#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:33:50 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: PREPROCESSOR 2.0 ***
*************************************************************************************
ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT
MODE MR_AUTO
HKLIN I432.mtz
LABIN F=FP SIGF=SIGFP
ENSEMBLE dna PDBFILE 131d.pdb IDENTITY 0.7
COMPOSITION PROTEIN MW 2000 NUM 2
SEARCH ENSEMBLE dna NUM 2
SGALTERNATIVE ALL
RESOLUTION 3.5
ROOT Betty
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 0.00 secs (0.00 secs)
Finished: Wed Jul 19 11:33:50 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:33:50 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: READ DATA FROM MTZ FILE 2.0 ***
*************************************************************************************
Data read from mtz file: I432.mtz
Space-Group Name (Hall Symbol): I 4 3 2 ( I 4 2 3)
Space-Group Number: 211
Unit Cell: 76.86 76.86 76.86 90.00 90.00 90.00
Column Labels Selected: FP SIGFP
Resolution on Mtz file: 1.62 38.43
Resolution Selected: 1.62 38.43
Number of Reflections in Selected Resolution Range: 5100
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 0.03 secs (0.03 secs)
Finished: Wed Jul 19 11:33:50 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:33:50 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.0 ***
*************************************************************************************
Steps:
Anisotropy correction
Fast Rotation Function
Fast Translation Function
Packing
Refinement (if data higher resolution than search resolution)
Number of search ensembles = 2
#1: Ensemble dna
#2: Ensemble dna
Number of permutations of search ensembles = 1
2 alternative space groups
Space group determined by highest LLG in search for FIRST ensemble
I 4 3 2
I 41 3 2
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 0.08 secs (0.08 secs)
Finished: Wed Jul 19 11:33:50 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:33:50 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: ANISOTROPY CORRECTION 2.0 ***
*************************************************************************************
------------------------------
DATA FOR ANISOTROPY CORRECTION
------------------------------
Space-Group Name (Number): I 4 3 2 (211)
Resolution of All Data (Number): 1.62 38.43 (5100)
Resolution of Selected Data (Number): 1.62 38.43 (5100)
---------------------
ANISOTROPY CORRECTION
---------------------
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
BIN SCALES: REFINE
ANISOTROPY: REFINE
SOLVENT K: FIX
SOLVENT B: FIX
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 26979.055
#1 26979.857 0.802 0.802
#2 26979.876 0.821 0.019
#3 26979.876 0.821 0.000
---CONVERGENCE OF MACROCYCLE---
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
0.000 0.0049 -0.0027 1.0000
0.000 1.0000 0.0016 -0.0049
0.000 -0.0016 1.0000 0.0028
Anisotropic deltaB (i.e. range of principal components): 0.000
Refined Anisotropy Parameters
-----------------------------
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
0.000 0.0049 -0.0027 1.0000
0.000 1.0000 0.0016 -0.0049
0.000 -0.0016 1.0000 0.0028
Anisotropic deltaB (i.e. range of principal components): 0.000
--------------
ABSOLUTE SCALE
--------------
Scale factor to put input Fs on absolute scale
Wilson Scale: 8.75926
Wilson B-factor: 22.3815
------------
OUTPUT FILES
------------
No mtz files output
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 0.31 secs (0.31 secs)
Finished: Wed Jul 19 11:33:50 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:33:50 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: CELL CONTENT ANALYSIS 2.0 ***
*************************************************************************************
Space-Group Name: I 4 3 2
Space-Group Number: 211
Unit Cell: 76.86 76.86 76.86 90.00 90.00 90.00
MW to which Matthews applies: 4000
Resolution for Matthews calculation: 1.62
Z MW VM % solvent rel. freq.
1 4000 2.36 47.98 0.808 <== most probable
Z is the number of multiples of the total composition
In most cases the most probable Z value should be 1
If it is not 1, you may need to consider other compositions
Histogram of relative frequencies of VM values
----------------------------------------------
Frequency of most common VM value normalized to 1
VM values plotted in increments of 1/VM (0.02)
<--- relative frequency --->
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
| | | | | | | | | | |
10.00 -
8.33 -
7.14 -
6.25 -
5.56 -
5.00 -
4.55 -
4.17 -
3.85 -
3.57 -
3.33 --
3.12 ----
2.94 --------
2.78 -------------
2.63 --------------------
2.50 ------------------------------
2.38 ----------------------------------------
2.27 *********************************************** (COMPOSITION*1)
2.17 --------------------------------------------------
2.08 -----------------------------------------------
2.00 ------------------------------------
1.92 -----------------------
1.85 ------------
1.79 -----
1.72 --
1.67 -
1.61 -
1.56 -
1.52 -
1.47 -
1.43 -
1.39 -
1.35 -
1.32 -
1.28 -
1.25 -
Most probable VM for resolution = 2.17808
Most probable MW of protein in asu for resolution = 4342.12
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 0.33 secs (0.33 secs)
Finished: Wed Jul 19 11:33:50 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:33:50 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.0 ***
*************************************************************************************
Loop over permutations
Permutation #1 of 1
Search order:
#1: Ensemble dna
#2: Ensemble dna
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 0.33 secs (0.33 secs)
Finished: Wed Jul 19 11:33:50 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:33:50 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT FAST ROTATION FUNCTION 2.0 ***
*************************************************************************************
-------------------------------
DATA FOR FAST ROTATION FUNCTION
-------------------------------
Outliers with a probability less than 1e-06 will be rejected
No reflections are outliers
Space-Group Name (Number): I 4 3 2 (211)
Resolution of All Data (Number): 1.62 38.43 (5100)
Resolution of Selected Data (Number): 3.50 38.43 (581)
--------------------------
ENSEMBLE FOR DECOMPOSITION
--------------------------
The RmsD of this model with respect to the real structure is 0.8
Unit Cell: 40.31 28.95 25.97 90.00 90.00 90.00
Calculating electron density...
Done
-------------------
WILSON DISTRIBUTION
-------------------
Parameters set for Wilson log-likelihood calculation
E = 0 and variance 1 for each reflection
Without correction for SigF to the variances,
Wilson log(likelihood) = - number of acentrics (358)
- half number of centrics (223/2)
= -469
With correction for SigF,
Wilson log(likelihood) = -462.199
------------
ENSEMBLE dna
------------
The RmsD of this model with respect to the real structure is 0.8
Unit Cell: 98.66 53.20 41.28 90.00 90.00 90.00
Calculating electron density...
Done
------------------------------
FAST ROTATION FUNCTION #1 OF 1
------------------------------
Search Ensemble: dna
Fixed MR solutions
(No solutions of this type)
Spherical Harmonics
-------------------
Elmn for Data
0% 100%
|===========================================================================| DONE
Elmn for Search Ensemble
0% 100%
|==========================================================================| DONE
Scanning the Range of Beta Angles
---------------------------------
Performing a 13.298 degree search.
0% 100%
|===============| DONE
Top 241 rotations before clustering will be rescored
0% 100%
|=============================================================| DONE
Scoring 500 randomly sampled rotations
0% 100%
|========================================================================| DONE
Mean Score (Sigma): -2.07683 (3.58516)
Highest Score (Z-score): 5.46667 (2.10409)
Top Peaks With Clustering From Rescoring of FRF #1
--------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 4 sites over 75% of top
The sites over 75% are:
# (#) Euler1 Euler2 Euler3 LLG Z-score Split #Group raw/top
1 5 45.5 47.2 108.3 +5.47 2.10 0.0 45 96.4/100.0
135.5 47.2 108.3
225.5 47.2 108.3
315.5 47.2 108.3
314.5 132.8 288.3
44.5 132.8 288.3
134.5 132.8 288.3
224.5 132.8 288.3
37.1 58.4 233.0
127.1 58.4 233.0
217.1 58.4 233.0
307.1 58.4 233.0
322.9 121.6 53.0
52.9 121.6 53.0
142.9 121.6 53.0
232.9 121.6 53.0
52.4 59.1 344.6
307.6 120.9 164.6
37.6 120.9 164.6
127.6 120.9 164.6
217.6 120.9 164.6
232.4 59.1 344.6
322.4 59.1 344.6
142.4 59.1 344.6
2 210 51.8 40.3 25.6 +5.21 2.03 44.6 31 70.5/ 99.9
141.8 40.3 25.6
231.8 40.3 25.6
321.8 40.3 25.6
308.2 139.7 205.6
38.2 139.7 205.6
128.2 139.7 205.6
218.2 139.7 205.6
27.7 59.4 159.8
117.7 59.4 159.8
207.7 59.4 159.8
297.7 59.4 159.8
332.3 120.6 339.8
62.3 120.6 339.8
152.3 120.6 339.8
242.3 120.6 339.8
56.3 66.4 264.7
303.7 113.6 84.7
33.7 113.6 84.7
123.7 113.6 84.7
213.7 113.6 84.7
236.3 66.4 264.7
326.3 66.4 264.7
146.3 66.4 264.7
3 90 36.4 44.9 169.0 +4.70 1.89 54.8 11 81.5/ 82.8
126.4 44.9 169.0
216.4 44.9 169.0
306.4 44.9 169.0
323.6 135.1 349.0
53.6 135.1 349.0
143.6 135.1 349.0
233.6 135.1 349.0
38.7 65.2 286.6
128.7 65.2 286.6
