013 886 12 626 11 45 19 436 7 0 0 892 6 0 0
=========
0 8 6 0.034 292 5 454 11 -2 23 711 3 0 0 182 3 0 0
=========
0 10 9 0.070 145 2 49 219 0 0 175 2 0 0 534 6 0 0
=========
0 12 4 0.034 349 7 357 17 -42 36 718 3 0 0 293 2 0 0
=========
0 13 3 0.034 414 8 341 19 50 42 882 6 0 0 272 6 0 0
=========
1 2 13 0.113 105 2 0 0 0 0 190 2 0 8 48 40 -97 77
=========
1 3 12 0.097 115 2 130 88 0 0 84 6 -8 13 71 37 97 80
=========
1 3 15 0.151 102 2 0 0 0 0 83 10 -12 16 127 34 102 68
=========
1 4 2 0.006 647 6 632 9 -23 17 321 5 -1 9 355 3 9 3
=========
1 9 14 0.144 202 2 0 0 0 0 197 4 2 8 65 45 123 90
=========
1 22 9 0.133 86 2 0 0 0 0 40 29 83 63 193 6 0 11
=========
2 1 0 0.001 782 6 1078 9 -11 17 815 10 0 0 0 0 0 0
=========
2 1 2 0.004 486 10 513 2 -15 9 453 5 3 11 104 3 14 3
=========
2 2 14 0.132 117 2 0 0 0 0 71 8 0 18 68 48 136 93
=========
2 6 13 0.119 266 5 0 0 0 0 255 2 10 5 142 25 104 45
=========
2 15 0 0.038 1002 14 923 11 8 22 705 9 0 0 546 6 0 0
=========
2 18 6 0.078 217 4 314 37 247 171 311 2 -13 2 274 6 2 8
=========
3 0 2 0.005 484 6 531 2 0 9 503 5 0 0 913 6 0 0
=========
3 5 14 0.136 79 2 0 0 0 0 92 10 -14 20 63 56 127 110
=========
3 9 2 0.018 84 1 116 51 -62 125 437 7 -31 12 91 6 54 14
=========
4 1 12 0.100 182 2 163 70 0 0 161 6 8 8 117 31 99 57
=========
4 2 0 0.004 774 6 733 9 20 17 652 8 0 0 1152 9 0 0
=========
4 2 1 0.005 444 6 511 9 17 17 465 5 -23 11 442 3 -158 6
=========
4 3 0 0.005 1167 9 1285 11 93 20 1063 12 0 0 744 9 0 0
=========
4 5 0 0.008 490 10 403 15 9 26 576 7 0 0 86 6 0 0
=========
4 5 1 0.009 800 9 784 9 15 17 857 9 13 19 761 3 112 9
=========
4 14 3 0.042 270 4 297 39 -251 214 366 2 -11 6 271 2 22 6
=========
5 0 10 0.072 513 7 664 16 32 30 873 6 0 0 350 3 0 0
=========
5 1 15 0.156 106 2 0 0 0 0 142 4 -4 12 63 54 119 104
=========
5 2 13 0.119 178 2 0 0 0 0 173 5 10 8 104 25 102 48
=========
5 3 2 0.010 56 1 169 20 -76 43 469 5 -5 12 223 3 18 3
=========
5 4 11 0.089 165 2 189 39 69 90 254 2 -17 6 117 23 -110 40
=========
5 15 0 0.043 7 10 288 30 95 74 168 6 0 0 61 19 0 0
=========
5 19 2 0.067 185 2 332 50 294 394 193 6 31 8 177 6 -8 13
=========
6 0 0 0.009 875 6 963 9 -9 17 846 11 0 0 417 6 0 0
=========
6 0 10 0.075 687 14 706 16 -80 30 556 2 0 0 144 3 0 0
=========
6 3 1 0.011 386 5 355 11 52 24 222 4 23 9 377 3 -114 6
=========
6 10 0 0.025 4 13 187 45 0 0 95 10 0 0 382 2 0 0
=========
7 1 14 0.142 163 2 0 0 0 0 220 4 -4 8 51 47 101 92
=========
7 3 12 0.109 163 2 0 0 0 0 76 5 -23 8 188 14 -112 31
=========
7 7 10 0.086 94 1 277 32 245 286 57 8 -32 17 98 9 0 0
=========
7 23 1 0.099 257 5 331 40 -263 201 215 7 31 15 176 6 0 13
=========
7 23 3 0.104 186 2 0 0 0 0 157 2 36 4 203 8 -98 13
=========
8 0 1 0.016 466 10 465 9 0 17 566 7 0 0 85 9 0 0
=========
8 6 0 0.021 148 4 238 26 0 52 582 7 0 0 71 11 0 0
=========
9 7 12 0.123 112 2 0 0 0 0 84 5 -23 8 88 42 -171 83
=========
9 23 3 0.111 105 2 0 0 0 0 80 23 -144 47 187 6 -2 10
=========
10 6 2 0.032 27 6 175 29 -52 61 43 28 88 53 50 11 -31 22
=========
11 19 2 0.090 236 4 297 61 -268 577 128 8 -2 16 179 6 2 10
=========
12 7 1 0.043 102 2 295 53 -248 262 354 3 18 9 314 2 -11 6
=========
13 3 0 0.042 39 7 346 56 0 0 177 9 0 0 139 8 0 0
=========
13 5 0 0.044 79 4 362 53 0 0 88 18 0 0 28 28 0 0
=========
13 13 3 0.074 197 4 329 45 247 190 261 6 -9 9 285 2 13 8
=========
13 21 7 0.145 40 4 0 0 0 0 62 48 121 91 62 12 -22 26
=========
13 23 4 0.137 132 2 0 0 0 0 57 32 -109 66 104 10 -5 20
=========
14 16 1 0.089 156 4 326 55 -285 440 64 24 48 48 100 8 31 18
=========
14 25 2 0.151 61 2 0 0 0 0 48 33 -92 64 44 19 25 39
=========
15 18 5 0.123 47 4 0 0 0 0 96 18 91 37 171 6 46 12
=========
17 10 4 0.096 52 2 203 50 86 115 42 33 83 69 98 10 0 20
=========
17 12 1 0.093 262 4 377 52 275 196 245 9 -17 13 255 8 -30 12
=========
17 14 6 0.124 135 2 0 0 0 0 82 21 -92 38 134 8 -6 16
=========
17 20 4 0.144 8 12 0 0 0 0 52 41 90 76 95 10 0 19
=========
18 2 2 0.080 118 2 191 46 -51 91 138 14 -94 26 96 10 10 18
=========
18 10 9 0.147 238 2 0 0 0 0 268 5 -23 8 97 20 139 40
=========
18 14 7 0.141 137 2 0 0 0 0 50 37 95 78 12 30 -25 60
=========
18 16 5 0.135 137 2 0 0 0 0 45 33 -88 67 207 8 -15 15
=========
19 2 9 0.140 56 2 0 0 0 0 54 32 -101 65 77 12 -33 23
=========
19 3 7 0.120 79 2 0 0 0 0 51 30 -101 62 178 8 41 12
=========
19 3 10 0.154 78 2 0 0 0 0 51 40 102 76 16 28 30 56
=========
19 5 10 0.156 107 2 0 0 0 0 46 33 88 63 167 6 33 10
=========
19 11 7 0.138 37 4 0 0 0 0 67 23 -74 46 62 30 -125 58
=========
19 12 5 0.126 56 2 0 0 0 0 117 15 49 32 69 45 137 87
=========
20 14 4 0.138 78 2 0 0 0 0 46 38 -86 76 73 15 -5 29
=========
21 8 6 0.139 55 5 0 0 0 0 42 28 87 58 57 17 -32 35
=========
21 14 3 0.143 46 4 0 0 0 0 59 21 36 46 53 34 -103 65
=========
21 14 5 0.153 121 2 0 0 0 0 45 37 89 70 0 34 0 67
=========
22 1 4 0.126 125 4 0 0 0 0 41 33 88 63 209 8 8 17
=========
22 4 1 0.118 97 4 0 0 0 0 106 22 -16 45 51 35 105 64
=========
22 5 6 0.143 214 2 0 0 0 0 64 50 125 98 197 5 -15 10
=========
22 7 7 0.155 38 3 0 0 0 0 49 28 95 59 70 17 -15 34
=========
22 11 1 0.135 293 4 0 0 0 0 219 11 -89 19 214 7 24 15
=========
22 11 2 0.137 37 4 0 0 0 0 87 29 -100 61 139 7 19 15
=========
23 1 3 0.132 18 16 0 0 0 0 63 27 -88 58 75 19 25 39
=========
24 2 1 0.138 64 7 0 0 0 0 43 38 88 79 40 26 12 50
=========
24 4 5 0.156 36 5 0 0 0 0 71 42 -139 82 43 34 0 0
=========
24 6 4 0.153 202 2 0 0 0 0 116 22 90 42 238 7 -5 15
=========
24 7 3 0.151 62 2 0 0 0 0 137 22 -90 44 68 15 30 26
=========
24 9 1 0.151 70 4 0 0 0 0 44 48 -84 92 225 7 -7 15
=========
HEADER INFORMATION FOR OUTPUT MTZ FILE ON INDEX 1
* Title:
Scaling RNAse SA Derivatives (mir tutorial step 1)
* Number of Datasets = 4
* Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
1 RNASE /
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
1.54200
2 RNASE /
DERIV_HG
64.9000 78.3200 38.7900 90.0000 90.0000 90.0000
1.54200
3 RNASE /
DERIV_PT
64.8500 78.5600 39.5100 90.0000 90.0000 90.0000
1.54200
4 RNASE /
DERIV_I
65.0000 78.6600 38.8100 90.0000 90.0000 90.0000
1.54200
* Number of Columns = 18
* Number of Reflections = 7262
* Missing value set to NaN in input mtz file
* Missing value set to NaN in output mtz file
* Column Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Column Types :
H H H F Q F Q D Q F Q D Q F Q D Q I
* Associated datasets :
1 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 1
* Cell Dimensions :
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.16000 ( 49.972 - 2.500 A )
* Sort Order :
1 2 3 0 0
* Space group = P212121 (number 19)
17803 STRUCTURE FACTORS SCALED AND WRITTEN TO OUTPUT FILE
ANALYSES OF SCALE FACTOR ON INTENSITIESAFTER CORRECTION
========================================================
------------------------------------------------------------------------------------------------------------------------
Scaling for derivative no. 1 Derivative title: FP= FNAT FPH= FHG2 SIGFHG2 DANOHG2 SIGDANOHG2
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= FNAT FPH= FHG2 SIGFHG2 DANOHG2 SIGDANOHG2
d -288 -252 -216 -180 -144 -108 -72 -36 0 36 72 108 144 180 216 252 288
15.81 1 1 1 2 4 2 2 5 4 3 6 4 4 0 0 1 0
9.13 0 0 0 3 5 11 27 18 20 20 15 8 5 6 1 1 0
7.07 0 1 1 2 3 19 33 36 38 27 17 6 4 1 0 1 0
5.98 0 0 1 3 4 20 36 49 51 33 14 11 3 1 0 0 0
5.27 0 0 1 1 13 25 36 48 59 39 24 7 1 0 0 0 0
4.77 2 0 0 3 14 19 26 50 68 48 23 18 2 0 0 0 0
4.39 1 1 4 2 5 25 40 59 63 57 24 11 3 1 1 0 0
4.08 0 0 1 1 12 27 32 57 82 48 35 11 6 1 1 0 0
3.83 0 1 2 8 14 17 34 72 90 43 36 9 3 0 0 0 0
3.63 0 0 2 6 21 25 44 65 76 66 29 10 6 0 1 0 0
3.45 0 2 5 6 19 23 51 84 98 55 27 11 1 1 0 0 0