218.7 65.2 286.6
308.7 65.2 286.6
321.3 114.8 106.6
51.3 114.8 106.6
141.3 114.8 106.6
231.3 114.8 106.6
59.4 55.4 35.2
300.6 124.6 215.2
30.6 124.6 215.2
120.6 124.6 215.2
210.6 124.6 215.2
239.4 55.4 35.2
329.4 55.4 35.2
149.4 55.4 35.2
4 155 44.2 38.0 62.1 +4.54 1.85 48.1 6 75.5/ 89.6
134.2 38.0 62.1
224.2 38.0 62.1
314.2 38.0 62.1
315.8 142.0 242.1
45.8 142.0 242.1
135.8 142.0 242.1
225.8 142.0 242.1
29.2 64.6 189.6
119.2 64.6 189.6
209.2 64.6 189.6
299.2 64.6 189.6
330.8 115.4 9.6
60.8 115.4 9.6
150.8 115.4 9.6
240.8 115.4 9.6
61.4 63.8 293.1
298.6 116.2 113.1
28.6 116.2 113.1
118.6 116.2 113.1
208.6 116.2 113.1
241.4 63.8 293.1
331.4 63.8 293.1
151.4 63.8 293.1
Fast Rotation Function Table
----------------------------
Top (Z) Second (Z) Third (Z)
5.47 ( 2.10) 5.21 ( 2.03) 4.70 ( 1.89)
---------------
FINAL SELECTION
---------------
Number of sets stored before final selection = 1
Number of solutions stored before final selection = 4
Number of sets stored (deleted) after final selection = 1 (0)
Number of solutions stored (deleted) after final selection = 4 (0)
$TABLE : Rotation Function Summary:
$GRAPHS :Graph1 RF Number vs LL-gain:AUTO:1,2:
:Graph2 RF Number vs Z-Score:AUTO:1,3:
$$
Number LL-gain Z-Score $$ loggraph $$
1 5.47 2.104
2 5.21 2.032
3 4.70 1.890
4 4.54 1.847
$$
------------
OUTPUT FILES
------------
No script files output
No pdb files output
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 6.76 secs (6.76 secs)
Finished: Wed Jul 19 11:33:57 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:33:57 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.0 ***
*************************************************************************************
Loop over space groups
SpaceGroup #1 of 2
Current space group : I 4 3 2
Permutation #1 of 1
Search Ensemble dna
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 6.77 secs (6.77 secs)
Finished: Wed Jul 19 11:33:57 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:33:57 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT FAST TRANSLATION FUNCTION 2.0 ***
*************************************************************************************
----------------------------------
DATA FOR FAST TRANSLATION FUNCTION
----------------------------------
Outliers with a probability less than 1e-06 will be rejected
No reflections are outliers
Space-Group Name (Number): I 4 3 2 (211)
Resolution of All Data (Number): 1.62 38.43 (5100)
Resolution of Selected Data (Number): 3.50 38.43 (581)
-------------------
WILSON DISTRIBUTION
-------------------
Parameters set for Wilson log-likelihood calculation
E = 0 and variance 1 for each reflection
Without correction for SigF to the variances,
Wilson log(likelihood) = - number of acentrics (358)
- half number of centrics (223/2)
= -469
With correction for SigF,
Wilson log(likelihood) = -462.199
-------------------
SPACE GROUP I 4 3 2
-------------------
Space Group Name (Number): I 4 3 2 (211)
---------------------------------
FAST TRANSLATION FUNCTION #1 OF 1
---------------------------------
Fixed MR solutions
(No solutions of this type)
This FTF set has 4 trial orientations
#TRIAL Euler1 Euler2 Euler3 Ensemble
1 45.5 47.2 108.3 dna
2 51.8 40.3 25.6 dna
3 36.4 44.9 169.0 dna
4 44.2 38.0 62.1 dna
SET #1 of 1 TRIAL #1 of 4
-------------------------
Search Euler = 45.5 47.2 108.3, Ensemble = dna
------------
ENSEMBLE dna
------------
The RmsD of this model with respect to the real structure is 0.8
Unit Cell: 98.66 53.20 41.28 90.00 90.00 90.00
Calculating electron density...
Done
Fixed MR solutions
(No solutions of this type)
Top 151 translations before clustering will be rescored
Highest Score (Z-score): 16.2014 (4.22824)
Top Peaks With Clustering From Rescoring of SET #1 of 1 TRIAL #1 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 36 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 95 0.246 0.797 0.914 +16.20 4.23 0 3 33.41/ 34.85
2 75 0.166 0.951 0.152 +14.05 3.93 8 2 34.01/ 34.01
3 52 0.422 0.617 0.787 +13.94 3.91 22 2 34.86/ 42.78
4 26 0.268 0.238 0.687 +13.50 3.85 14 1 36.58/ 36.58
5 78 0.465 0.183 0.685 +13.46 3.85 20 1 33.85/ 33.85
6 5 0.190 0.856 0.721 +13.14 3.80 5 1 42.52/ 42.52
7 132 0.391 0.868 0.995 +12.62 3.73 14 1 32.89/ 32.89
8 42 0.369 0.967 0.076 +12.51 3.71 14 1 35.45/ 35.45
9 65 0.554 0.167 0.837 +12.45 3.71 17 2 34.26/ 34.26
10 62 0.494 0.048 0.889 +12.15 3.66 21 1 34.38/ 34.38
11 143 0.420 0.003 0.420 +11.84 3.62 22 1 32.57/ 32.57
12 129 0.432 0.093 0.222 +11.65 3.59 18 1 32.92/ 32.92
13 41 0.313 0.394 0.849 +11.65 3.59 15 1 35.48/ 35.48
14 56 0.500 0.049 0.724 +11.58 3.58 21 2 34.75/ 34.75
15 99 0.211 0.501 0.889 +11.57 3.58 20 1 33.36/ 33.36
16 106 0.473 0.861 0.870 +11.51 3.57 18 3 33.29/ 35.80
17 40 0.516 0.749 0.878 +11.45 3.57 21 1 35.57/ 35.57
18 63 0.287 0.755 0.715 +11.36 3.55 14 2 34.27/ 34.27
19 117 0.391 0.863 0.520 +11.26 3.54 23 1 33.07/ 33.07
20 6 0.243 0.006 0.052 +11.20 3.53 14 1 42.04/ 42.04
21 120 0.067 0.636 0.920 +11.16 3.53 13 2 33.01/ 38.62
22 39 0.432 0.598 0.717 +11.07 3.51 26 1 35.74/ 35.74
23 107 0.544 0.515 0.415 +10.79 3.47 37 1 33.24/ 33.24
24 81 0.156 0.637 0.837 +10.76 3.47 11 2 33.82/ 35.17
25 30 0.505 0.984 0.886 +10.68 3.46 21 1 36.40/ 36.40
26 103 0.078 0.174 0.303 +10.63 3.45 9 1 33.32/ 33.32
27 34 0.486 0.217 0.908 +10.36 3.41 21 3 35.98/ 35.98
28 71 0.462 0.196 0.634 +10.17 3.39 22 1 34.05/ 34.05
29 133 0.279 0.325 0.145 +10.13 3.38 11 1 32.86/ 32.86
30 98 0.462 0.426 0.318 +9.98 3.36 30 1 33.38/ 33.38
31 125 0.404 0.623 0.639 +9.49 3.29 28 1 32.97/ 32.97
32 131 0.470 0.200 0.335 +9.23 3.26 23 1 32.91/ 32.91
33 46 0.063 0.179 0.521 +9.05 3.23 18 1 35.20/ 35.20
34 12 0.309 0.888 0.183 +9.03 3.23 5 1 39.21/ 39.21
35 73 0.142 0.485 0.976 +8.84 3.20 20 1 34.04/ 34.04
36 104 0.234 0.469 0.162 +8.64 3.17 21 1 33.30/ 33.30
SET #1 of 1 TRIAL #2 of 4
-------------------------
Search Euler = 51.8 40.3 25.6, Ensemble = dna
Fixed MR solutions
(No solutions of this type)
Top 10 translations before clustering will be rescored
Highest Score (Z-score): -11.7249 (0.404727)
Top Peaks With Clustering From Rescoring of SET #1 of 1 TRIAL #2 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There was 1 site over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 4 0.123 0.611 0.795 -11.72 0.40 0 1 53.00/ 53.00
SET #1 of 1 TRIAL #3 of 4
-------------------------
Search Euler = 36.4 44.9 169.0, Ensemble = dna
Fixed MR solutions
(No solutions of this type)
Top 41 translations before clustering will be rescored
Highest Score (Z-score): 16.4033 (4.33813)
Top Peaks With Clustering From Rescoring of SET #1 of 1 TRIAL #3 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 11 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 37 0.961 0.286 0.994 +16.40 4.34 0 3 37.18/ 38.20
2 27 0.116 0.270 0.091 +15.58 4.22 9 1 38.12/ 38.12
3 12 0.228 0.034 0.868 +14.48 4.07 9 2 40.23/ 40.29
4 38 0.879 0.805 0.743 +13.18 3.89 16 1 37.17/ 37.17
5 40 0.221 0.938 0.531 +11.51 3.66 22 1 37.02/ 37.02
6 26 0.876 0.810 0.616 +11.37 3.64 17 1 38.19/ 38.19
7 34 0.269 0.521 0.753 +9.80 3.42 30 1 37.50/ 37.50
8 15 0.138 0.446 0.116 +9.78 3.41 17 1 39.99/ 39.99
9 41 0.257 0.251 0.406 +9.33 3.35 27 1 37.00/ 37.00
10 21 0.230 0.104 0.425 +9.22 3.34 20 1 38.49/ 38.49
11 32 0.886 0.136 0.318 +8.80 3.28 12 1 37.72/ 37.72
SET #1 of 1 TRIAL #4 of 4
-------------------------
Search Euler = 44.2 38.0 62.1, Ensemble = dna
Fixed MR solutions
(No solutions of this type)
Top 95 translations before clustering will be rescored
Highest Score (Z-score): 13.3239 (4.10411)
Top Peaks With Clustering From Rescoring of SET #1 of 1 TRIAL #4 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 24 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 23 0.345 0.058 0.622 +13.32 4.10 0 1 42.54/ 42.54
2 28 0.171 0.853 0.065 +13.03 4.06 22 2 41.67/ 41.67
3 10 0.450 0.164 0.211 +12.78 4.02 14 1 45.15/ 45.15
4 78 0.237 0.365 0.420 +12.72 4.01 14 1 38.04/ 38.04
5 89 0.373 0.479 0.773 +12.23 3.94 17 2 37.16/ 38.16
6 73 0.526 0.593 0.920 +11.91 3.89 9 1 38.17/ 38.17
7 32 0.291 0.787 0.065 +11.86 3.89 12 1 40.96/ 40.96
8 53 0.585 0.221 0.978 +11.58 3.85 12 1 39.14/ 39.14
9 11 0.285 0.361 0.007 +10.56 3.69 6 1 44.86/ 44.86
10 42 0.348 0.360 0.124 +10.12 3.63 5 1 39.96/ 39.96
11 67 0.408 0.304 0.113 +9.41 3.52 9 1 38.36/ 38.36
12 75 0.182 0.669 0.997 +8.99 3.46 14 1 38.12/ 38.12
13 8 0.536 0.082 0.122 +8.74 3.42 21 1 46.42/ 46.42
14 24 0.346 0.798 0.252 +8.60 3.40 15 1 42.46/ 42.46
15 95 0.281 0.427 0.618 +8.42 3.38 18 1 36.84/ 36.84
16 56 0.584 0.218 0.767 +8.37 3.37 15 1 39.00/ 39.00
17 92 0.532 0.777 0.824 +8.25 3.35 15 1 36.97/ 36.97
18 40 0.537 0.174 0.934 +8.17 3.34 17 1 40.47/ 40.47
19 64 0.535 0.359 0.502 +7.27 3.21 27 1 38.60/ 38.60
20 38 0.538 0.984 0.120 +7.02 3.17 19 1 40.65/ 40.65
21 82 0.473 0.666 0.755 +6.96 3.16 18 1 37.88/ 37.88
22 79 0.339 0.363 0.010 +6.90 3.15 4 1 37.96/ 37.96
23 66 0.468 0.169 0.755 +6.66 3.12 16 1 38.53/ 38.53
24 85 0.486 0.669 0.068 +6.56 3.10 8 1 37.79/ 37.79
---------------
FINAL SELECTION
---------------
Mean used for final selection = -14.3881
Number of solutions stored before final selection = 72
Percentage of top value for final selection = 75
LLG value for final selection = 8.70546
Number of solutions stored (deleted) after final selection = 59 (13)
$TABLE : Translation Function Summary:
$GRAPHS :Graph1 TF Number vs LL-gain:AUTO:1,2:
:Graph2 TF Number vs Z-Score:AUTO:1,3:
$$
Number LL-gain Z-Score $$ loggraph $$
1 16.40 4.34
2 16.20 4.23
3 15.58 4.22
4 14.48 4.07
5 14.05 3.93
6 13.94 3.91
7 13.50 3.85
8 13.46 3.85
9 13.32 4.10
10 13.18 3.89
11 13.14 3.80
12 13.03 4.06
13 12.78 4.02
14 12.72 4.01
15 12.62 3.73
16 12.51 3.71
17 12.45 3.71
18 12.23 3.94
19 12.15 3.66
20 11.91 3.89
21 11.86 3.89
22 11.84 3.62
23 11.65 3.59
24 11.65 3.59
25 11.58 3.58
26 11.58 3.85
27 11.57 3.58
28 11.51 3.66
29 11.51 3.57
30 11.45 3.57
31 11.37 3.64
32 11.36 3.55
33 11.26 3.54
34 11.20 3.53
35 11.16 3.53
36 11.07 3.51
37 10.79 3.47
38 10.76 3.47
39 10.68 3.46
40 10.63 3.45
41 10.56 3.69
42 10.36 3.41
43 10.17 3.39
44 10.13 3.38
45 10.12 3.63
46 9.98 3.36
47 9.80 3.42
48 9.78 3.41
49 9.49 3.29
50 9.41 3.52
51 9.33 3.35
52 9.23 3.26
53 9.22 3.34
54 9.05 3.23
55 9.03 3.23
56 8.99 3.46
57 8.84 3.20
58 8.80 3.28
59 8.74 3.42
$$
-----------------
TABLES OF RESULTS
-----------------
Fast Translation Function Table: Space Group I 4 3 2
----------------------------------------------------
#SET #TRIAL Top (Z) Second (Z) Third (Z) Ensemble
1 1 16.20 ( 4.23) 14.05 ( 3.93) 13.94 ( 3.91) dna
1 2 -11.72 ( 0.40) - - - - dna
1 3 16.40 ( 4.34) 15.58 ( 4.22) 14.48 ( 4.07) dna
1 4 13.32 ( 4.10) 13.03 ( 4.06) 12.78 ( 4.02) dna
---- ------
------------
OUTPUT FILES
------------
No script files output
No pdb files output
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 25.21 secs (25.21 secs)
Finished: Wed Jul 19 11:34:15 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:34:16 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT PACKING 2.0 ***
*************************************************************************************
Space Group Name (Number): I 4 3 2 (211)
Unit Cell: 76.86 76.86 76.86 90.00 90.00 90.00
----------------------
STRUCTURES FOR PACKING
----------------------
Packing will be performed with "trace" atoms (C-alphas for protein, P and selected
N for nucleic acid). When a protein molecule consists of more than one structure,
the structure with the highest homology is selected for packing. The structure is
then trimmed of loops that diverge more than 3A from other atoms in the molecule.
Ensemble: dna
-------------
Structure with lowest rms = 131d.pdb (0.8)
Trace length before selecting conserved = 41
Trace length after selecting conserved = 41
-------------------------
PACKING FUNCTION #1 OF 59
-------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.961 0.286 0.994
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC -0.039 0.286 -0.006
In total there were no clashes between trace atoms
-------------------------
PACKING FUNCTION #2 OF 59
-------------------------
ANNOTATION: RFZ=2.1 TFZ=4.2
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.246 0.797 0.914
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 135.5 47.2 108.3 FRAC 0.203 0.246 -0.086
There was 1 clash between trace atoms for models 1:1
In total there was 1 clash between trace atoms
-------------------------
PACKING FUNCTION #3 OF 59
-------------------------
ANNOTATION: RFZ=1.9 TFZ=4.2
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.116 0.270 0.091
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 126.4 44.9 169.0 FRAC 0.230 -0.384 -0.409
There were 12 clashes between trace atoms for models 1:1
In total there were 12 clashes between trace atoms
-------------------------
PACKING FUNCTION #4 OF 59
-------------------------
ANNOTATION: RFZ=1.9 TFZ=4.1
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.228 0.034 0.868
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 38.7 65.2 286.6 FRAC -0.132 0.228 0.034
There were 14 clashes between trace atoms for models 1:1
In total there were 14 clashes between trace atoms
-------------------------
PACKING FUNCTION #5 OF 59
-------------------------
ANNOTATION: RFZ=2.1 TFZ=3.9
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.166 0.951 0.152
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 315.5 47.2 108.3 FRAC -0.049 -0.166 -0.848
There were 14 clashes between trace atoms for models 1:1
In total there were 14 clashes between trace atoms
-------------------------
PACKING FUNCTION #6 OF 59
-------------------------
ANNOTATION: RFZ=2.1 TFZ=3.9
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.422 0.617 0.787
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 134.5 132.8 288.3 FRAC 0.078 0.117 0.713
There were 7 clashes between trace atoms for models 1:1
In total there were 7 clashes between trace atoms
-------------------------
PACKING FUNCTION #7 OF 59
-------------------------
ANNOTATION: RFZ=2.1 TFZ=3.9
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.268 0.238 0.687
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 135.5 47.2 108.3 FRAC -0.238 0.268 -0.313
In total there were no clashes between trace atoms
-------------------------
PACKING FUNCTION #8 OF 59
-------------------------
ANNOTATION: RFZ=2.1 TFZ=3.8
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.465 0.183 0.685
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 127.1 58.4 233.0 FRAC 0.035 -0.815 -0.317
There were 6 clashes between trace atoms for models 1:1
In total there were 6 clashes between trace atoms
-------------------------
PACKING FUNCTION #9 OF 59
-------------------------
ANNOTATION: RFZ=1.8 TFZ=4.1
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.345 0.058 0.622
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.345 0.058 -0.378
There was 1 clash between trace atoms for models 1:1
In total there was 1 clash between trace atoms
--------------------------
PACKING FUNCTION #10 OF 59
--------------------------
ANNOTATION: RFZ=1.9 TFZ=3.9
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.879 0.805 0.743
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 216.4 44.9 169.0 FRAC 0.121 0.195 -0.257
There were 8 clashes between trace atoms for models 1:1
In total there were 8 clashes between trace atoms
--------------------------
PACKING FUNCTION #11 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.8
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.190 0.856 0.721
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.190 -0.144 -0.279
There were 39 clashes between trace atoms for models 1:1
In total there were 39 clashes between trace atoms
--------------------------
PACKING FUNCTION #12 OF 59
--------------------------
ANNOTATION: RFZ=1.8 TFZ=4.1
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.171 0.853 0.065
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.171 -0.147 0.065
There were 2 clashes between trace atoms for models 1:1
In total there were 2 clashes between trace atoms
--------------------------
PACKING FUNCTION #13 OF 59
--------------------------
ANNOTATION: RFZ=1.8 TFZ=4.0
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.450 0.164 0.211
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 330.8 115.4 9.6 FRAC -0.289 0.050 0.336
There were 33 clashes between trace atoms for models 1:1
In total there were 33 clashes between trace atoms
--------------------------
PACKING FUNCTION #14 OF 59
--------------------------
ANNOTATION: RFZ=1.8 TFZ=4.0
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.237 0.365 0.420
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.237 -0.635 -0.580
There were 9 clashes between trace atoms for models 1:1
In total there were 9 clashes between trace atoms
--------------------------
PACKING FUNCTION #15 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.7
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.391 0.868 0.995
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 135.5 47.2 108.3 FRAC -0.368 -0.109 -0.505
There was 1 clash between trace atoms for models 1:1
In total there was 1 clash between trace atoms
--------------------------
PACKING FUNCTION #16 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.7
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.369 0.967 0.076
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC -0.131 -0.533 -0.424
There were 27 clashes between trace atoms for models 1:1
In total there were 27 clashes between trace atoms
--------------------------
PACKING FUNCTION #17 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.7
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.554 0.167 0.837
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.054 -0.333 -0.663
There were 3 clashes between trace atoms for models 1:1
In total there were 3 clashes between trace atoms
--------------------------
PACKING FUNCTION #18 OF 59
--------------------------
ANNOTATION: RFZ=1.8 TFZ=3.9
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.373 0.479 0.773
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.373 -0.521 -0.227
There was 1 clash between trace atoms for models 1:1
In total there was 1 clash between trace atoms
--------------------------
PACKING FUNCTION #19 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.7
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.494 0.048 0.889
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 322.9 121.6 53.0 FRAC -0.611 0.006 0.452