3.30 0 0 3 10 19 31 75 77 96 53 22 1 0 0 0 0 0
3.16 0 1 0 8 25 36 71 103 101 55 12 4 1 0 0 0 0
3.04 0 0 0 3 7 5 18 24 24 12 6 2 0 0 0 0 0
2.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Total 4 7 21 58 165 285 525 747 870 559 290 113 39 11 4 3 0
Anomolous Differences
---------------------
d -256 -224 -192 -160 -128 -96 -64 -32 0 32 64 96 128 160 192 224 256
15.81 0 0 0 0 0 3 4 11 9 10 1 2 0 0 0 0 0
9.13 0 0 0 0 2 2 9 30 58 28 10 1 0 0 0 0 0
7.07 0 0 0 0 1 1 13 31 79 47 15 1 1 0 0 0 0
5.98 0 0 0 0 1 5 18 45 69 55 25 5 2 1 0 0 0
5.27 0 0 0 2 1 9 27 51 81 47 28 5 1 2 0 0 0
4.77 2 0 0 1 2 9 20 59 94 52 19 10 3 0 1 1 0
4.39 0 1 0 2 4 10 31 48 96 49 30 14 7 4 1 0 0
4.08 0 1 1 1 7 12 37 56 106 43 26 15 5 2 0 2 0
3.83 0 1 2 5 4 12 30 54 91 55 38 11 14 8 2 1 1
3.63 0 1 3 7 9 10 37 66 98 52 30 20 10 4 3 0 1
3.45 0 1 1 4 11 19 35 65 97 62 42 19 14 6 3 3 1
3.30 2 0 5 3 13 23 41 56 98 50 45 27 12 7 3 1 1
3.16 2 1 2 4 16 23 54 50 103 69 45 22 16 6 3 0 1
3.04 0 0 1 0 3 6 14 10 28 15 14 7 2 1 0 0 0
2.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Total 6 6 15 29 74 144 370 632 1107 634 368 159 87 41 16 8 5
THE TOTALS 3701. 131445. 0.996 0.977 0.175 0.253 0.010 55.0 307. 3405. 1.4 47.7 293. 2.2178
1
------------------------------------------------------------------------------------------------------------------------
Scaling for derivative no. 2 Derivative title: FP= FNAT FPH= FPTNCD25 SIGFPTNCD25 DANOPTNCD25 SIGDANOPTNCD25
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= FNAT FPH= FPTNCD25 SIGFPTNCD25 DANOPTNCD25 SIGDANOPTNCD25
d -320 -280 -240 -200 -160 -120 -80 -40 0 40 80 120 160 200 240 280 320
15.81 1 1 2 1 2 2 2 7 5 3 3 4 0 1 1 1 3
9.13 2 2 4 7 9 7 16 19 16 24 6 10 3 7 4 1 3
7.07 3 3 7 14 14 19 22 29 24 19 18 8 7 1 1 0 1
5.98 3 5 4 9 14 26 35 44 30 16 18 13 5 2 2 0 0
5.27 3 1 7 13 18 23 26 34 40 34 16 13 4 1 0 1 0
4.77 1 0 8 5 29 15 39 28 45 39 30 15 8 4 2 1 0
4.39 1 1 7 7 9 20 38 54 48 39 33 23 6 4 0 1 0
4.08 1 1 0 4 11 21 40 42 62 54 37 17 11 3 3 1 2
3.83 1 0 2 6 17 23 42 54 58 56 32 21 14 4 2 0 1
3.63 1 1 2 2 11 18 42 52 57 75 44 25 10 9 0 2 0
3.45 0 2 1 4 11 20 44 65 76 74 51 23 12 2 2 0 1
3.30 0 0 1 6 7 28 38 69 67 77 44 27 13 8 2 0 0
3.16 0 0 0 4 9 14 59 75 92 83 44 20 10 1 0 0 0
3.04 0 0 1 0 9 16 44 68 108 77 65 14 12 5 0 0 0
2.94 0 0 0 0 3 19 45 90 108 99 60 15 2 0 0 0 0
2.84 0 0 0 1 1 5 34 88 119 115 60 20 7 2 0 0 0
2.75 0 0 0 0 3 13 43 93 117 106 65 19 2 1 0 0 0
2.67 0 0 0 0 1 9 42 87 145 111 59 18 1 0 0 0 0
2.60 0 0 0 0 0 7 27 106 132 126 55 17 7 0 0 0 0
2.53 0 0 0 0 4 8 37 124 213 159 58 20 3 0 0 0 0
Total 17 17 46 83 182 313 715 1228 1562 1386 798 342 137 55 19 8 11
Anomolous Differences
---------------------
d -88 -77 -66 -55 -44 -33 -22 -11 0 11 22 33 44 55 66 77 88
15.81 0 0 0 0 1 0 3 0 30 1 3 1 0 0 0 0 0
9.13 0 0 0 2 3 2 8 11 79 17 8 5 3 2 0 0 0
7.07 0 0 1 0 4 9 19 21 86 23 11 12 3 1 0 0 0
5.98 0 0 3 1 4 10 21 28 102 27 13 12 3 1 0 1 0
5.27 0 0 0 1 1 9 14 19 102 40 29 14 2 2 0 0 1
4.77 0 1 1 0 1 9 22 39 101 43 27 22 1 1 1 0 0
4.39 0 0 0 2 5 7 12 37 113 53 30 19 8 2 3 0 0
4.08 0 0 1 1 1 11 15 42 116 56 35 21 8 2 0 1 0
3.83 0 0 1 1 4 5 22 48 126 56 40 20 8 2 0 0 0
3.63 0 0 1 2 2 9 23 46 121 69 47 25 4 2 0 0 0
3.45 1 0 0 3 3 6 25 69 123 68 61 17 9 2 1 0 0
3.30 0 1 3 1 1 9 30 62 125 89 46 15 3 1 0 1 0
3.16 0 0 0 1 5 11 21 61 154 89 42 17 4 1 3 1 1
3.04 0 1 2 3 3 10 27 59 163 84 41 15 6 2 2 1 0
2.94 1 0 0 2 6 8 28 51 193 72 53 18 4 3 0 2 0
2.84 1 1 1 3 4 11 25 51 186 86 44 22 6 2 2 6 1
2.75 2 0 0 3 3 13 29 56 207 71 51 12 9 2 0 3 1
2.67 5 2 3 4 7 16 19 57 207 78 47 14 4 5 2 0 3
2.60 1 0 3 5 5 10 33 74 182 86 42 19 4 6 2 1 4
2.53 4 1 3 5 7 16 30 77 247 128 49 26 10 12 4 2 5
Total 15 7 23 40 70 181 426 908 2763 1236 719 326 99 51 20 19 16
THE TOTALS 6919. 90708. 1.056 0.993 0.240 0.382 0.166 60.6 468. 5746. 3.0 15.0 144. 7.4020
1
------------------------------------------------------------------------------------------------------------------------
Scaling for derivative no. 3 Derivative title: FP= FNAT FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
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= FNAT FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
d -368 -322 -276 -230 -184 -138 -92 -46 0 46 92 138 184 230 276 322 368
15.81 1 0 0 0 1 1 2 6 3 5 0 4 1 0 1 0 2
9.13 2 1 1 6 6 13 10 20 18 18 14 10 2 9 3 1 5
7.07 0 0 1 3 9 17 17 28 33 30 21 16 8 4 1 1 1
5.98 1 0 1 5 4 21 21 34 43 36 23 22 7 5 1 0 0
5.27 1 0 1 4 11 15 34 43 36 36 33 25 4 7 2 0 0
4.77 0 1 2 6 6 17 43 46 42 41 32 19 14 2 2 0 2
4.39 0 2 1 4 10 26 30 52 55 51 28 14 17 6 0 0 0
4.08 1 3 2 1 12 22 36 51 55 66 30 18 12 2 2 0 0
3.83 0 1 7 9 9 26 37 62 61 42 44 16 12 4 3 0 0
3.63 1 1 2 8 15 23 44 52 55 56 41 28 15 6 2 3 2
3.45 0 2 2 5 8 26 48 70 75 61 40 35 11 4 2 0 0
3.30 0 0 2 2 10 31 36 71 62 62 57 23 20 6 7 1 0
3.16 0 0 1 2 8 26 62 72 87 66 46 28 17 3 0 0 0
3.04 0 0 0 1 7 24 51 76 90 76 54 33 4 2 2 1 0
2.94 0 0 1 2 7 20 50 98 90 73 72 29 3 3 1 0 0
2.84 0 0 1 2 5 17 51 83 111 103 47 33 5 0 0 1 0
2.75 0 0 0 1 6 16 54 85 124 118 41 15 5 0 0 0 0
2.67 0 0 0 1 2 16 50 98 134 97 50 14 4 0 0 0 0
2.60 0 0 0 0 1 9 45 80 153 122 51 11 6 0 0 0 0
2.53 0 0 0 0 2 14 51 114 156 135 61 18 3 1 1 0 0
Total 7 11 25 62 139 380 772 1241 1483 1294 785 411 170 64 30 8 12
Anomolous Differences
---------------------
d -96 -84 -72 -60 -48 -36 -24 -12 0 12 24 36 48 60 72 84 96
15.81 0 0 0 1 0 2 1 1 19 1 1 0 0 1 0 0 0
9.13 3 1 2 5 4 5 5 12 70 6 6 7 2 3 4 3 1
7.07 0 2 5 3 12 8 10 23 77 21 9 8 9 2 1 0 0
5.98 0 0 0 5 13 8 10 32 95 34 10 7 7 2 0 1 0
5.27 0 3 1 4 10 11 20 27 88 29 34 13 7 4 1 0 0
4.77 0 0 2 8 5 20 24 30 93 40 30 14 4 4 0 1 0
4.39 0 0 0 3 5 14 32 40 109 37 23 19 8 4 2 0 0
4.08 0 0 2 0 7 18 45 44 104 50 25 10 5 2 1 0 0
3.83 0 0 0 1 7 10 28 59 137 42 31 9 6 2 1 0 0
3.63 0 0 0 0 3 11 35 60 128 48 46 13 8 2 0 0 0
3.45 0 0 0 1 4 9 45 67 140 64 42 11 5 0 1 0 0
3.30 1 0 1 3 3 7 42 57 146 57 45 19 6 1 0 2 0
3.16 0 1 0 1 6 20 36 66 156 50 58 15 5 2 0 0 2
3.04 1 0 1 1 3 21 29 53 162 69 44 26 7 3 1 0 0
2.94 2 0 1 2 7 18 42 65 176 67 32 21 10 2 3 1 0
2.84 1 2 0 7 3 13 32 68 179 84 34 18 11 2 2 0 3
2.75 0 1 0 2 3 24 49 71 175 72 41 17 5 2 0 1 2
2.67 1 1 1 2 4 19 50 69 171 67 49 19 4 4 4 0 1
2.60 1 0 2 2 12 24 44 74 168 61 42 23 13 4 3 1 4
2.53 0 2 4 8 10 24 47 93 196 85 42 22 11 4 3 2 3
Total 10 13 22 59 121 286 626 1011 2589 984 644 291 133 50 27 12 16
THE TOTALS 6894. 89995. 1.101 1.008 0.281 0.442 0.170 70.9 627. 5652. 0.2 18.1 171. 7.3796
1
SCALEIT: Normal termination of SCALEIT
Times: User: 0.6s System: 0.0s Elapsed: 0:01
SCALEIT
1###############################################################
###############################################################
###############################################################
### CCP4 4.2: SCALEIT version 4.2 : 07/08/02##
###############################################################
User: mgwt Run date: 24/ 6/03 Run time:13:24:25
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--- refine isotropic
Data line--- LABIN FP=FNAT SIGFP=SIGFNAT FPH1=FHG2 SIGFPH1=SIGFHG2 DPH1=DANOHG2 SIGDPH1=SIGDANOHG2
FP=
FP= FNAT
FP= FNAT FPH= FHG2 SIGFHG2
Comment line--- ## This script run with the command ##########
Comment line--- # scaleit HKLIN /y/people/mgwt/TEST/rnase25_scaleit1.mtz HKLOUT /y/people/mgwt/work/2003test_32_3_mtz.tmp
Comment line--- ################################################
Input MTZ File
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: HKLIN Filename: /y/people/mgwt/TEST/rnase25_scaleit1.mtz
HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 1
* Title:
Scaling RNAse SA Derivatives (mir tutorial step 1).