There were 2 clashes between trace atoms for models 1:1
In total there were 2 clashes between trace atoms
--------------------------
PACKING FUNCTION #20 OF 59
--------------------------
ANNOTATION: RFZ=1.8 TFZ=3.9
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.526 0.593 0.920
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 225.8 142.0 242.1 FRAC 0.407 -0.526 0.080
There were 13 clashes between trace atoms for models 1:1
In total there were 13 clashes between trace atoms
--------------------------
PACKING FUNCTION #21 OF 59
--------------------------
ANNOTATION: RFZ=1.8 TFZ=3.9
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.291 0.787 0.065
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 119.2 64.6 189.6 FRAC -0.291 0.065 -0.213
There were 7 clashes between trace atoms for models 1:1
In total there were 7 clashes between trace atoms
--------------------------
PACKING FUNCTION #22 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.6
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.420 0.003 0.420
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.420 0.003 -0.580
In total there were no clashes between trace atoms
--------------------------
PACKING FUNCTION #23 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.6
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.432 0.093 0.222
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 217.6 120.9 164.6 FRAC 0.278 0.407 0.068
In total there were no clashes between trace atoms
--------------------------
PACKING FUNCTION #24 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.6
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.313 0.394 0.849
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 52.4 59.1 344.6 FRAC -0.106 -0.651 -0.187
There were 3 clashes between trace atoms for models 1:1
In total there were 3 clashes between trace atoms
--------------------------
PACKING FUNCTION #25 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.6
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.500 0.049 0.724
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 127.1 58.4 233.0 FRAC -0.000 -0.776 -0.451
In total there were no clashes between trace atoms
--------------------------
PACKING FUNCTION #26 OF 59
--------------------------
ANNOTATION: RFZ=1.8 TFZ=3.8
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.585 0.221 0.978
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.085 -0.279 -0.522
There were 26 clashes between trace atoms for models 1:1
In total there were 26 clashes between trace atoms
--------------------------
PACKING FUNCTION #27 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.6
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.211 0.501 0.889
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 134.5 132.8 288.3 FRAC 0.289 0.001 0.611
There were 3 clashes between trace atoms for models 1:1
In total there were 3 clashes between trace atoms
--------------------------
PACKING FUNCTION #28 OF 59
--------------------------
ANNOTATION: RFZ=1.9 TFZ=3.7
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.221 0.938 0.531
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.221 -0.062 -0.469
There were 10 clashes between trace atoms for models 1:1
In total there were 10 clashes between trace atoms
--------------------------
PACKING FUNCTION #29 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.6
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.473 0.861 0.870
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 322.9 121.6 53.0 FRAC -0.130 -0.473 0.139
There were 8 clashes between trace atoms for models 1:1
In total there were 8 clashes between trace atoms
--------------------------
PACKING FUNCTION #30 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.6
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.516 0.749 0.878
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 52.4 59.1 344.6 FRAC 0.249 -0.622 0.016
There was 1 clash between trace atoms for models 1:1
In total there was 1 clash between trace atoms
--------------------------
PACKING FUNCTION #31 OF 59
--------------------------
ANNOTATION: RFZ=1.9 TFZ=3.6
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.876 0.810 0.616
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC -0.124 -0.190 -0.384
There were 35 clashes between trace atoms for models 1:1
In total there were 35 clashes between trace atoms
--------------------------
PACKING FUNCTION #32 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.6
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.287 0.755 0.715
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 225.5 47.2 108.3 FRAC -0.287 0.245 -0.285
There were 14 clashes between trace atoms for models 1:1
In total there were 14 clashes between trace atoms
--------------------------
PACKING FUNCTION #33 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.5
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.391 0.863 0.520
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.391 -0.137 -0.480
There were 10 clashes between trace atoms for models 1:1
In total there were 10 clashes between trace atoms
--------------------------
PACKING FUNCTION #34 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.5
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.243 0.006 0.052
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC -0.257 -0.494 -0.448
There were 9 clashes between trace atoms for models 1:1
In total there were 9 clashes between trace atoms
--------------------------
PACKING FUNCTION #35 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.5
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.067 0.636 0.920
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.067 -0.364 -0.080
There were 3 clashes between trace atoms for models 1:1
In total there were 3 clashes between trace atoms
--------------------------
PACKING FUNCTION #36 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.5
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.432 0.598 0.717
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 225.5 47.2 108.3 FRAC 0.068 -0.098 -0.783
There were 18 clashes between trace atoms for models 1:1
In total there were 18 clashes between trace atoms
--------------------------
PACKING FUNCTION #37 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.5
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.544 0.515 0.415
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.044 0.015 -0.085
There were 4 clashes between trace atoms for models 1:1
In total there were 4 clashes between trace atoms
--------------------------
PACKING FUNCTION #38 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.5
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.156 0.637 0.837
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 37.6 120.9 164.6 FRAC -0.163 -0.363 -0.156
In total there were no clashes between trace atoms
--------------------------
PACKING FUNCTION #39 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.5
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.505 0.984 0.886
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 135.5 47.2 108.3 FRAC 0.516 0.005 -0.614
In total there were no clashes between trace atoms
--------------------------
PACKING FUNCTION #40 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.5
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.078 0.174 0.303
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.078 0.174 -0.697
There were 16 clashes between trace atoms for models 1:1
In total there were 16 clashes between trace atoms
--------------------------
PACKING FUNCTION #41 OF 59
--------------------------
ANNOTATION: RFZ=1.8 TFZ=3.7
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.285 0.361 0.007
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC -0.215 -0.139 -0.493
There were 4 clashes between trace atoms for models 1:1
In total there were 4 clashes between trace atoms
--------------------------
PACKING FUNCTION #42 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.4
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.486 0.217 0.908
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 135.5 47.2 108.3 FRAC 0.283 -0.014 -0.592
There were 12 clashes between trace atoms for models 1:1
In total there were 12 clashes between trace atoms
--------------------------
PACKING FUNCTION #43 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.4
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.462 0.196 0.634
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC -0.038 -0.304 -0.866
In total there were no clashes between trace atoms
--------------------------
PACKING FUNCTION #44 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.4
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.279 0.325 0.145
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC -0.221 -0.175 -0.355
There were 4 clashes between trace atoms for models 1:1
In total there were 4 clashes between trace atoms
--------------------------
PACKING FUNCTION #45 OF 59
--------------------------
ANNOTATION: RFZ=1.8 TFZ=3.6
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.348 0.360 0.124
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC -0.152 -0.140 -0.376
In total there were no clashes between trace atoms
--------------------------
PACKING FUNCTION #46 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.4
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.462 0.426 0.318
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 225.5 47.2 108.3 FRAC 0.038 0.074 -0.182
There were 12 clashes between trace atoms for models 1:1
In total there were 12 clashes between trace atoms
--------------------------
PACKING FUNCTION #47 OF 59
--------------------------
ANNOTATION: RFZ=1.9 TFZ=3.4
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.269 0.521 0.753
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC -0.231 0.021 -0.747
There were 2 clashes between trace atoms for models 1:1
In total there were 2 clashes between trace atoms
--------------------------
PACKING FUNCTION #48 OF 59
--------------------------
ANNOTATION: RFZ=1.9 TFZ=3.4
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.138 0.446 0.116
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 323.6 135.1 349.0 FRAC -0.362 0.054 0.384
There were 12 clashes between trace atoms for models 1:1
In total there were 12 clashes between trace atoms
--------------------------
PACKING FUNCTION #49 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.3
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.404 0.623 0.639
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 225.5 47.2 108.3 FRAC -0.404 0.377 -0.361
There was 1 clash between trace atoms for models 1:1
In total there was 1 clash between trace atoms
--------------------------
PACKING FUNCTION #50 OF 59
--------------------------
ANNOTATION: RFZ=1.8 TFZ=3.5
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.408 0.304 0.113
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 150.8 115.4 9.6 FRAC 0.387 -0.092 0.196
There were 2 clashes between trace atoms for models 1:1
In total there were 2 clashes between trace atoms
--------------------------
PACKING FUNCTION #51 OF 59
--------------------------
ANNOTATION: RFZ=1.9 TFZ=3.4
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.257 0.251 0.406
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 306.4 44.9 169.0 FRAC 0.251 -0.257 -0.594
There were 5 clashes between trace atoms for models 1:1
In total there were 5 clashes between trace atoms
--------------------------
PACKING FUNCTION #52 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.3
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.470 0.200 0.335
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 134.5 132.8 288.3 FRAC 0.030 -0.300 0.165
In total there were no clashes between trace atoms
--------------------------
PACKING FUNCTION #53 OF 59
--------------------------
ANNOTATION: RFZ=1.9 TFZ=3.3
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.230 0.104 0.425
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.230 0.104 -0.575
There were 4 clashes between trace atoms for models 1:1
In total there were 4 clashes between trace atoms
--------------------------
PACKING FUNCTION #54 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.2
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.063 0.179 0.521
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 307.1 58.4 233.0 FRAC 0.063 0.479 0.179
There were 18 clashes between trace atoms for models 1:1
In total there were 18 clashes between trace atoms
--------------------------
PACKING FUNCTION #55 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.2
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.309 0.888 0.183
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.309 -0.112 -0.817
There were 6 clashes between trace atoms for models 1:1
In total there were 6 clashes between trace atoms
--------------------------
PACKING FUNCTION #56 OF 59
--------------------------
ANNOTATION: RFZ=1.8 TFZ=3.5
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.182 0.669 0.997
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.182 -0.331 -0.003
There were 22 clashes between trace atoms for models 1:1
In total there were 22 clashes between trace atoms
--------------------------
PACKING FUNCTION #57 OF 59
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.2
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.142 0.485 0.976
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC -0.358 -0.015 -0.524
There were 4 clashes between trace atoms for models 1:1
In total there were 4 clashes between trace atoms
--------------------------
PACKING FUNCTION #58 OF 59
--------------------------
ANNOTATION: RFZ=1.9 TFZ=3.3
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.886 0.136 0.318
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC -0.114 0.136 -0.682
There were 35 clashes between trace atoms for models 1:1
In total there were 35 clashes between trace atoms
--------------------------
PACKING FUNCTION #59 OF 59
--------------------------
ANNOTATION: RFZ=1.8 TFZ=3.4
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.536 0.082 0.122
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 60.8 115.4 9.6 FRAC 0.036 -0.378 0.418
There were 51 clashes between trace atoms for models 1:1
In total there were 51 clashes between trace atoms
-------------
PACKING TABLE
-------------
Solutions rejected if number of clashes > 0
# #CLASHES # ACCEPTED
1 0 1 YES
2 1 NO
3 12 NO
4 14 NO
5 14 NO
6 7 NO
7 0 2 YES
8 6 NO
9 1 NO
10 8 NO
11 39 NO
12 2 NO
13 33 NO
14 9 NO
15 1 NO
16 27 NO
17 3 NO
18 1 NO
19 2 NO
20 13 NO
21 7 NO
22 0 3 YES
23 0 4 YES
24 3 NO
25 0 5 YES
26 26 NO
27 3 NO
28 10 NO
29 8 NO
30 1 NO
31 35 NO
32 14 NO
33 10 NO
34 9 NO
35 3 NO
36 18 NO
37 4 NO
38 0 6 YES
39 0 7 YES
40 16 NO
41 4 NO
42 12 NO
43 0 8 YES
44 4 NO
45 0 9 YES
46 12 NO
47 2 NO
48 12 NO
49 1 NO
50 2 NO
51 5 NO
52 0 10 YES
53 4 NO
54 18 NO
55 6 NO
56 22 NO
57 4 NO
58 35 NO
59 51 NO
10 accepted of 59 solutions
------------
OUTPUT FILES
------------
No script files output
No pdb files output
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 27.83 secs (27.83 secs)
Finished: Wed Jul 19 11:34:18 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:34:18 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.0 ***
*************************************************************************************
-------------------------------
DATA FOR REFINEMENT AND PHASING
-------------------------------
Outliers with a probability less than 1e-06 will be rejected
No reflections are outliers
Space-Group Name (Number): I 4 3 2 (211)
Resolution of All Data (Number): 1.62 38.43 (5100)
Resolution of Selected Data (Number): 3.50 38.43 (581)
-------------------
WILSON DISTRIBUTION
-------------------
Parameters set for Wilson log-likelihood calculation
E = 0 and variance 1 for each reflection
Without correction for SigF to the variances,
Wilson log(likelihood) = - number of acentrics (358)
- half number of centrics (223/2)
= -469
With correction for SigF,
Wilson log(likelihood) = -462.199
------------
ENSEMBLE dna
------------
The RmsD of this model with respect to the real structure is 0.8
Unit Cell: 98.66 53.20 41.28 90.00 90.00 90.00
Calculating electron density...
Done
-------------------
REFINEMENT #1 OF 10
-------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC -0.039 0.286 -0.006
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 16.403
#1 17.062 0.659 0.659
#2 17.129 0.726 0.067
#3 17.129 0.726 0.000
#4 17.129 0.726 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna -0.1689 -0.7085 -0.2771 +0.0565 -0.0441 -0.0426
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 35.6 45.2 169.3 FRAC -0.040 0.286 -0.006
The log(likelihood) gain = 17.1294 (at start 16.4033)
The R-factor = 59.00 (at start 59.34)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
-------------------
REFINEMENT #2 OF 10
-------------------
ANNOTATION: RFZ=2.1 TFZ=3.9 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 135.5 47.2 108.3 FRAC -0.238 0.268 -0.313
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 13.504
#1 15.515 2.011 2.011
#2 16.315 2.812 0.801
#3 16.341 2.837 0.025
#4 16.540 3.036 0.199
#5 16.929 3.426 0.389
#6 16.932 3.428 0.003
#7 16.932 3.428 0.000
#8 16.941 3.437 0.009
#9 16.942 3.438 0.001
#10 16.942 3.438 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna -5.4336 +0.6243 +2.9717 -0.0814 -0.3917 +0.2255
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 141.8 44.0 101.0 FRAC -0.233 0.310 -0.298
The log(likelihood) gain = 16.9419 (at start 13.5037)
The R-factor = 62.17 (at start 68.23)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
-------------------
REFINEMENT #3 OF 10
-------------------
ANNOTATION: RFZ=2.1 TFZ=3.6 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.420 0.003 -0.580
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 11.837
#1 13.864 2.028 2.028
#2 14.205 2.368 0.341
#3 14.228 2.391 0.023
#4 14.234 2.397 0.006
#5 14.234 2.397 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna +4.0621 +0.4714 +0.6169 +0.0490 +0.0460 +0.1102
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 44.3 48.6 112.9 FRAC 0.399 0.016 -0.584
The log(likelihood) gain = 14.2337 (at start 11.8366)
The R-factor = 62.87 (at start 64.82)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