* Number of Datasets = 4
* Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
1 RNASE /
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
1.54200
2 RNASE /
DERIV_HG
64.9000 78.3200 38.7900 90.0000 90.0000 90.0000
1.54200
3 RNASE /
DERIV_PT
64.8500 78.5600 39.5100 90.0000 90.0000 90.0000
1.54200
4 RNASE /
DERIV_I
65.0000 78.6600 38.8100 90.0000 90.0000 90.0000
1.54200
* Number of Columns = 18
* Number of Reflections = 7262
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Column Types :
H H H F Q F Q D Q F Q D Q F Q D Q I
* Associated datasets :
1 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 1
* Cell Dimensions :
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.16000 ( 50.000 - 2.500 A )
* Sort Order :
1 2 3 0 0
* Space group = P212121 (number 19)
* Input Program Labels :
H K L FP SIGFP FPH1 SIGFPH1 DPH1 SIGDPH1 FPH1(+) SIGFPH1(+) FPH1(-) SIGFPH1(-)
IMEAN1 SIGIMEAN1 I1(+) SIGI1(+) I1(-) SIGI1(-)
* Input File Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Lookup Table : the number indicates the input column no.
* Array element n corresponds to the nth program label
1 2 3 4 5 6 7 8 9 0 0 0 0 0 0
0 0 0 0
Centric Zone 1 Reflections of Type 0kl
Centric Zone 2 Reflections of Type h0l
Centric Zone 3 Reflections of Type hk0
Output File
(Q)QOPEN: file opened on unit 2 Status: UNKNOWN
Logical Name: HKLOUT Filename: /y/people/mgwt/work/2003test_32_3_mtz.tmp
SPACE GROUP NUMBER 19
SPACE GROUP NAME P212121
POINT GROUP NAME PG222
NUMBER OF SYMMETRY OPERATORS 4
NUMBER OF PRIMITIVE SYMMETRY OPERATORS 4
ISOTROPIC DERIVATIVE TO NATIVE SCALING
========================================
Position of Native F 4
Position of Derivative F 6
Number of Cycles 4
Convergence Limit 0.001000
Derivative has Anomalous Difference to be Scaled
Derivative: FP= FNAT FPH= FHG2 SIGFHG2 DANOHG2 SIGDANOHG2
Initial derivative scale factor (for F) = 0.9772 from 3701 reflections
The isotropic scale is applied to the derivative F as
(derivative scale)* exp( - B (sin theta/lambda)**2)
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) : 1332717972.71639 FOR 3701 REFLECTIONS
SCALES (for F)
NATIVE DERIVATIVE B11
SHIFTS 0.0000 0.0000 -0.000068
SD 'S 0.0019 0.0019 0.280580
RMS isomorphous difference for derivative 1 is 71.11
Number of observations: 3701
RMS anomalous difference for derivative 1 is 63.49
Number of observations: 3405
APPLICATION OF SCALES AND ANALYSIS OF DIFFERENCES
SCALE (F) B11
Derivative 1 0.997 0.11230
----------------------------------------------------------
----------------------------------------------------------
Isomorphous Differences
Derivative title: FP= FNAT FPH= FHG2 SIGFHG2 DANOHG2 SIGDANOHG2
Differences greater than 3.8323 * RMSDIF are unlikely,
ie acceptable differences are less than 272.51
Maximum difference 306.00
Difference interval for Histogram 36
----------------------------------------------------------
Anomalous Differences
Differences greater than 3.8120 * RMSDIF are unlikely,
ie acceptable differences are less than 242.02
Maximum difference 292.00
Difference interval for Histogram 32
1 sort keys, in columns 8
************************************************************************************************************************
Large differences (isomorphous & anomalous)
H K L RES FP SIGP FPH1 SIGF1 DPH1 SIGD1
2 1 0 0.001 782 6 1074 9 -11 17
=========
2 18 6 0.078 217 4 313 37 247 170
=========
4 14 3 0.042 270 4 296 39 -250 213
=========
5 15 0 0.043 7 10 287 30 95 74
=========
5 19 2 0.067 185 2 331 50 293 392
=========
7 7 10 0.086 94 1 276 32 244 285
=========
7 23 1 0.099 257 5 329 40 -262 200
=========
11 19 2 0.090 236 4 296 61 -267 575
=========
12 7 1 0.043 102 2 294 52 -247 261
=========
13 3 0 0.042 39 7 345 56 0 0
=========
13 5 0 0.044 79 4 361 53 0 0
=========
13 13 3 0.074 197 4 328 45 246 190
=========
14 16 1 0.089 156 4 325 55 -284 439
=========
17 12 1 0.093 262 4 375 51 274 196
=========
HEADER INFORMATION FOR OUTPUT MTZ FILE ON INDEX 1
* Title:
Scaling RNAse SA Derivatives (mir tutorial step 1).
* Number of Datasets = 4
* Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
1 RNASE /
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
1.54200
2 RNASE /
DERIV_HG
64.9000 78.3200 38.7900 90.0000 90.0000 90.0000
1.54200
3 RNASE /
DERIV_PT
64.8500 78.5600 39.5100 90.0000 90.0000 90.0000
1.54200
4 RNASE /
DERIV_I
65.0000 78.6600 38.8100 90.0000 90.0000 90.0000
1.54200
* Number of Columns = 18
* Number of Reflections = 7262
* Missing value set to NaN in input mtz file
* Missing value set to NaN in output mtz file
* Column Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Column Types :
H H H F Q F Q D Q F Q D Q F Q D Q I
* Associated datasets :
1 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 1
* Cell Dimensions :
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.16000 ( 49.972 - 2.500 A )
* Sort Order :
1 2 3 0 0
* Space group = P212121 (number 19)
3766 STRUCTURE FACTORS SCALED AND WRITTEN TO OUTPUT FILE
ANALYSES OF SCALE FACTOR ON INTENSITIESAFTER CORRECTION
========================================================
3701 records passed to sort
2917 acentric, 784 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) 784 3.833 1.044 1375.2 496 2.517 1.090 1.9
Total (acen) 2917 2.592 0.411 1132.6 1843 2.049 0.444 3.5
------------------------------------------------------------------------------------------------------------------------
Scaling for derivative no. 1 Derivative title: FP= FNAT FPH= FHG2 SIGFHG2 DANOHG2 SIGDANOHG2
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= FNAT FPH= FHG2 SIGFHG2 DANOHG2 SIGDANOHG2
d -288 -252 -216 -180 -144 -108 -72 -36 0 36 72 108 144 180 216 252 288
15.81 1 1 1 2 4 2 2 5 4 2 7 4 3 1 0 1 0
9.13 0 0 0 3 4 12 27 18 19 20 16 8 5 6 0 2 0
7.07 0 1 1 2 3 18 33 37 36 29 17 5 5 1 0 1 0
5.98 0 0 1 2 4 21 35 48 52 33 15 11 3 1 0 0 0
5.27 0 0 1 1 13 25 34 48 59 40 25 7 1 0 0 0 0
4.77 2 0 0 3 13 19 27 50 64 50 24 19 2 0 0 0 0
4.39 1 1 3 3 4 24 41 58 63 59 24 11 3 1 1 0 0
4.08 0 0 1 1 11 26 32 59 77 52 35 12 6 1 1 0 0
3.83 0 1 2 8 13 16 34 73 89 45 35 10 3 0 0 0 0
3.63 0 0 2 5 22 24 44 62 79 66 30 10 6 0 1 0 0
3.45 0 2 5 6 18 20 49 87 98 56 28 12 1 1 0 0 0
3.30 0 0 3 10 19 30 75 72 100 54 23 1 0 0 0 0 0
3.16 0 1 0 8 24 35 72 101 103 56 12 4 1 0 0 0 0
3.04 0 0 0 2 7 5 19 24 24 11 7 2 0 0 0 0 0
2.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Total 4 7 20 56 159 277 524 742 867 573 298 116 39 12 3 4 0
Anomolous Differences
---------------------
d -256 -224 -192 -160 -128 -96 -64 -32 0 32 64 96 128 160 192 224 256
15.81 0 0 0 0 0 3 4 11 9 10 1 2 0 0 0 0 0
9.13 0 0 0 0 2 2 9 30 58 28 10 1 0 0 0 0 0
7.07 0 0 0 0 1 1 13 31 79 47 15 1 1 0 0 0 0
5.98 0 0 0 0 1 5 18 45 69 55 25 5 2 1 0 0 0
5.27 0 0 0 2 1 9 27 51 81 48 27 5 1 2 0 0 0
4.77 2 0 0 1 2 9 20 59 94 52 19 10 3 0 1 1 0
4.39 0 1 0 2 4 9 32 48 96 49 30 14 7 4 1 0 0
4.08 0 1 1 1 7 12 37 56 106 43 26 15 5 2 0 2 0
3.83 0 1 2 5 4 12 29 55 92 54 38 11 14 8 2 1 1
3.63 0 1 3 7 9 10 37 66 98 53 29 20 10 4 3 0 1
3.45 0 1 1 4 11 18 35 66 97 64 40 19 14 6 3 3 1
3.30 2 0 5 3 13 23 41 56 98 50 45 27 12 7 3 1 1
3.16 2 0 3 4 16 23 54 50 103 70 44 23 16 5 3 0 1
3.04 0 0 1 0 3 6 14 10 28 15 14 7 2 1 0 0 0
2.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Total 6 5 16 29 74 142 370 634 1108 638 363 160 87 40 16 8 5
THE TOTALS 3701. 131445. 0.999 0.980 0.175 0.252 0.010 54.8 306. 3405. 1.4 47.5 292. 2.2171
1
SCALEIT: Normal termination of SCALEIT
Times: User: 0.1s System: 0.0s Elapsed: 0:01
SCALEIT
1###############################################################
###############################################################
###############################################################
### CCP4 4.2: SCALEIT version 4.2 : 07/08/02##
###############################################################
User: mgwt Run date: 24/ 6/03 Run time:13:24:26
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--- refine isotropic
Data line--- LABIN FP=FNAT SIGFP=SIGFNAT FPH1=FPTNCD25 SIGFPH1=SIGFPTNCD25 DPH1=DANOPTNCD25 SIGDPH1=SIGDANOPTNCD25
FP=
FP= FNAT
FP= FNAT FPH= FPTNCD25 SIGFPTNCD25
Comment line--- ## This script run with the command ##########
Comment line--- # scaleit HKLIN /y/people/mgwt/TEST/rnase25_scaleit1.mtz HKLOUT /y/people/mgwt/work/2003test_32_3_mtz.tmp
Comment line--- ################################################
Input MTZ File
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: HKLIN Filename: /y/people/mgwt/TEST/rnase25_scaleit1.mtz
HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 1
* Title:
Scaling RNAse SA Derivatives (mir tutorial step 1).
* Number of Datasets = 4
* Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
1 RNASE /
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
1.54200
2 RNASE /
DERIV_HG
64.9000 78.3200 38.7900 90.0000 90.0000 90.0000
1.54200
3 RNASE /
DERIV_PT
64.8500 78.5600 39.5100 90.0000 90.0000 90.0000
1.54200
4 RNASE /
DERIV_I
65.0000 78.6600 38.8100 90.0000 90.0000 90.0000
1.54200
* Number of Columns = 18
* Number of Reflections = 7262
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Column Types :
H H H F Q F Q D Q F Q D Q F Q D Q I
* Associated datasets :
1 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 1
* Cell Dimensions :
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.16000 ( 50.000 - 2.500 A )
* Sort Order :
1 2 3 0 0
* Space group = P212121 (number 19)
* Input Program Labels :
H K L FP SIGFP FPH1 SIGFPH1 DPH1 SIGDPH1 FPH1(+) SIGFPH1(+) FPH1(-) SIGFPH1(-)
IMEAN1 SIGIMEAN1 I1(+) SIGI1(+) I1(-) SIGI1(-)
* Input File Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Lookup Table : the number indicates the input column no.
* Array element n corresponds to the nth program label
1 2 3 4 5 10 11 12 13 0 0 0 0 0 0
0 0 0 0
Centric Zone 1 Reflections of Type 0kl
Centric Zone 2 Reflections of Type h0l
Centric Zone 3 Reflections of Type hk0
Output File
(Q)QOPEN: file opened on unit 2 Status: UNKNOWN
Logical Name: HKLOUT Filename: /y/people/mgwt/work/2003test_32_3_mtz.tmp
SPACE GROUP NUMBER 19
SPACE GROUP NAME P212121
POINT GROUP NAME PG222
NUMBER OF SYMMETRY OPERATORS 4
NUMBER OF PRIMITIVE SYMMETRY OPERATORS 4
ISOTROPIC DERIVATIVE TO NATIVE SCALING
========================================
Position of Native F 4
Position of Derivative F 10
Number of Cycles 4
Convergence Limit 0.001000
Derivative has Anomalous Difference to be Scaled
Derivative: FP= FNAT FPH= FPTNCD25 SIGFPTNCD25 DANOPTNCD25 SIGDANOPTNCD25
Initial derivative scale factor (for F) = 0.9928 from 6919 reflections
The isotropic scale is applied to the derivative F as
(derivative scale)* exp( - B (sin theta/lambda)**2)
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) : 1909721308.99882 FOR 6919 REFLECTIONS
SCALES (for F)
NATIVE DERIVATIVE B11
SHIFTS 0.0000 0.0000 -0.000656
SD 'S 0.0022 0.0023 0.283852
RMS isomorphous difference for derivative 1 is 80.92
Number of observations: 6919
RMS anomalous difference for derivative 1 is 20.98
Number of observations: 5746
APPLICATION OF SCALES AND ANALYSIS OF DIFFERENCES
SCALE (F) B11
Derivative 1 1.005 1.38403
----------------------------------------------------------
----------------------------------------------------------
Isomorphous Differences
Derivative title: FP= FNAT FPH= FPTNCD25 SIGFPTNCD25 DANOPTNCD25 SIGDANOPTNCD25
Differences greater than 3.9807 * RMSDIF are unlikely,
ie acceptable differences are less than 322.11
Maximum difference 470.00
Difference interval for Histogram 40
----------------------------------------------------------
Anomalous Differences
Differences greater than 3.9380 * RMSDIF are unlikely,
ie acceptable differences are less than 82.62
Maximum difference 143.00
Difference interval for Histogram 10
1 sort keys, in columns 8
************************************************************************************************************************
Large differences (isomorphous & anomalous)
H K L RES FP SIGP FPH1 SIGF1 DPH1 SIGD1
0 2 0 0.001 1486 17 1029 11 0 0
=========
0 2 1 0.001 1139 9 776 8 0 0
=========
0 3 8 0.044 13 14 362 3 0 0
=========
0 5 3 0.010 112 2 532 7 0 0
=========
0 8 2 0.013 886 12 437 7 0 0
=========
0 8 6 0.034 292 5 712 3 0 0
=========
0 12 4 0.034 349 7 719 3 0 0
=========
0 13 3 0.034 414 8 884 6 0 0
=========
1 4 2 0.006 647 6 322 5 -1 10
=========
3 9 2 0.018 84 1 439 7 -32 12
=========
5 0 10 0.072 513 7 873 6 0 0
=========
5 3 2 0.010 56 1 471 5 -5 12
=========
8 6 0 0.021 148 4 584 7 0 0
=========
9 23 3 0.111 105 2 80 23 -144 47
=========
10 6 2 0.032 27 6 44 28 89 53
=========
13 21 7 0.145 40 4 62 47 120 91
=========
13 23 4 0.137 132 2 56 32 -109 66
=========
14 25 2 0.151 61 2 47 33 -91 63
=========
15 18 5 0.123 47 4 96 18 90 36
=========
17 10 4 0.096 52 2 42 33 83 68
=========
17 14 6 0.124 135 2 81 21 -91 38
=========
17 20 4 0.144 8 12 52 40 89 75
=========
18 2 2 0.080 118 2 137 14 -94 26
=========
18 14 7 0.141 137 2 49 37 94 77
=========
18 16 5 0.135 137 2 45 32 -87 67
=========
19 2 9 0.140 56 2 54 32 -101 64
=========
19 3 7 0.120 79 2 51 30 -100 62
=========
19 3 10 0.154 78 2 50 40 101 76
=========
19 5 10 0.156 107 2 45 33 87 62
=========
20 14 4 0.138 78 2 46 38 -86 75
=========
21 8 6 0.139 55 5 41 28 86 58
=========
21 14 5 0.153 121 2 45 37 89 70
=========
22 1 4 0.126 125 4 41 33 87 63
=========
22 5 6 0.143 214 2 63 50 124 98
=========
22 7 7 0.155 38 3 49 28 94 58
=========
22 11 1 0.135 293 4 218 11 -89 19
=========
22 11 2 0.137 37 4 86 28 -99 60
=========
23 1 3 0.132 18 16 63 27 -87 58
=========
24 2 1 0.138 64 7 43 38 87 79
=========
24 4 5 0.156 36 5 70 42 -138 81
=========
24 6 4 0.153 202 2 115 21 89 42
=========
24 7 3 0.151 62 2 136 21 -89 44
=========
24 9 1 0.151 70 4 44 47 -83 91
=========
HEADER INFORMATION FOR OUTPUT MTZ FILE ON INDEX 1
* Title:
Scaling RNAse SA Derivatives (mir tutorial step 1).
* Number of Datasets = 4
* Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
1 RNASE /
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
1.54200
2 RNASE /
DERIV_HG
64.9000 78.3200 38.7900 90.0000 90.0000 90.0000
1.54200
3 RNASE /
DERIV_PT
64.8500 78.5600 39.5100 90.0000 90.0000 90.0000
1.54200
4 RNASE /
DERIV_I
65.0000 78.6600 38.8100 90.0000 90.0000 90.0000
1.54200
* Number of Columns = 18
* Number of Reflections = 7262
* Missing value set to NaN in input mtz file
* Missing value set to NaN in output mtz file
* Column Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Column Types :
H H H F Q F Q D Q F Q D Q F Q D Q I
* Associated datasets :
1 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 1
* Cell Dimensions :
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.16000 ( 49.972 - 2.500 A )
* Sort Order :
1 2 3 0 0
* Space group = P212121 (number 19)
7041 STRUCTURE FACTORS SCALED AND WRITTEN TO OUTPUT FILE
ANALYSES OF SCALE FACTOR ON INTENSITIESAFTER CORRECTION
========================================================
6919 records passed to sort
5759 acentric, 1160 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) 1160 13.068 3.430 18942.8 732 9.523 1.825 334.0
Total (acen) 5759 12.991 0.609 66660.3 3639 9.453 -0.390 444.1
------------------------------------------------------------------------------------------------------------------------
Scaling for derivative no. 1 Derivative title: FP= FNAT FPH= FPTNCD25 SIGFPTNCD25 DANOPTNCD25 SIGDANOPTNCD25
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= FNAT FPH= FPTNCD25 SIGFPTNCD25 DANOPTNCD25 SIGDANOPTNCD25
d -320 -280 -240 -200 -160 -120 -80 -40 0 40 80 120 160 200 240 280 320
15.81 1 1 2 1 2 2 2 7 6 2 3 4 0 1 1 1 3
9.13 2 2 4 7 9 7 17 19 17 23 6 9 3 7 4 1 3
7.07 3 4 6 15 13 22 19 31 22 20 17 8 7 1 1 0 1
5.98 3 5 4 9 15 26 34 44 30 16 18 13 5 2 2 0 0
5.27 3 1 7 13 18 24 27 32 41 33 17 12 4 1 0 1 0
4.77 1 0 8 5 30 16 38 27 46 38 30 16 7 4 2 1 0
4.39 1 1 8 6 9 22 36 55 48 38 33 23 6 4 0 1 0
4.08 1 1 0 4 11 21 40 42 62 54 37 17 11 3 3 1 2
3.83 1 0 2 6 17 23 42 54 58 56 32 21 14 4 2 0 1
3.63 1 1 2 2 11 17 43 52 55 75 46 25 10 9 0 2 0
3.45 0 1 2 4 11 20 43 64 77 75 51 23 12 2 2 0 1
3.30 0 0 1 6 7 28 37 70 66 77 45 27 13 8 2 0 0
3.16 0 0 0 4 9 14 58 75 91 82 45 22 10 1 0 0 0
3.04 0 0 1 0 7 18 42 70 106 76 68 14 12 5 0 0 0
2.94 0 0 0 0 3 19 41 93 106 101 59 17 2 0 0 0 0
2.84 0 0 0 1 1 5 33 85 122 115 60 21 7 2 0 0 0
2.75 0 0 0 0 2 13 43 92 117 107 65 20 2 1 0 0 0
2.67 0 0 0 0 1 9 37 92 140 114 61 18 1 0 0 0 0
2.60 0 0 0 0 0 6 27 104 132 126 56 19 7 0 0 0 0
2.53 0 0 0 0 3 7 37 121 211 162 61 21 3 0 0 0 0
Total 17 17 47 83 179 319 696 1229 1553 1390 810 350 136 55 19 8 11
Anomolous Differences
---------------------
d -80 -70 -60 -50 -40 -30 -20 -10 0 10 20 30 40 50 60 70 80
15.81 0 0 0 1 0 1 2 0 30 1 1 2 1 0 0 0 0
9.13 0 0 1 2 2 3 8 13 73 14 13 4 4 3 0 0 0
7.07 0 0 1 1 4 14 17 20 81 25 7 15 2 2 1 0 0
5.98 0 2 1 2 7 8 21 31 92 28 12 13 6 1 1 0 1
5.27 0 0 1 1 0 10 19 13 102 28 34 20 1 2 2 0 1
4.77 0 2 0 1 2 13 21 34 101 38 27 23 5 1 1 0 0
4.39 0 0 1 3 6 6 12 35 113 44 34 20 11 3 2 1 0
4.08 0 0 1 1 3 13 12 41 116 53 31 21 11 6 0 0 1
3.83 0 1 1 1 4 5 22 47 126 56 32 22 10 5 1 0 0
3.63 0 1 1 2 4 10 20 45 121 67 40 30 7 3 0 0 0
3.45 1 0 3 0 3 10 29 61 123 66 60 16 8 6 1 1 0
3.30 1 1 2 2 2 11 32 57 122 88 44 15 6 2 1 1 0
3.16 0 0 0 3 4 12 23 61 149 83 44 18 8 0 3 1 2
3.04 1 2 0 4 4 10 28 58 160 76 43 20 5 5 1 2 0
2.94 1 0 1 2 6 9 29 48 193 67 49 24 6 2 2 2 0
2.84 2 0 4 2 6 10 26 47 186 77 47 25 5 4 2 6 3
2.75 2 0 0 4 4 17 25 54 207 63 53 18 6 4 1 2 2
2.67 5 5 0 4 10 19 17 53 207 71 48 15 7 6 2 1 3
2.60 1 1 4 6 4 16 31 68 182 77 45 21 7 3 6 1 4
2.53 5 2 2 5 10 13 35 71 247 116 55 26 13 11 6 2 7
Total 19 17 24 47 85 210 429 857 2731 1138 719 368 129 69 33 20 24
THE TOTALS 6919. 90708. 1.057 0.993 0.241 0.383 0.166 60.7 470. 5746. 3.0 15.0 143. 7.4347
1
SCALEIT: Normal termination of SCALEIT
Times: User: 0.1s System: 0.0s Elapsed: 0:00
SCALEIT
1###############################################################
###############################################################
###############################################################
### CCP4 4.2: SCALEIT version 4.2 : 07/08/02##
###############################################################
User: mgwt Run date: 24/ 6/03 Run time:13:24:26
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--- refine isotropic
Data line--- LABIN FP=FNAT SIGFP=SIGFNAT FPH1=FIOD25 SIGFPH1=SIGFIOD25 DPH1=DANOIOD25 SIGDPH1=SIGDANOIOD25
FP=
FP= FNAT
FP= FNAT FPH= FIOD25 SIGFIOD25
Comment line--- ## This script run with the command ##########
Comment line--- # scaleit HKLIN /y/people/mgwt/TEST/rnase25_scaleit1.mtz HKLOUT /y/people/mgwt/work/2003test_32_3_mtz.tmp
Comment line--- ################################################
Input MTZ File
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: HKLIN Filename: /y/people/mgwt/TEST/rnase25_scaleit1.mtz
HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 1
* Title:
Scaling RNAse SA Derivatives (mir tutorial step 1).