-------------------
REFINEMENT #4 OF 10
-------------------
ANNOTATION: RFZ=2.1 TFZ=3.6 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 217.6 120.9 164.6 FRAC 0.278 0.407 0.068
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 11.654
#1 12.633 0.979 0.979
#2 12.983 1.329 0.350
#3 13.426 1.772 0.443
#4 13.426 1.772 0.000
#5 13.426 1.772 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna -0.4330 -1.4025 -1.5528 +0.0750 -0.2132 +0.1615
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 216.4 122.2 162.7 FRAC 0.279 0.405 0.075
The log(likelihood) gain = 13.4262 (at start 11.6540)
The R-factor = 61.22 (at start 62.69)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
-------------------
REFINEMENT #5 OF 10
-------------------
ANNOTATION: RFZ=2.1 TFZ=3.6 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 127.1 58.4 233.0 FRAC -0.000 -0.776 -0.451
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 11.584
#1 13.069 1.485 1.485
#2 13.201 1.617 0.132
#3 13.208 1.624 0.007
#4 13.226 1.642 0.018
#5 13.237 1.653 0.012
#6 13.314 1.730 0.076
#7 13.340 1.756 0.026
#8 13.438 1.854 0.098
#9 13.438 1.854 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna +1.0232 -0.2182 -1.3001 +0.1928 +0.0254 +0.2433
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 128.9 58.9 232.2 FRAC 0.015 -0.777 -0.449
The log(likelihood) gain = 13.4384 (at start 11.5840)
The R-factor = 60.21 (at start 61.82)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
-------------------
REFINEMENT #6 OF 10
-------------------
ANNOTATION: RFZ=2.1 TFZ=3.5 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 37.6 120.9 164.6 FRAC -0.163 -0.363 -0.156
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 10.756
#1 11.124 0.367 0.367
#2 11.124 0.367 0.000
#3 11.124 0.367 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna -0.0968 +0.6221 -0.0615 -0.0124 -0.0032 -0.0426
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 38.3 120.8 164.9 FRAC -0.162 -0.367 -0.157
The log(likelihood) gain = 11.1235 (at start 10.7563)
The R-factor = 62.99 (at start 63.90)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
-------------------
REFINEMENT #7 OF 10
-------------------
ANNOTATION: RFZ=2.1 TFZ=3.5 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 135.5 47.2 108.3 FRAC 0.516 0.005 -0.614
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 10.678
#1 13.100 2.422 2.422
#2 14.048 3.370 0.948
#3 14.565 3.887 0.517
#4 14.662 3.984 0.097
#5 14.693 4.014 0.030
#6 14.763 4.085 0.070
#7 14.763 4.085 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna +0.7468 +2.5342 +4.4651 +0.0472 -0.0363 +0.0242
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 141.2 46.3 107.5 FRAC 0.508 0.022 -0.613
The log(likelihood) gain = 14.7628 (at start 10.6781)
The R-factor = 62.50 (at start 61.84)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
-------------------
REFINEMENT #8 OF 10
-------------------
ANNOTATION: RFZ=2.1 TFZ=3.4 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC -0.038 -0.304 -0.866
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 10.166
#1 14.217 4.051 4.051
#2 14.958 4.792 0.741
#3 15.203 5.037 0.245
#4 15.204 5.038 0.001
#5 15.204 5.038 0.000
#6 15.204 5.038 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna +2.4498 +2.3740 -0.6456 +0.1380 +0.5758 -0.1635
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 46.0 50.1 109.9 FRAC -0.054 -0.305 -0.868
The log(likelihood) gain = 15.2039 (at start 10.1659)
The R-factor = 62.61 (at start 62.72)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
-------------------
REFINEMENT #9 OF 10
-------------------
ANNOTATION: RFZ=1.8 TFZ=3.6 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC -0.152 -0.140 -0.376
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 10.121
#1 11.080 0.959 0.959
#2 11.403 1.282 0.323
#3 11.793 1.671 0.390
#4 12.248 2.126 0.455
#5 12.257 2.136 0.009
#6 12.291 2.170 0.034
#7 12.650 2.529 0.359
#8 12.650 2.529 0.000
#9 12.670 2.549 0.020
#10 12.676 2.555 0.006
#11 12.677 2.555 0.000
#12 12.677 2.555 0.000
#13 12.685 2.563 0.008
#14 12.685 2.563 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna +3.0900 +3.4644 -2.8683 -0.0288 -0.1663 +0.1351
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 37.9 41.5 68.3 FRAC -0.189 -0.141 -0.388
The log(likelihood) gain = 12.6847 (at start 10.1214)
The R-factor = 62.28 (at start 65.52)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
--------------------
REFINEMENT #10 OF 10
--------------------
ANNOTATION: RFZ=2.1 TFZ=3.3 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 134.5 132.8 288.3 FRAC 0.030 -0.300 0.165
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 9.232
#1 16.526 7.294 7.294
#2 18.028 8.797 1.503
#3 18.202 8.971 0.174
#4 18.329 9.097 0.126
#5 18.418 9.187 0.090
#6 18.419 9.187 0.001
#7 18.421 9.189 0.002
#8 18.426 9.195 0.005
#9 18.429 9.197 0.002
#10 18.429 9.197 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna +9.5404 +1.5979 -2.0168 -0.1982 +0.5715 -0.0185
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 139.0 126.9 298.3 FRAC 0.096 -0.280 0.174
The log(likelihood) gain = 18.4285 (at start 9.2316)
The R-factor = 60.87 (at start 63.02)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
----------------
PRUNE DUPLICATES
----------------
Check for nearly equivalent solutions
No duplicate solutions pruned
Refinement Table: Space Group I 4 3 2
-------------------------------------
#+ = input number #* = output number
Unsorted (refinement order) Sorted in LL-gain order
Initial Refined Initial Refined
#+ LL-gain LL-gain Unique #* #+ LL-gain LL-gain Unique =#*
1 16.40 17.13 YES 1 10 9.23 18.43 YES
2 13.50 16.94 YES 2 1 16.40 17.13 YES
3 11.84 14.23 YES 3 2 13.50 16.94 YES
4 11.65 13.43 YES 4 8 10.17 15.20 YES
5 11.58 13.44 YES 5 7 10.68 14.76 YES
6 10.76 11.12 YES 6 3 11.84 14.23 YES
7 10.68 14.76 YES 7 5 11.58 13.44 YES
8 10.17 15.20 YES 8 4 11.65 13.43 YES
9 10.12 12.68 YES 9 9 10.12 12.68 YES
10 9.23 18.43 YES 10 6 10.76 11.12 YES
------------
OUTPUT FILES
------------
No script files output
No pdb files output
No mtz files output
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 50.91 secs (50.91 secs)
Finished: Wed Jul 19 11:34:41 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:34:41 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.0 ***
*************************************************************************************
Purge solutions according to highest LLG
Top LLG value from Translation Function = 16.4033
Percent used for purge = 0.75
Top LLG value used for purge = 18.4285
Mean LLG used for purge = -14.3881
Number of solutions stored before purge = 10
Number of solutions stored (deleted) after purge = 10 (0)
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 50.91 secs (50.91 secs)
Finished: Wed Jul 19 11:34:41 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:34:41 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.0 ***
*************************************************************************************
New Best Solution: TOP LL-GAIN 18.428548
Permutation #1
Search Ensemble dna
Space Group: I 4 3 2
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 50.92 secs (50.92 secs)
Finished: Wed Jul 19 11:34:41 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:34:41 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.0 ***
*************************************************************************************
Loop over space groups
SpaceGroup #2 of 2
Current space group : I 41 3 2
Permutation #1 of 1
Search Ensemble dna
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 50.93 secs (50.93 secs)
Finished: Wed Jul 19 11:34:41 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:34:41 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT FAST TRANSLATION FUNCTION 2.0 ***
*************************************************************************************
----------------------------------
DATA FOR FAST TRANSLATION FUNCTION
----------------------------------
Outliers with a probability less than 1e-06 will be rejected
No reflections are outliers
Space-Group Name (Number): I 41 3 2 (214)
Resolution of All Data (Number): 1.62 38.43 (5100)
Resolution of Selected Data (Number): 3.50 38.43 (581)
-------------------
WILSON DISTRIBUTION
-------------------
Parameters set for Wilson log-likelihood calculation
E = 0 and variance 1 for each reflection
Without correction for SigF to the variances,
Wilson log(likelihood) = - number of acentrics (358)
- half number of centrics (223/2)
= -469
With correction for SigF,
Wilson log(likelihood) = -462.199
--------------------
SPACE GROUP I 41 3 2
--------------------
Space Group Name (Number): I 41 3 2 (214)
---------------------------------
FAST TRANSLATION FUNCTION #1 OF 1
---------------------------------
Fixed MR solutions
(No solutions of this type)
This FTF set has 4 trial orientations
#TRIAL Euler1 Euler2 Euler3 Ensemble
1 45.5 47.2 108.3 dna
2 51.8 40.3 25.6 dna
3 36.4 44.9 169.0 dna
4 44.2 38.0 62.1 dna
SET #1 of 1 TRIAL #1 of 4
-------------------------
Search Euler = 45.5 47.2 108.3, Ensemble = dna
------------
ENSEMBLE dna
------------
The RmsD of this model with respect to the real structure is 0.8
Unit Cell: 98.66 53.20 41.28 90.00 90.00 90.00
Calculating electron density...
Done
Fixed MR solutions
(No solutions of this type)
Top 374 translations before clustering will be rescored
Highest Score (Z-score): 16.1727 (4.36752)
Top Peaks With Clustering From Rescoring of SET #1 of 1 TRIAL #1 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 63 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 32 0.537 0.270 0.642 +16.17 4.37 0 1 37.28/ 37.28
2 36 0.517 0.617 0.926 +15.86 4.32 10 2 36.90/ 36.90
3 9 0.079 0.451 0.954 +15.56 4.28 15 1 39.68/ 39.68
4 18 0.430 0.026 0.601 +14.84 4.17 14 1 38.77/ 38.77
5 122 0.443 0.641 0.021 +14.61 4.14 16 2 34.01/ 36.25
6 63 0.372 0.458 0.161 +13.84 4.03 18 1 35.54/ 35.54
7 189 0.107 0.517 0.183 +13.43 3.97 20 1 32.66/ 32.66
8 74 0.318 0.770 0.914 +13.21 3.93 11 2 35.22/ 40.12
9 31 0.516 0.981 0.727 +12.43 3.82 7 3 37.39/ 37.39
10 20 0.522 0.980 0.642 +12.39 3.81 9 3 38.28/ 38.28
11 73 0.510 0.888 0.929 +12.33 3.81 13 1 35.28/ 35.28
12 54 0.520 0.248 0.384 +12.22 3.79 20 1 35.98/ 35.98
13 229 0.554 0.690 0.458 +12.16 3.78 6 2 32.21/ 32.21
14 166 0.496 0.137 0.383 +12.10 3.77 18 1 33.05/ 33.05
15 23 0.431 0.524 0.106 +12.04 3.76 19 1 37.98/ 37.98
16 41 0.079 0.437 0.490 +12.02 3.76 19 4 36.75/ 36.75
17 2 0.214 0.444 0.898 +11.91 3.74 9 1 42.57/ 42.57
18 95 0.361 0.244 0.682 +11.84 3.73 14 2 34.68/ 34.68
19 223 0.305 0.894 0.174 +11.72 3.72 13 1 32.28/ 32.28
20 289 0.406 0.195 0.517 +11.59 3.70 11 2 31.69/ 35.00
21 17 0.421 0.378 0.815 +11.54 3.69 8 1 38.96/ 38.96
22 111 0.305 0.185 0.284 +11.52 3.69 13 2 34.26/ 34.26
23 69 0.370 0.035 0.155 +11.45 3.68 6 2 35.39/ 35.39
24 149 0.425 0.866 0.040 +11.01 3.61 12 1 33.42/ 33.42
25 144 0.500 0.234 0.288 +10.92 3.60 15 1 33.59/ 33.59
26 110 0.464 0.746 0.329 +10.83 3.59 7 1 34.27/ 34.27
27 296 0.128 0.982 0.421 +10.80 3.58 17 1 31.60/ 31.60
28 6 0.559 0.291 0.465 +10.70 3.57 14 2 41.13/ 41.13
29 261 0.300 0.749 0.414 +10.65 3.56 13 1 31.91/ 31.91
30 194 0.293 0.190 0.981 +10.53 3.54 13 1 32.58/ 32.58
31 199 0.483 0.972 0.724 +10.52 3.54 10 1 32.50/ 32.50
32 75 0.343 0.607 0.260 +10.30 3.51 19 1 35.22/ 35.22
33 90 0.152 0.235 0.948 +10.29 3.51 13 1 34.80/ 34.80
34 259 0.540 0.020 0.149 +10.28 3.51 15 2 31.92/ 36.15
35 87 0.156 0.245 0.885 +10.26 3.50 14 2 34.84/ 34.84
36 39 0.068 0.302 0.651 +10.26 3.50 20 1 36.81/ 36.81
37 15 0.124 0.669 0.344 +10.19 3.49 19 1 39.10/ 39.10
38 309 0.153 0.638 0.827 +10.08 3.48 22 1 31.48/ 31.48
39 56 0.435 0.219 0.598 +10.02 3.47 9 1 35.84/ 35.84
40 68 0.212 0.988 0.508 +9.98 3.46 11 1 35.39/ 35.39
41 348 0.114 0.004 0.337 +9.88 3.45 20 1 31.19/ 31.19
42 80 0.311 0.755 0.887 +9.75 3.43 13 1 35.06/ 35.06
43 71 0.204 0.669 0.833 +9.72 3.43 21 1 35.35/ 35.35
44 226 0.151 0.764 0.963 +9.65 3.41 14 1 32.24/ 32.24
45 82 0.160 0.317 0.141 +9.53 3.40 16 1 35.02/ 35.02
46 240 0.090 0.481 0.245 +9.51 3.39 21 1 32.10/ 32.10
47 247 0.074 0.859 0.690 +9.48 3.39 10 1 32.03/ 32.03
48 180 0.200 0.812 0.818 +9.34 3.37 14 1 32.83/ 32.83
49 307 0.511 0.138 0.137 +9.29 3.36 12 1 31.50/ 31.50
50 13 0.301 0.637 0.293 +9.25 3.36 19 1 39.30/ 39.30
51 258 0.168 0.076 0.100 +9.17 3.34 18 1 31.93/ 31.93
52 29 0.415 0.702 0.645 +9.16 3.34 15 1 37.43/ 37.43
53 99 0.069 0.390 0.315 +9.11 3.34 13 1 34.60/ 34.60
54 85 0.154 0.322 0.850 +9.09 3.33 13 1 34.92/ 34.92
55 34 0.145 0.255 0.566 +9.08 3.33 16 1 37.11/ 37.11
56 211 0.509 0.770 0.429 +9.08 3.33 5 1 32.39/ 32.39
57 264 0.135 0.110 0.021 +9.07 3.33 21 1 31.89/ 31.89
58 19 0.065 0.856 0.471 +9.00 3.32 17 1 38.61/ 38.61
59 225 0.457 0.565 0.261 +8.92 3.31 14 1 32.24/ 32.24
60 25 0.398 0.616 0.318 +8.90 3.30 13 1 37.85/ 37.85
61 318 0.368 0.636 0.164 +8.86 3.30 22 1 31.40/ 31.40
62 27 0.077 0.817 0.140 +8.83 3.29 11 1 37.65/ 37.65
63 202 0.147 0.304 0.574 +8.75 3.28 19 1 32.48/ 32.48
SET #1 of 1 TRIAL #2 of 4
-------------------------
Search Euler = 51.8 40.3 25.6, Ensemble = dna
Fixed MR solutions
(No solutions of this type)
Top 164 translations before clustering will be rescored
Highest Score (Z-score): 21.2564 (5.49821)
Top Peaks With Clustering From Rescoring of SET #1 of 1 TRIAL #2 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 4 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 5 0.432 0.537 0.835 +21.26 5.50 0 2 42.09/ 42.58
2 4 0.186 0.943 0.195 +16.74 4.79 18 1 42.55/ 42.55
3 20 0.182 0.274 0.292 +14.88 4.50 8 2 38.42/ 40.58
4 126 0.559 0.904 0.655 +13.84 4.33 18 1 34.16/ 34.16
SET #1 of 1 TRIAL #3 of 4
-------------------------
Search Euler = 36.4 44.9 169.0, Ensemble = dna
Fixed MR solutions
(No solutions of this type)
Top 117 translations before clustering will be rescored
Highest Score (Z-score): 14.1344 (4.44378)
Top Peaks With Clustering From Rescoring of SET #1 of 1 TRIAL #3 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 56 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 21 0.073 0.085 0.903 +14.13 4.44 0 1 37.35/ 37.35
2 8 0.042 0.973 0.597 +13.04 4.27 5 1 40.44/ 40.44
3 5 0.289 0.602 0.104 +12.89 4.25 20 1 42.57/ 42.57
4 62 0.057 0.787 0.973 +12.72 4.22 12 1 34.99/ 34.99
5 85 0.907 0.285 0.723 +12.48 4.19 24 2 34.47/ 34.76
6 1 0.077 0.265 0.574 +12.45 4.18 17 2 46.85/ 46.85
7 87 0.042 0.885 0.897 +12.40 4.17 14 1 34.27/ 34.27
8 15 0.122 0.897 0.519 +12.15 4.14 7 1 38.02/ 38.02
9 69 0.093 0.743 0.784 +12.10 4.13 12 1 34.87/ 34.87
10 77 0.089 0.441 0.476 +12.03 4.12 11 1 34.70/ 34.70
11 12 0.858 0.105 0.668 +11.65 4.06 23 2 38.85/ 38.85
12 28 0.901 0.511 0.097 +11.40 4.02 7 1 36.86/ 36.86
13 93 0.324 0.017 0.826 +11.39 4.02 15 2 34.15/ 36.80
14 79 0.007 0.019 0.650 +11.29 4.00 10 1 34.58/ 34.58
15 100 0.043 0.650 0.676 +11.29 4.00 17 2 33.99/ 33.99
16 45 0.037 0.875 0.130 +11.26 4.00 6 1 35.95/ 35.95
17 99 0.152 0.386 0.469 +10.88 3.94 16 2 34.00/ 37.55
18 17 0.014 0.069 0.493 +10.76 3.92 8 2 37.74/ 37.74
19 38 0.906 0.821 0.396 +10.61 3.90 8 1 36.46/ 36.46
20 54 0.337 0.581 0.850 +10.54 3.89 14 1 35.38/ 35.38
21 19 0.087 0.522 0.150 +10.14 3.82 15 1 37.55/ 37.55
22 80 0.886 0.099 0.508 +10.11 3.82 17 1 34.56/ 34.56
23 71 0.310 0.018 0.651 +10.08 3.81 12 1 34.81/ 34.81
24 16 0.107 0.896 0.971 +9.99 3.80 8 2 37.76/ 37.76
25 3 0.026 0.395 0.815 +9.97 3.80 25 2 44.29/ 44.68
26 27 0.028 0.153 0.057 +9.93 3.79 12 2 36.89/ 37.10
27 13 0.225 0.712 0.608 +9.32 3.70 12 1 38.81/ 38.81
28 14 0.298 0.079 0.145 +9.18 3.67 8 1 38.03/ 38.03
29 63 0.916 0.086 0.866 +9.06 3.66 12 1 34.97/ 34.97
30 52 0.290 0.721 0.351 +9.02 3.65 10 1 35.48/ 35.48
31 35 0.979 0.595 0.745 +8.99 3.64 23 1 36.64/ 36.64
32 68 0.018 0.117 0.599 +8.78 3.61 14 2 34.89/ 34.89
33 44 0.234 0.776 0.562 +8.78 3.61 12 1 36.02/ 36.02
34 89 0.157 0.174 0.490 +8.73 3.60 9 1 34.26/ 34.26
35 41 0.124 0.934 0.819 +8.71 3.60 14 2 36.10/ 39.05
36 26 0.850 0.568 0.651 +8.35 3.55 22 1 36.98/ 36.98
37 104 0.143 0.022 0.560 +8.20 3.52 10 1 33.83/ 33.83
38 39 0.961 0.878 0.285 +8.18 3.52 12 1 36.26/ 36.26
39 33 0.345 0.598 0.996 +8.15 3.51 15 1 36.75/ 36.75
40 110 0.010 0.121 0.407 +8.01 3.49 6 1 33.73/ 33.73
41 51 0.890 0.515 0.555 +8.00 3.49 13 1 35.50/ 35.50
42 76 0.030 0.159 0.007 +7.91 3.48 10 1 34.73/ 34.73
43 9 0.851 0.214 0.852 +7.84 3.47 20 1 40.20/ 40.20
44 32 0.860 0.880 0.390 +7.78 3.46 6 1 36.76/ 36.76
45 49 0.908 0.190 0.963 +7.72 3.45 13 1 35.70/ 35.70
46 70 0.968 0.598 0.068 +7.72 3.45 4 1 34.81/ 34.81
47 10 0.165 0.543 0.954 +7.63 3.43 21 1 40.19/ 40.19
48 31 0.975 0.969 0.863 +7.58 3.43 12 1 36.77/ 36.77
49 98 0.902 0.013 0.294 +7.42 3.40 14 1 34.00/ 34.00
50 43 0.034 0.839 0.681 +7.41 3.40 9 1 36.06/ 36.06
51 53 0.177 0.644 0.742 +7.32 3.39 16 1 35.45/ 35.45
52 36 0.159 0.864 0.642 +7.32 3.39 4 1 36.47/ 36.47
53 75 0.040 0.969 0.060 +7.30 3.38 6 1 34.75/ 34.75
54 24 0.856 0.698 0.162 +7.28 3.38 11 1 37.06/ 37.06
55 66 0.036 0.967 0.910 +7.09 3.35 9 1 34.91/ 34.91
56 84 0.056 0.732 0.617 +7.07 3.35 12 1 34.47/ 34.47
SET #1 of 1 TRIAL #4 of 4
-------------------------
Search Euler = 44.2 38.0 62.1, Ensemble = dna
Fixed MR solutions
(No solutions of this type)
Top 298 translations before clustering will be rescored
Highest Score (Z-score): 16.621 (4.61623)
Top Peaks With Clustering From Rescoring of SET #1 of 1 TRIAL #4 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 28 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 9 0.192 0.919 0.499 +16.62 4.62 0 1 42.38/ 42.38
2 2 0.200 0.898 0.338 +16.24 4.56 8 1 44.55/ 44.55
3 92 0.557 0.232 0.940 +13.13 4.09 6 1 35.96/ 35.96
4 83 0.267 0.787 0.199 +12.34 3.98 15 1 36.10/ 36.10
5 29 0.392 0.595 0.998 +12.25 3.96 33 1 38.78/ 38.78
6 144 0.269 0.606 0.266 +12.11 3.94 20 1 34.76/ 34.76
7 255 0.359 0.080 0.485 +11.85 3.90 13 1 33.04/ 33.04
8 89 0.244 0.509 0.955 +11.00 3.78 30 1 36.00/ 36.00
9 271 0.520 0.273 0.182 +10.62 3.72 21 1 32.87/ 32.87
10 66 0.520 0.779 0.492 +10.61 3.72 10 1 36.80/ 36.80
11 290 0.475 0.056 0.384 +10.34 3.68 19 1 32.68/ 32.68
12 228 0.555 0.100 0.756 +10.11 3.64 15 1 33.30/ 33.30
13 8 0.600 0.294 0.695 +10.08 3.64 20 2 42.55/ 42.55
14 275 0.404 0.656 0.017 +10.05 3.63 31 1 32.83/ 32.83
15 287 0.606 0.448 0.384 +10.02 3.63 21 2 32.69/ 34.01
16 288 0.603 0.744 0.733 +9.94 3.62 15 1 32.69/ 32.69
17 180 0.371 0.242 0.794 +9.87 3.61 14 1 34.01/ 34.01
18 230 0.384 0.326 0.066 +9.84 3.60 18 1 33.29/ 33.29