* Number of Datasets = 4
* Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
1 RNASE /
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
1.54200
2 RNASE /
DERIV_HG
64.9000 78.3200 38.7900 90.0000 90.0000 90.0000
1.54200
3 RNASE /
DERIV_PT
64.8500 78.5600 39.5100 90.0000 90.0000 90.0000
1.54200
4 RNASE /
DERIV_I
65.0000 78.6600 38.8100 90.0000 90.0000 90.0000
1.54200
* Number of Columns = 18
* Number of Reflections = 7262
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Column Types :
H H H F Q F Q D Q F Q D Q F Q D Q I
* Associated datasets :
1 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 1
* Cell Dimensions :
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.16000 ( 50.000 - 2.500 A )
* Sort Order :
1 2 3 0 0
* Space group = P212121 (number 19)
* Input Program Labels :
H K L FP SIGFP FPH1 SIGFPH1 DPH1 SIGDPH1 FPH1(+) SIGFPH1(+) FPH1(-) SIGFPH1(-)
IMEAN1 SIGIMEAN1 I1(+) SIGI1(+) I1(-) SIGI1(-)
* Input File Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Lookup Table : the number indicates the input column no.
* Array element n corresponds to the nth program label
1 2 3 4 5 14 15 16 17 0 0 0 0 0 0
0 0 0 0
Centric Zone 1 Reflections of Type 0kl
Centric Zone 2 Reflections of Type h0l
Centric Zone 3 Reflections of Type hk0
Output File
(Q)QOPEN: file opened on unit 2 Status: UNKNOWN
Logical Name: HKLOUT Filename: /y/people/mgwt/work/2003test_32_3_mtz.tmp
SPACE GROUP NUMBER 19
SPACE GROUP NAME P212121
POINT GROUP NAME PG222
NUMBER OF SYMMETRY OPERATORS 4
NUMBER OF PRIMITIVE SYMMETRY OPERATORS 4
ISOTROPIC DERIVATIVE TO NATIVE SCALING
========================================
Position of Native F 4
Position of Derivative F 14
Number of Cycles 4
Convergence Limit 0.001000
Derivative has Anomalous Difference to be Scaled
Derivative: FP= FNAT FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
Initial derivative scale factor (for F) = 1.0078 from 6894 reflections
The isotropic scale is applied to the derivative F as
(derivative scale)* exp( - B (sin theta/lambda)**2)
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) : 2299159130.67643 FOR 6894 REFLECTIONS
SCALES (for F)
NATIVE DERIVATIVE B11
SHIFTS 0.0000 0.0000 -0.000588
SD 'S 0.0027 0.0028 0.333836
RMS isomorphous difference for derivative 1 is 92.72
Number of observations: 6894
RMS anomalous difference for derivative 1 is 24.61
Number of observations: 5652
APPLICATION OF SCALES AND ANALYSIS OF DIFFERENCES
SCALE (F) B11
Derivative 1 1.008 1.32800
----------------------------------------------------------
----------------------------------------------------------
Isomorphous Differences
Derivative title: FP= FNAT FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
Differences greater than 3.9798 * RMSDIF are unlikely,
ie acceptable differences are less than 369.02
Maximum difference 621.00
Difference interval for Histogram 46
----------------------------------------------------------
Anomalous Differences
Differences greater than 3.9341 * RMSDIF are unlikely,
ie acceptable differences are less than 96.83
Maximum difference 170.00
Difference interval for Histogram 12
1 sort keys, in columns 8
************************************************************************************************************************
Large differences (isomorphous & anomalous)
H K L RES FP SIGP FPH1 SIGF1 DPH1 SIGD1
0 0 2 0.003 29 88 627 9 0 0
=========
0 2 9 0.054 367 7 890 11 0 0
=========
0 6 0 0.006 1391 12 769 9 0 0
=========
0 7 1 0.009 625 12 182 3 0 0
=========
0 10 9 0.070 145 2 535 6 0 0
=========
1 2 13 0.113 105 2 48 40 -97 77
=========
1 3 12 0.097 115 2 71 37 97 80
=========
1 3 15 0.151 102 2 127 34 102 68
=========
1 9 14 0.144 202 2 65 45 123 89
=========
2 1 2 0.004 486 10 105 3 14 3
=========
2 2 14 0.132 117 2 68 48 136 93
=========
2 6 13 0.119 266 5 142 25 104 45
=========
2 15 0 0.038 1002 14 549 6 0 0
=========
3 0 2 0.005 484 6 920 6 0 0
=========
3 5 14 0.136 79 2 63 56 126 110
=========
4 1 12 0.100 182 2 117 31 99 57
=========
4 2 0 0.004 774 6 1161 9 0 0
=========
4 2 1 0.005 444 6 446 3 -159 6
=========
4 3 0 0.005 1167 9 750 9 0 0
=========
4 5 0 0.008 490 10 86 6 0 0
=========
4 5 1 0.009 800 9 766 3 113 9
=========
5 1 15 0.156 106 2 62 54 118 103
=========
5 2 13 0.119 178 2 104 25 101 48
=========
5 4 11 0.089 165 2 117 23 -110 40
=========
6 0 0 0.009 875 6 420 6 0 0
=========
6 0 10 0.075 687 14 144 3 0 0
=========
6 3 1 0.011 386 5 379 3 -115 6
=========
6 10 0 0.025 4 13 384 2 0 0
=========
7 1 14 0.142 163 2 51 47 100 92
=========
7 3 12 0.109 163 2 188 14 -112 31
=========
7 23 3 0.104 186 2 203 8 -98 13
=========
8 0 1 0.016 466 10 85 9 0 0
=========
9 7 12 0.123 112 2 88 41 -171 83
=========
18 10 9 0.147 238 2 96 20 139 40
=========
19 11 7 0.138 37 4 62 30 -125 57
=========
19 12 5 0.126 56 2 69 45 136 87
=========
21 14 3 0.143 46 4 53 34 -103 65
=========
22 4 1 0.118 97 4 51 35 105 64
=========
HEADER INFORMATION FOR OUTPUT MTZ FILE ON INDEX 1
* Title:
Scaling RNAse SA Derivatives (mir tutorial step 1).
* Number of Datasets = 4
* Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
1 RNASE /
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
1.54200
2 RNASE /
DERIV_HG
64.9000 78.3200 38.7900 90.0000 90.0000 90.0000
1.54200
3 RNASE /
DERIV_PT
64.8500 78.5600 39.5100 90.0000 90.0000 90.0000
1.54200
4 RNASE /
DERIV_I
65.0000 78.6600 38.8100 90.0000 90.0000 90.0000
1.54200
* Number of Columns = 18
* Number of Reflections = 7262
* Missing value set to NaN in input mtz file
* Missing value set to NaN in output mtz file
* Column Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Column Types :
H H H F Q F Q D Q F Q D Q F Q D Q I
* Associated datasets :
1 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 1
* Cell Dimensions :
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.16000 ( 49.972 - 2.500 A )
* Sort Order :
1 2 3 0 0
* Space group = P212121 (number 19)
6996 STRUCTURE FACTORS SCALED AND WRITTEN TO OUTPUT FILE
ANALYSES OF SCALE FACTOR ON INTENSITIESAFTER CORRECTION
========================================================
6894 records passed to sort
5718 acentric, 1176 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) 1176 12.497 0.950 13613.5 744 8.941 0.181 135.7
Total (acen) 5718 14.639 1.391 89967.9 3614 10.869 0.150 819.9
------------------------------------------------------------------------------------------------------------------------
Scaling for derivative no. 1 Derivative title: FP= FNAT FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
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= FNAT FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
d -368 -322 -276 -230 -184 -138 -92 -46 0 46 92 138 184 230 276 322 368
15.81 1 0 0 0 1 1 2 6 3 5 0 4 1 0 1 0 2
9.13 2 1 1 6 7 13 10 21 16 20 12 10 4 7 4 0 5
7.07 0 0 1 3 10 18 15 28 34 31 19 16 8 4 1 1 1
5.98 1 0 2 4 4 22 21 35 42 35 23 22 7 5 1 0 0
5.27 1 0 1 4 11 19 32 41 37 35 34 24 6 5 2 0 0
4.77 0 1 2 7 5 18 43 46 41 42 33 17 14 2 2 0 2
4.39 0 2 1 4 11 28 27 54 54 50 29 13 17 6 0 0 0
4.08 1 3 2 2 11 22 39 48 56 65 31 17 12 2 2 0 0
3.83 0 1 8 8 9 26 40 60 61 43 43 15 12 4 3 0 0
3.63 1 1 2 8 15 23 44 53 55 56 41 27 15 6 2 3 2
3.45 0 2 2 5 8 26 48 71 75 60 40 35 11 4 2 0 0
3.30 0 0 2 2 10 31 37 71 61 63 56 23 20 6 7 1 0
3.16 0 0 1 2 8 26 62 72 87 66 46 28 17 3 0 0 0
3.04 0 0 0 1 7 24 51 75 90 77 53 34 4 2 2 1 0
2.94 0 0 1 2 6 21 50 98 90 73 71 29 4 3 1 0 0
2.84 0 0 1 2 5 16 51 83 112 102 48 33 5 0 0 1 0
2.75 0 0 0 1 6 15 53 83 126 119 42 15 5 0 0 0 0
2.67 0 0 0 1 2 16 49 96 137 95 52 14 4 0 0 0 0
2.60 0 0 0 0 1 9 45 79 153 122 52 11 6 0 0 0 0
2.53 0 0 0 0 1 15 48 113 156 137 63 18 3 1 1 0 0
Total 7 11 27 62 138 389 767 1233 1486 1296 788 405 175 60 31 7 12
Anomolous Differences
---------------------
d -96 -84 -72 -60 -48 -36 -24 -12 0 12 24 36 48 60 72 84 96
15.81 0 0 0 1 0 2 1 1 19 1 1 0 0 1 0 0 0
9.13 3 1 3 4 4 5 5 12 70 6 6 7 2 3 4 3 1
7.07 0 2 5 6 9 8 10 23 77 21 9 8 8 3 1 0 0
5.98 0 0 0 6 12 8 10 32 95 34 10 7 5 4 0 1 0
5.27 0 3 1 5 9 11 20 27 88 29 34 13 7 4 1 0 0
4.77 0 0 2 8 5 20 24 30 93 40 30 14 4 4 0 1 0
4.39 0 0 0 3 5 15 31 40 109 37 23 19 7 4 3 0 0
4.08 0 0 2 1 6 19 44 45 103 50 25 10 4 3 1 0 0
3.83 0 0 0 1 7 10 28 60 135 43 30 10 5 3 1 0 0
3.63 0 0 0 0 3 11 35 61 127 48 46 13 8 2 0 0 0
3.45 0 0 0 1 4 9 45 67 140 64 42 11 5 0 1 0 0
3.30 1 0 1 3 3 7 42 57 146 57 45 19 6 1 0 2 0
3.16 0 1 0 1 6 20 36 66 156 50 58 15 5 2 0 0 2
3.04 1 0 1 1 3 21 29 53 162 69 44 26 7 3 1 0 0
2.94 2 0 1 2 7 18 42 65 176 67 32 21 10 2 3 1 0
2.84 1 2 0 7 3 13 32 68 180 83 34 18 11 2 2 0 3
2.75 0 1 0 2 3 24 48 72 175 72 41 17 5 2 0 1 2
2.67 1 1 1 2 4 19 50 69 171 67 49 19 5 3 4 0 1
2.60 1 0 1 3 12 24 43 75 169 61 41 23 13 4 3 1 4
2.53 0 2 4 8 10 24 47 93 197 85 42 21 11 4 3 2 3
Total 10 13 22 65 115 288 622 1016 2588 984 642 291 128 54 28 12 16
THE TOTALS 6894. 89995. 1.098 1.006 0.282 0.443 0.171 70.9 621. 5652. 0.2 18.1 170. 7.3852
1
SCALEIT: Normal termination of SCALEIT
Times: User: 0.2s System: 0.0s Elapsed: 0:00
SCALEIT
1###############################################################
###############################################################
###############################################################
### CCP4 4.2: SCALEIT version 4.2 : 07/08/02##
###############################################################
User: mgwt Run date: 24/ 6/03 Run time:13:24:26
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--- refine isotropic
Data line--- LABIN FP=FHG2 SIGFP=SIGFHG2 FPH1=FPTNCD25 SIGFPH1=SIGFPTNCD25 DPH1=DANOPTNCD25 SIGDPH1=SIGDANOPTNCD25
FP=
FP= FHG2
FP= FHG2 FPH= FPTNCD25 SIGFPTNCD25
Comment line--- ## This script run with the command ##########
Comment line--- # scaleit HKLIN /y/people/mgwt/TEST/rnase25_scaleit1.mtz HKLOUT /y/people/mgwt/work/2003test_32_3_mtz.tmp
Comment line--- ################################################
Input MTZ File
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: HKLIN Filename: /y/people/mgwt/TEST/rnase25_scaleit1.mtz
HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 1
* Title:
Scaling RNAse SA Derivatives (mir tutorial step 1).
* Number of Datasets = 4
* Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
1 RNASE /
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
1.54200
2 RNASE /
DERIV_HG
64.9000 78.3200 38.7900 90.0000 90.0000 90.0000
1.54200
3 RNASE /
DERIV_PT
64.8500 78.5600 39.5100 90.0000 90.0000 90.0000
1.54200
4 RNASE /
DERIV_I
65.0000 78.6600 38.8100 90.0000 90.0000 90.0000
1.54200
* Number of Columns = 18
* Number of Reflections = 7262
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Column Types :
H H H F Q F Q D Q F Q D Q F Q D Q I
* Associated datasets :
1 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 1
* Cell Dimensions :
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.16000 ( 50.000 - 2.500 A )
* Sort Order :
1 2 3 0 0
* Space group = P212121 (number 19)
* Input Program Labels :
H K L FP SIGFP FPH1 SIGFPH1 DPH1 SIGDPH1 FPH1(+) SIGFPH1(+) FPH1(-) SIGFPH1(-)
IMEAN1 SIGIMEAN1 I1(+) SIGI1(+) I1(-) SIGI1(-)
* Input File Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Lookup Table : the number indicates the input column no.
* Array element n corresponds to the nth program label
1 2 3 6 7 10 11 12 13 0 0 0 0 0 0
0 0 0 0
Centric Zone 1 Reflections of Type 0kl
Centric Zone 2 Reflections of Type h0l
Centric Zone 3 Reflections of Type hk0
Output File
(Q)QOPEN: file opened on unit 2 Status: UNKNOWN
Logical Name: HKLOUT Filename: /y/people/mgwt/work/2003test_32_3_mtz.tmp
SPACE GROUP NUMBER 19
SPACE GROUP NAME P212121
POINT GROUP NAME PG222
NUMBER OF SYMMETRY OPERATORS 4
NUMBER OF PRIMITIVE SYMMETRY OPERATORS 4
ISOTROPIC DERIVATIVE TO NATIVE SCALING
========================================
Position of Native F 6
Position of Derivative F 10
Number of Cycles 4
Convergence Limit 0.001000
Derivative has Anomalous Difference to be Scaled
Derivative: FP= FHG2 FPH= FPTNCD25 SIGFPTNCD25 DANOPTNCD25 SIGDANOPTNCD25
Initial derivative scale factor (for F) = 1.0034 from 3674 reflections
The isotropic scale is applied to the derivative F as
(derivative scale)* exp( - B (sin theta/lambda)**2)
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) : 3490589261.56753 FOR 3674 REFLECTIONS
SCALES (for F)
NATIVE DERIVATIVE B11
SHIFTS 0.0000 0.0000 -0.002125
SD 'S 0.0033 0.0033 0.470080
RMS isomorphous difference for derivative 1 is 97.08
Number of observations: 3674
RMS anomalous difference for derivative 1 is 20.01
Number of observations: 2890
APPLICATION OF SCALES AND ANALYSIS OF DIFFERENCES
SCALE (F) B11
Derivative 1 1.022 5.90556
----------------------------------------------------------
----------------------------------------------------------
Isomorphous Differences
Derivative title: FP= FHG2 FPH= FPTNCD25 SIGFPTNCD25 DANOPTNCD25 SIGDANOPTNCD25
Differences greater than 3.8306 * RMSDIF are unlikely,
ie acceptable differences are less than 371.87
Maximum difference 701.00
Difference interval for Histogram 49
----------------------------------------------------------
Anomalous Differences
Differences greater than 3.7718 * RMSDIF are unlikely,
ie acceptable differences are less than 75.49
Maximum difference 93.00
Difference interval for Histogram 10
1 sort keys, in columns 8
************************************************************************************************************************
Large differences (isomorphous & anomalous)
H K L RES FP SIGP FPH1 SIGF1 DPH1 SIGD1
0 1 1 0.001 1500 9 1084 13 0 0
=========
0 2 0 0.001 1748 11 1046 11 0 0
=========
0 13 3 0.034 341 19 891 6 0 0
=========
5 11 1 0.026 162 40 40 30 81 60
=========
5 16 3 0.054 268 35 113 11 77 19
=========
10 6 2 0.032 175 29 44 28 89 53
=========
17 9 5 0.098 190 48 39 30 76 63
=========
17 10 4 0.096 203 50 41 33 82 68
=========
17 11 2 0.091 283 65 41 39 -77 77
=========
18 2 2 0.080 191 46 137 14 -93 26
=========
HEADER INFORMATION FOR OUTPUT MTZ FILE ON INDEX 1
* Title:
Scaling RNAse SA Derivatives (mir tutorial step 1).
* Number of Datasets = 4
* Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
1 RNASE /
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
1.54200
2 RNASE /
DERIV_HG
64.9000 78.3200 38.7900 90.0000 90.0000 90.0000
1.54200
3 RNASE /
DERIV_PT
64.8500 78.5600 39.5100 90.0000 90.0000 90.0000
1.54200
4 RNASE /
DERIV_I
65.0000 78.6600 38.8100 90.0000 90.0000 90.0000
1.54200
* Number of Columns = 18
* Number of Reflections = 7262
* Missing value set to NaN in input mtz file
* Missing value set to NaN in output mtz file
* Column Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Column Types :
H H H F Q F Q D Q F Q D Q F Q D Q I
* Associated datasets :
1 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 1
* Cell Dimensions :
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.16000 ( 49.972 - 2.500 A )
* Sort Order :
1 2 3 0 0
* Space group = P212121 (number 19)
7041 STRUCTURE FACTORS SCALED AND WRITTEN TO OUTPUT FILE
ANALYSES OF SCALE FACTOR ON INTENSITIESAFTER CORRECTION
========================================================
3674 records passed to sort
2892 acentric, 782 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) 782 5.837 -0.145 2792.3 494 3.483 -0.464 18.3
Total (acen) 2892 4.151 -0.189 2525.2 1828 3.123 -0.440 12.1
------------------------------------------------------------------------------------------------------------------------
Scaling for derivative no. 1 Derivative title: FP= FHG2 FPH= FPTNCD25 SIGFPTNCD25 DANOPTNCD25 SIGDANOPTNCD25
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= FHG2 FPH= FPTNCD25 SIGFPTNCD25 DANOPTNCD25 SIGDANOPTNCD25
d -392 -343 -294 -245 -196 -147 -98 -49 0 49 98 147 196 245 294 343 392
15.81 0 0 0 0 2 3 6 8 6 6 3 1 1 1 0 0 2
9.13 0 0 3 4 3 14 20 18 30 18 15 7 6 0 1 1 0
7.07 0 2 1 4 19 15 19 40 28 25 25 5 6 0 0 0 0
5.98 0 2 1 2 16 23 34 38 42 34 21 11 1 0 0 1 0
5.27 2 0 0 7 10 19 33 41 37 45 27 11 2 0 0 0 0
4.77 0 0 0 3 12 20 36 48 48 42 26 28 3 0 0 0 0
4.39 0 0 1 2 11 16 38 52 53 45 47 15 8 3 1 0 0
4.08 0 0 1 5 5 18 29 63 64 55 36 32 15 4 0 0 0
3.83 0 0 0 1 4 20 22 65 76 65 51 16 10 3 0 0 0
3.63 0 0 1 0 5 15 23 50 83 69 47 38 15 3 2 0 0
3.45 0 0 1 1 3 10 24 55 88 98 64 27 10 2 0 1 0
3.30 0 0 0 1 1 5 21 54 75 82 78 46 12 8 0 0 0
3.16 0 0 0 0 1 5 25 44 105 117 57 42 13 1 0 0 0
3.04 0 0 0 0 0 1 3 16 17 33 17 10 3 0 0 0 0
2.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Total 2 4 9 30 92 184 333 592 752 734 514 289 105 25 4 3 2
Anomolous Differences
---------------------
d -80 -70 -60 -50 -40 -30 -20 -10 0 10 20 30 40 50 60 70 80
15.81 0 0 0 1 0 1 2 0 30 1 1 2 1 0 0 0 0
9.13 0 0 1 2 2 3 8 13 73 13 14 4 4 2 1 0 0
7.07 0 0 1 1 4 14 17 20 80 24 8 15 2 2 1 0 0
5.98 0 2 1 2 7 8 21 31 92 28 11 14 6 1 1 0 1
5.27 0 0 1 1 0 10 19 13 102 28 34 20 1 2 2 0 1
4.77 0 2 0 1 2 13 20 34 100 37 27 23 5 1 1 0 0
4.39 0 0 1 3 7 5 12 35 113 43 35 21 11 3 2 1 0
4.08 0 0 1 1 3 12 12 41 128 54 33 21 13 7 0 0 1
3.83 0 1 1 1 4 5 22 45 128 56 32 22 10 5 1 0 0
3.63 0 1 1 1 4 9 20 46 121 68 41 29 7 3 0 0 0
3.45 1 0 2 1 3 10 29 59 121 66 60 16 9 5 1 1 0
3.30 1 1 2 2 2 11 32 57 120 87 44 14 6 2 1 1 0
3.16 0 0 0 2 4 13 23 60 149 84 43 18 8 0 3 1 2
3.04 0 0 0 0 0 2 11 18 34 23 8 2 1 1 0 0 0
2.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Total 2 7 12 19 42 116 248 472 1391 612 391 221 84 34 14 4 5
THE TOTALS 3674. 143490. 1.049 1.001 0.225 0.365 0.020 76.3 701. 2890. 3.4 15.1 93. 9.4646
1
SCALEIT: Normal termination of SCALEIT
Times: User: 0.1s System: 0.0s Elapsed: 0:00
SCALEIT
1###############################################################
###############################################################
###############################################################
### CCP4 4.2: SCALEIT version 4.2 : 07/08/02##
###############################################################
User: mgwt Run date: 24/ 6/03 Run time:13:24:27
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--- refine isotropic
Data line--- LABIN FP=FHG2 SIGFP=SIGFHG2 FPH1=FIOD25 SIGFPH1=SIGFIOD25 DPH1=DANOIOD25 SIGDPH1=SIGDANOIOD25
FP=
FP= FHG2
FP= FHG2 FPH= FIOD25 SIGFIOD25
Comment line--- ## This script run with the command ##########
Comment line--- # scaleit HKLIN /y/people/mgwt/TEST/rnase25_scaleit1.mtz HKLOUT /y/people/mgwt/work/2003test_32_3_mtz.tmp
Comment line--- ################################################
Input MTZ File
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: HKLIN Filename: /y/people/mgwt/TEST/rnase25_scaleit1.mtz
HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 1
* Title:
Scaling RNAse SA Derivatives (mir tutorial step 1).
* Number of Datasets = 4
* Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
1 RNASE /
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
1.54200
2 RNASE /
DERIV_HG
64.9000 78.3200 38.7900 90.0000 90.0000 90.0000
1.54200
3 RNASE /
DERIV_PT
64.8500 78.5600 39.5100 90.0000 90.0000 90.0000
1.54200
4 RNASE /
DERIV_I
65.0000 78.6600 38.8100 90.0000 90.0000 90.0000
1.54200
* Number of Columns = 18
* Number of Reflections = 7262
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Column Types :
H H H F Q F Q D Q F Q D Q F Q D Q I
* Associated datasets :
1 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 1
* Cell Dimensions :
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.16000 ( 50.000 - 2.500 A )
* Sort Order :
1 2 3 0 0
* Space group = P212121 (number 19)
* Input Program Labels :
H K L FP SIGFP FPH1 SIGFPH1 DPH1 SIGDPH1 FPH1(+) SIGFPH1(+) FPH1(-) SIGFPH1(-)
IMEAN1 SIGIMEAN1 I1(+) SIGI1(+) I1(-) SIGI1(-)
* Input File Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Lookup Table : the number indicates the input column no.
* Array element n corresponds to the nth program label
1 2 3 6 7 14 15 16 17 0 0 0 0 0 0
0 0 0 0
Centric Zone 1 Reflections of Type 0kl
Centric Zone 2 Reflections of Type h0l
Centric Zone 3 Reflections of Type hk0
Output File
(Q)QOPEN: file opened on unit 2 Status: UNKNOWN
Logical Name: HKLOUT Filename: /y/people/mgwt/work/2003test_32_3_mtz.tmp
SPACE GROUP NUMBER 19
SPACE GROUP NAME P212121
POINT GROUP NAME PG222
NUMBER OF SYMMETRY OPERATORS 4
NUMBER OF PRIMITIVE SYMMETRY OPERATORS 4
ISOTROPIC DERIVATIVE TO NATIVE SCALING
========================================
Position of Native F 6
Position of Derivative F 14
Number of Cycles 4
Convergence Limit 0.001000
Derivative has Anomalous Difference to be Scaled
Derivative: FP= FHG2 FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
Initial derivative scale factor (for F) = 1.0260 from 3704 reflections
The isotropic scale is applied to the derivative F as
(derivative scale)* exp( - B (sin theta/lambda)**2)
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) : 4703327517.47677 FOR 3704 REFLECTIONS
SCALES (for F)
NATIVE DERIVATIVE B11
SHIFTS 0.0000 0.0001 0.005656
SD 'S 0.0045 0.0044 0.612661
RMS isomorphous difference for derivative 1 is 119.93
Number of observations: 3704
RMS anomalous difference for derivative 1 is 24.91
Number of observations: 2900
APPLICATION OF SCALES AND ANALYSIS OF DIFFERENCES
SCALE (F) B11
Derivative 1 0.981 -5.07756
----------------------------------------------------------
----------------------------------------------------------
Isomorphous Differences
Derivative title: FP= FHG2 FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
Differences greater than 3.8325 * RMSDIF are unlikely,
ie acceptable differences are less than 459.64
Maximum difference 692.00
Difference interval for Histogram 60
----------------------------------------------------------
Anomalous Differences
Differences greater than 3.7727 * RMSDIF are unlikely,
ie acceptable differences are less than 94.00
Maximum difference 155.00
Difference interval for Histogram 12
1 sort keys, in columns 8
************************************************************************************************************************
Large differences (isomorphous & anomalous)
H K L RES FP SIGP FPH1 SIGF1 DPH1 SIGD1
0 0 2 0.003 104 17 610 9 0 0
=========
0 2 9 0.054 193 41 885 11 0 0
=========
0 10 9 0.070 49 219 535 6 0 0
=========
1 3 12 0.097 130 88 72 37 98 80
=========
4 1 12 0.100 163 70 118 32 101 57
=========
4 2 1 0.005 511 9 435 2 -155 6
=========
4 3 0 0.005 1285 11 731 9 0 0
=========
4 5 1 0.009 784 9 748 2 110 9
=========
5 4 11 0.089 189 39 118 23 -111 40
=========
6 0 0 0.009 963 9 410 6 0 0
=========
6 0 10 0.075 706 16 145 3 0 0
=========
6 3 1 0.011 355 11 370 2 -112 6
=========
HEADER INFORMATION FOR OUTPUT MTZ FILE ON INDEX 1
* Title:
Scaling RNAse SA Derivatives (mir tutorial step 1).
* Number of Datasets = 4
* Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
1 RNASE /
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
1.54200
2 RNASE /
DERIV_HG
64.9000 78.3200 38.7900 90.0000 90.0000 90.0000
1.54200
3 RNASE /
DERIV_PT
64.8500 78.5600 39.5100 90.0000 90.0000 90.0000
1.54200
4 RNASE /
DERIV_I
65.0000 78.6600 38.8100 90.0000 90.0000 90.0000
1.54200
* Number of Columns = 18
* Number of Reflections = 7262
* Missing value set to NaN in input mtz file
* Missing value set to NaN in output mtz file
* Column Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Column Types :
H H H F Q F Q D Q F Q D Q F Q D Q I
* Associated datasets :
1 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 1
* Cell Dimensions :
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.16000 ( 49.972 - 2.500 A )
* Sort Order :
1 2 3 0 0
* Space group = P212121 (number 19)
6996 STRUCTURE FACTORS SCALED AND WRITTEN TO OUTPUT FILE
ANALYSES OF SCALE FACTOR ON INTENSITIESAFTER CORRECTION
========================================================
3704 records passed to sort
2927 acentric, 777 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) 777 7.751 -2.241 13343.9 491 4.050 -1.642 21.0
Total (acen) 2927 5.506 -0.918 15196.9 1849 3.805 -0.670 22.4
------------------------------------------------------------------------------------------------------------------------
Scaling for derivative no. 1 Derivative title: FP= FHG2 FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
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= FHG2 FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
d -480 -420 -360 -300 -240 -180 -120 -60 0 60 120 180 240 300 360 420 480
15.81 1 0 0 0 1 1 2 2 7 2 4 4 1 1 0 1 0
9.13 0 1 5 2 3 8 15 16 20 20 24 11 4 5 3 0 2
7.07 0 0 0 1 4 6 17 33 34 48 17 16 9 1 2 1 0
5.98 0 0 0 3 4 9 22 30 44 51 34 20 2 3 2 0 0
5.27 0 0 2 1 4 13 18 35 44 60 48 20 4 3 0 0 0
4.77 0 0 0 0 5 17 24 52 55 51 39 19 8 1 1 0 0
4.39 0 0 1 4 6 6 35 48 63 63 38 19 10 1 1 2 0
4.08 1 1 0 1 11 17 35 49 76 65 43 17 7 5 2 0 0
3.83 0 0 1 5 11 13 33 52 72 67 41 26 10 1 1 0 0
3.63 1 0 0 1 8 22 34 58 56 76 55 18 14 9 1 0 1
3.45 0 0 0 2 3 13 41 59 83 77 69 25 10 2 0 1 0
3.30 0 0 1 0 3 10 29 53 75 87 65 32 22 8 1 0 0
3.16 0 0 1 1 1 10 39 62 85 92 75 38 11 1 0 0 0
3.04 0 0 0 0 2 2 7 12 19 25 24 7 1 1 0 0 0
2.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Total 3 2 11 21 66 147 351 561 733 784 576 272 113 42 14 5 3
Anomolous Differences
---------------------
d -96 -84 -72 -60 -48 -36 -24 -12 0 12 24 36 48 60 72 84 96
15.81 0 0 0 1 0 2 1 1 19 1 1 0 0 1 0 0 0
9.13 3 1 2 3 6 5 5 12 70 6 6 7 2 3 4 3 1
7.07 0 2 5 3 9 11 10 23 76 21 9 9 8 2 1 0 0
5.98 0 0 0 5 11 10 10 32 95 34 10 7 7 2 0 1 0
5.27 0 3 0 5 8 13 20 27 88 29 34 13 7 4 1 0 0
4.77 0 0 2 8 5 20 24 29 92 40 30 14 3 4 0 1 0
4.39 0 0 0 3 5 14 33 39 110 37 23 19 8 4 2 0 0
4.08 0 0 2 0 8 17 47 47 116 48 27 10 5 2 1 0 0
3.83 0 0 0 1 7 10 28 57 138 41 33 9 6 2 1 0 0
3.63 0 0 0 0 2 11 35 60 127 49 46 14 8 2 0 0 0
3.45 0 0 0 1 4 9 44 67 137 64 42 11 5 0 1 0 0
3.30 1 0 1 3 3 8 41 57 142 58 41 22 6 1 0 2 0
3.16 0 1 0 1 6 19 39 67 150 50 59 14 6 2 0 0 2
3.04 0 0 1 1 1 6 10 14 35 17 5 7 2 1 0 0 0
2.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2.53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Total 4 7 13 35 75 155 347 532 1395 495 366 156 73 30 11 7 3
THE TOTALS 3704. 140668. 1.117 1.028 0.279 0.451 0.027 94.0 692. 2900. -0.3 18.9 155. 9.2299
1
SCALEIT: Normal termination of SCALEIT
Times: User: 0.2s System: 0.0s Elapsed: 0:01
SCALEIT
1###############################################################
###############################################################
###############################################################
### CCP4 4.2: SCALEIT version 4.2 : 07/08/02##
###############################################################
User: mgwt Run date: 24/ 6/03 Run time:13:24:27
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--- refine isotropic
Data line--- LABIN FP=FPTNCD25 SIGFP=SIGFPTNCD25 FPH1=FIOD25 SIGFPH1=SIGFIOD25 DPH1=DANOIOD25 SIGDPH1=SIGDANOIOD25
FP=
FP= FPTNCD25
FP= FPTNCD25 FPH= FIOD25 SIGFIOD25
Comment line--- ## This script run with the command ##########
Comment line--- # scaleit HKLIN /y/people/mgwt/TEST/rnase25_scaleit1.mtz HKLOUT /y/people/mgwt/work/2003test_32_3_mtz.tmp
Comment line--- ################################################
Input MTZ File
(Q)QOPEN: file opened on unit 1 Status: READONLY
Logical Name: HKLIN Filename: /y/people/mgwt/TEST/rnase25_scaleit1.mtz
HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 1
* Title:
Scaling RNAse SA Derivatives (mir tutorial step 1).
* Number of Datasets = 4
* Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
1 RNASE /
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
1.54200
2 RNASE /
DERIV_HG
64.9000 78.3200 38.7900 90.0000 90.0000 90.0000
1.54200
3 RNASE /
DERIV_PT
64.8500 78.5600 39.5100 90.0000 90.0000 90.0000
1.54200
4 RNASE /
DERIV_I
65.0000 78.6600 38.8100 90.0000 90.0000 90.0000
1.54200
* Number of Columns = 18
* Number of Reflections = 7262
* Missing value set to NaN in input mtz file
* Column Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Column Types :
H H H F Q F Q D Q F Q D Q F Q D Q I
* Associated datasets :
1 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 1
* Cell Dimensions :
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.16000 ( 50.000 - 2.500 A )
* Sort Order :
1 2 3 0 0
* Space group = P212121 (number 19)
* Input Program Labels :
H K L FP SIGFP FPH1 SIGFPH1 DPH1 SIGDPH1 FPH1(+) SIGFPH1(+) FPH1(-) SIGFPH1(-)
IMEAN1 SIGIMEAN1 I1(+) SIGI1(+) I1(-) SIGI1(-)
* Input File Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Lookup Table : the number indicates the input column no.
* Array element n corresponds to the nth program label
1 2 3 10 11 14 15 16 17 0 0 0 0 0 0
0 0 0 0
Centric Zone 1 Reflections of Type 0kl
Centric Zone 2 Reflections of Type h0l
Centric Zone 3 Reflections of Type hk0
Output File
(Q)QOPEN: file opened on unit 2 Status: UNKNOWN
Logical Name: HKLOUT Filename: /y/people/mgwt/work/2003test_32_3_mtz.tmp
SPACE GROUP NUMBER 19
SPACE GROUP NAME P212121
POINT GROUP NAME PG222
NUMBER OF SYMMETRY OPERATORS 4
NUMBER OF PRIMITIVE SYMMETRY OPERATORS 4
ISOTROPIC DERIVATIVE TO NATIVE SCALING
========================================
Position of Native F 10
Position of Derivative F 14
Number of Cycles 4
Convergence Limit 0.001000
Derivative has Anomalous Difference to be Scaled
Derivative: FP= FPTNCD25 FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
Initial derivative scale factor (for F) = 1.0172 from 6781 reflections
The isotropic scale is applied to the derivative F as
(derivative scale)* exp( - B (sin theta/lambda)**2)
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) : 3579516833.86808 FOR 6781 REFLECTIONS
SCALES (for F)
NATIVE DERIVATIVE B11
SHIFTS 0.0000 -0.0002 -0.015954
SD 'S 0.0034 0.0035 0.425319
RMS isomorphous difference for derivative 1 is 115.28
Number of observations: 6781
RMS anomalous difference for derivative 1 is 24.36
Number of observations: 5603
APPLICATION OF SCALES AND ANALYSIS OF DIFFERENCES
SCALE (F) B11
Derivative 1 1.039 8.25809
----------------------------------------------------------
----------------------------------------------------------
Isomorphous Differences
Derivative title: FP= FPTNCD25 FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
Differences greater than 3.9757 * RMSDIF are unlikely,
ie acceptable differences are less than 458.32
Maximum difference 604.00
Difference interval for Histogram 58
----------------------------------------------------------
Anomalous Differences
Differences greater than 3.9320 * RMSDIF are unlikely,
ie acceptable differences are less than 95.78
Maximum difference 166.00
Difference interval for Histogram 12
1 sort keys, in columns 8
************************************************************************************************************************
Large differences (isomorphous & anomalous)
H K L RES FP SIGP FPH1 SIGF1 DPH1 SIGD1
0 0 2 0.003 63 8 645 9 0 0
=========
0 5 3 0.010 529 7 21 18 0 0
=========
0 5 10 0.071 568 2 66 29 0 0
=========
0 6 8 0.048 866 3 405 3 0 0
=========
0 8 0 0.010 589 8 121 9 0 0
=========
0 8 2 0.013 436 7 920 6 0 0
=========
0 8 6 0.034 711 3 186 3 0 0
=========
0 13 3 0.034 882 6 277 6 0 0
=========
1 3 12 0.097 84 6 70 36 96 79
=========
1 3 15 0.151 83 10 122 33 98 65
=========
1 9 14 0.144 197 4 62 43 119 87
=========
2 2 14 0.132 71 8 66 47 132 91
=========
2 6 13 0.119 255 2 139 25 102 44
=========
3 5 14 0.136 92 10 61 55 123 107
=========
4 1 12 0.100 161 6 116 31 98 56
=========
4 2 0 0.004 652 8 1194 9 0 0
=========
4 2 1 0.005 465 5 459 3 -164 7
=========
4 5 0 0.008 576 7 89 7 0 0
=========
4 5 1 0.009 857 9 787 3 116 9
=========
5 0 10 0.072 873 6 350 3 0 0
=========
5 1 15 0.156 142 4 60 52 114 100
=========
5 2 13 0.119 173 5 102 24 99 47
=========
5 4 11 0.089 254 2 116 22 -109 40
=========
6 3 1 0.011 222 4 389 3 -118 6
=========
7 1 14 0.142 220 4 49 46 97 89
=========
7 3 12 0.109 76 5 184 13 -110 31
=========
7 23 3 0.104 157 2 200 8 -97 12
=========
8 0 1 0.016 566 7 87 9 0 0
=========
8 6 0 0.021 582 7 73 11 0 0
=========
9 7 12 0.123 84 5 86 41 -167 81
=========
10 0 2 0.026 533 7 34 20 0 0
=========
18 10 9 0.147 268 5 93 19 134 39
=========
19 11 7 0.138 67 23 60 29 -121 56
=========
19 12 5 0.126 117 15 68 44 133 85
=========
21 14 3 0.143 59 21 51 33 -100 63
=========
22 4 1 0.118 106 22 50 34 103 62
=========
HEADER INFORMATION FOR OUTPUT MTZ FILE ON INDEX 1
* Title:
Scaling RNAse SA Derivatives (mir tutorial step 1).
* Number of Datasets = 4
* Dataset ID, project/crystal name, dataset name, cell dimensions, wavelength:
1 RNASE /
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
1.54200
2 RNASE /
DERIV_HG
64.9000 78.3200 38.7900 90.0000 90.0000 90.0000
1.54200
3 RNASE /
DERIV_PT
64.8500 78.5600 39.5100 90.0000 90.0000 90.0000
1.54200
4 RNASE /
DERIV_I
65.0000 78.6600 38.8100 90.0000 90.0000 90.0000
1.54200
* Number of Columns = 18
* Number of Reflections = 7262
* Missing value set to NaN in input mtz file
* Missing value set to NaN in output mtz file
* Column Labels :
H K L FNAT SIGFNAT FHG2 SIGFHG2 DANOHG2 SIGDANOHG2 FPTNCD25 SIGFPTNCD25
DANOPTNCD25 SIGDANOPTNCD25 FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25 FreeR_flag
* Column Types :
H H H F Q F Q D Q F Q D Q F Q D Q I
* Associated datasets :
1 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 4 1
* Cell Dimensions :
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.16000 ( 49.972 - 2.500 A )
* Sort Order :
1 2 3 0 0
* Space group = P212121 (number 19)
6996 STRUCTURE FACTORS SCALED AND WRITTEN TO OUTPUT FILE
ANALYSES OF SCALE FACTOR ON INTENSITIESAFTER CORRECTION
========================================================
6781 records passed to sort
5664 acentric, 1117 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) 1117 16.197 -2.679 55917.4 705 9.967 -1.480 194.9
Total (acen) 5664 17.953 -0.408 131275.8 3578 11.488 -0.135 971.0
------------------------------------------------------------------------------------------------------------------------
Scaling for derivative no. 1 Derivative title: FP= FPTNCD25 FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
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= FPTNCD25 FPH= FIOD25 SIGFIOD25 DANOIOD25 SIGDANOIOD25
d -464 -406 -348 -290 -232 -174 -116 -58 0 58 116 174 232 290 348 406 464
15.81 1 0 0 0 1 1 0 5 5 6 1 3 1 1 1 1 0
9.13 4 1 2 6 3 6 12 21 26 14 16 5 10 5 1 3 4
7.07 1 0 3 3 3 5 13 34 29 29 26 19 14 3 5 2 1
5.98 0 0 1 5 12 8 13 24 37 44 34 22 12 3 5 2 2
5.27 0 0 1 5 7 14 23 32 30 36 34 21 11 11 4 1 3
4.77 0 1 2 5 9 14 31 43 48 45 24 14 15 11 6 0 0
4.39 0 1 1 4 9 8 44 53 57 43 27 21 11 5 4 2 1
4.08 0 2 4 7 12 26 35 62 51 45 41 28 5 6 0 1 1
3.83 0 0 4 4 14 22 50 43 75 56 34 14 13 4 4 0 0
3.63 0 0 7 7 17 20 46 50 62 51 50 23 14 1 2 1 3
3.45 0 0 1 4 14 23 45 68 82 57 43 38 11 1 1 1 0
3.30 0 1 2 1 14 21 46 72 69 55 50 28 19 7 0 1 0
3.16 0 0 0 3 15 12 46 68 95 85 54 19 7 6 0 0 0
3.04 0 0 0 1 7 25 48 82 88 76 57 20 8 2 0 0 0
2.94 0 0 0 0 6 14 54 76 111 89 62 17 9 2 0 0 0
2.84 0 0 0 2 8 21 37 94 122 101 44 15 4 0 0 0 0
2.75 0 0 1 1 5 15 36 102 144 87 49 10 1 0 0 0 0
2.67 0 0 0 0 2 12 41 117 141 91 41 9 1 0 0 0 0
2.60 0 0 0 0 0 13 32 104 162 101 39 13 1 0 0 0 0
2.53 0 0 0 0 0 9 36 115 192 114 46 16 6 0 0 0 0
Total 6 6 29 58 158 289 688 1265 1626 1225 772 355 173 68 33 15 15
Anomolous Differences
---------------------
d -96 -84 -72 -60 -48 -36 -24 -12 0 12 24 36 48 60 72 84 96
15.81 0 0 0 1 0 2 2 0 19 1 1 0 0 1 0 0 0
9.13 4 1 2 4 5 4 9 8 70 5 7 7 2 3 4 3 1
7.07 0 3 4 7 8 8 16 17 77 13 17 8 8 3 1 0 0
5.98 0 0 1 5 12 8 13 29 95 30 14 7 3 6 0 1 0
5.27 0 3 1 4 10 9 20 22 82 28 33 8 7 5 1 0 0
4.77 0 0 2 8 5 18 24 29 90 40 30 12 5 4 0 1 0
4.39 0 0 0 2 5 14 32 42 105 36 23 18 7 4 3 0 0
4.08 0 0 2 1 7 19 43 49 111 49 27 10 4 3 1 0 0
3.83 0 0 0 1 7 10 27 60 137 44 32 10 5 3 1 0 0
3.63 0 0 0 0 3 11 35 60 127 48 46 14 8 2 0 0 0
3.45 0 0 0 1 4 9 45 66 140 65 43 10 5 0 1 0 0
3.30 1 0 1 3 2 8 40 56 147 55 45 19 6 1 0 2 0
3.16 0 1 0 1 5 19 35 67 152 49 57 15 6 1 0 0 2
3.04 1 0 1 0 4 20 28 52 160 69 44 25 7 2 1 0 0
2.94 2 0 1 1 8 19 41 66 169 68 30 22 9 2 2 0 0
2.84 1 1 1 6 3 12 34 65 179 78 33 20 10 0 2 0 3
2.75 0 1 0 1 4 21 44 76 168 71 39 17 5 1 0 1 2
2.67 1 1 1 1 5 17 47 71 166 67 52 13 6 2 4 0 1
2.60 1 0 1 2 11 23 41 77 160 61 42 25 9 5 2 1 4
2.53 0 1 4 5 14 20 45 93 190 84 44 17 7 3 3 1 3
Total 11 12 22 54 122 271 621 1005 2544 961 659 277 119 51 26 10 16
THE TOTALS 6781. 95261. 1.165 1.015 0.338 0.535 0.253 87.0 604. 5603. 0.2 17.9 166. 9.1405
1
SCALEIT: Normal termination of SCALEIT
Times: User: 0.1s System: 0.0s Elapsed: 0:00
#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 24 Jun 2003 13:24:27
#CCP4I TERMINATION OUTPUT_FILES /y/people/mgwt/TEST/2003test_32_scaleit.summary 2003test
#CCP4I MESSAGE Task completed successfully