19 124 0.273 0.972 0.262 +9.51 3.55 8 1 35.24/ 35.24
20 291 0.493 0.148 0.011 +9.47 3.55 8 1 32.67/ 32.67
21 37 0.220 0.663 0.927 +9.40 3.54 27 1 37.96/ 37.96
22 55 0.271 0.675 0.621 +9.26 3.52 18 1 37.24/ 37.24
23 249 0.542 0.800 0.116 +9.22 3.51 31 1 33.08/ 33.08
24 18 0.566 0.144 0.896 +9.12 3.49 7 1 39.77/ 39.77
25 47 0.592 0.911 0.743 +9.09 3.49 20 1 37.48/ 37.48
26 3 0.352 0.600 0.997 +9.06 3.49 33 1 44.12/ 44.12
27 77 0.345 0.977 0.311 +9.01 3.48 15 1 36.27/ 36.27
28 238 0.469 0.164 0.464 +8.94 3.47 23 1 33.20/ 33.20
---------------
FINAL SELECTION
---------------
Mean used for final selection = -14.0447
Number of solutions stored before final selection = 151
Percentage of top value for final selection = 75
LLG value for final selection = 12.4311
Number of solutions stored (deleted) after final selection = 22 (129)
$TABLE : Translation Function Summary:
$GRAPHS :Graph1 TF Number vs LL-gain:AUTO:1,2:
:Graph2 TF Number vs Z-Score:AUTO:1,3:
$$
Number LL-gain Z-Score $$ loggraph $$
1 21.26 5.50
2 16.74 4.79
3 16.62 4.62
4 16.24 4.56
5 16.17 4.37
6 15.86 4.32
7 15.56 4.28
8 14.88 4.50
9 14.84 4.17
10 14.61 4.14
11 14.13 4.44
12 13.84 4.33
13 13.84 4.03
14 13.43 3.97
15 13.21 3.93
16 13.13 4.09
17 13.04 4.27
18 12.89 4.25
19 12.72 4.22
20 12.48 4.19
21 12.45 4.18
22 12.43 3.82
$$
-----------------
TABLES OF RESULTS
-----------------
Fast Translation Function Table: Space Group I 41 3 2
-----------------------------------------------------
#SET #TRIAL Top (Z) Second (Z) Third (Z) Ensemble
1 1 16.17 ( 4.37) 15.86 ( 4.32) 15.56 ( 4.28) dna
1 2 21.26 ( 5.50) 16.74 ( 4.79) 14.88 ( 4.50) dna
1 3 14.13 ( 4.44) 13.04 ( 4.27) 12.89 ( 4.25) dna
1 4 16.62 ( 4.62) 16.24 ( 4.56) 13.13 ( 4.09) dna
---- ------
------------
OUTPUT FILES
------------
No script files output
No pdb files output
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 1 mins 55.70 secs (115.70 secs)
Finished: Wed Jul 19 11:35:46 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:35:46 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.0 ***
*************************************************************************************
Purge solutions according to highest LLG from TFs in other spacegroups
Percent used for purge = 0.75
Top LLG value from TF = 21.2564
Top LLG value for purge = 21.2564
Mean LLG used for purge = -14.0447
Number of solutions stored before purge = 22
Number of solutions stored (deleted) after purge = 22 (0)
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 1 mins 55.71 secs (115.71 secs)
Finished: Wed Jul 19 11:35:46 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:35:46 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT PACKING 2.0 ***
*************************************************************************************
Space Group Name (Number): I 41 3 2 (214)
Unit Cell: 76.86 76.86 76.86 90.00 90.00 90.00
----------------------
STRUCTURES FOR PACKING
----------------------
Packing will be performed with "trace" atoms (C-alphas for protein, P and selected
N for nucleic acid). When a protein molecule consists of more than one structure,
the structure with the highest homology is selected for packing. The structure is
then trimmed of loops that diverge more than 3A from other atoms in the molecule.
Ensemble: dna
-------------
Structure with lowest rms = 131d.pdb (0.8)
Trace length before selecting conserved = 41
Trace length after selecting conserved = 41
-------------------------
PACKING FUNCTION #1 OF 22
-------------------------
ANNOTATION: RFZ=2.0 TFZ=5.5
SOLU 6DIM ENSE dna EULER 51.8 40.3 25.6 FRAC 0.432 0.537 0.835
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 128.2 139.7 205.6 FRAC 0.068 -0.463 0.165
There were 3 clashes between trace atoms for models 1:1
In total there were 3 clashes between trace atoms
-------------------------
PACKING FUNCTION #2 OF 22
-------------------------
ANNOTATION: RFZ=2.0 TFZ=4.8
SOLU 6DIM ENSE dna EULER 51.8 40.3 25.6 FRAC 0.186 0.943 0.195
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 218.2 139.7 205.6 FRAC 0.307 0.064 0.055
There were 12 clashes between trace atoms for models 1:1
In total there were 12 clashes between trace atoms
-------------------------
PACKING FUNCTION #3 OF 22
-------------------------
ANNOTATION: RFZ=1.8 TFZ=4.6
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.192 0.919 0.499
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 134.2 38.0 62.1 FRAC 0.331 -0.058 -0.251
There were 13 clashes between trace atoms for models 1:1
In total there were 13 clashes between trace atoms
-------------------------
PACKING FUNCTION #4 OF 22
-------------------------
ANNOTATION: RFZ=1.8 TFZ=4.6
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.200 0.898 0.338
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 60.8 115.4 9.6 FRAC -0.050 -0.412 0.352
There were 40 clashes between trace atoms for models 1:1
In total there were 40 clashes between trace atoms
-------------------------
PACKING FUNCTION #5 OF 22
-------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.537 0.270 0.642
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 232.4 59.1 344.6 FRAC 0.230 0.358 0.037
In total there were no clashes between trace atoms
-------------------------
PACKING FUNCTION #6 OF 22
-------------------------
ANNOTATION: RFZ=2.1 TFZ=4.3
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.517 0.617 0.926
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 315.5 47.2 108.3 FRAC -0.133 -0.267 -0.324
There were 2 clashes between trace atoms for models 1:1
In total there were 2 clashes between trace atoms
-------------------------
PACKING FUNCTION #7 OF 22
-------------------------
ANNOTATION: RFZ=2.1 TFZ=4.3
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.079 0.451 0.954
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 134.5 132.8 288.3 FRAC -0.079 -0.049 0.546
There were 4 clashes between trace atoms for models 1:1
In total there were 4 clashes between trace atoms
-------------------------
PACKING FUNCTION #8 OF 22
-------------------------
ANNOTATION: RFZ=2.0 TFZ=4.5
SOLU 6DIM ENSE dna EULER 51.8 40.3 25.6 FRAC 0.182 0.274 0.292
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 303.7 113.6 84.7 FRAC -0.226 0.208 -0.182
There were 2 clashes between trace atoms for models 1:1
In total there were 2 clashes between trace atoms
-------------------------
PACKING FUNCTION #9 OF 22
-------------------------
ANNOTATION: RFZ=2.1 TFZ=4.2
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.430 0.026 0.601
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 217.1 58.4 233.0 FRAC 0.399 0.070 0.026
There were 4 clashes between trace atoms for models 1:1
In total there were 4 clashes between trace atoms
--------------------------
PACKING FUNCTION #10 OF 22
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.1
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.443 0.641 0.021
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 37.6 120.9 164.6 FRAC -0.229 -0.109 -0.193
There were 4 clashes between trace atoms for models 1:1
In total there were 4 clashes between trace atoms
--------------------------
PACKING FUNCTION #11 OF 22
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.4
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.073 0.085 0.903
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 128.7 65.2 286.6 FRAC 0.177 -0.347 0.335
There were 3 clashes between trace atoms for models 1:1
In total there were 3 clashes between trace atoms
--------------------------
PACKING FUNCTION #12 OF 22
--------------------------
ANNOTATION: RFZ=2.0 TFZ=4.3
SOLU 6DIM ENSE dna EULER 51.8 40.3 25.6 FRAC 0.559 0.904 0.655
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 236.3 66.4 264.7 FRAC 0.596 0.345 0.059
There were 10 clashes between trace atoms for models 1:1
In total there were 10 clashes between trace atoms
--------------------------
PACKING FUNCTION #13 OF 22
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.0
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.372 0.458 0.161
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 37.1 58.4 233.0 FRAC -0.339 -0.128 -0.042
There were 7 clashes between trace atoms for models 1:1
In total there were 7 clashes between trace atoms
--------------------------
PACKING FUNCTION #14 OF 22
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.0
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.107 0.517 0.183
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 307.6 120.9 164.6 FRAC 0.017 0.317 -0.107
In total there were no clashes between trace atoms
--------------------------
PACKING FUNCTION #15 OF 22
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.9
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.318 0.770 0.914
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 127.1 58.4 233.0 FRAC -0.068 -0.336 0.020
There were 36 clashes between trace atoms for models 1:1
In total there were 36 clashes between trace atoms
--------------------------
PACKING FUNCTION #16 OF 22
--------------------------
ANNOTATION: RFZ=1.8 TFZ=4.1
SOLU 6DIM ENSE dna EULER 44.2 38.0 62.1 FRAC 0.557 0.232 0.940
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 61.4 63.8 293.1 FRAC -0.268 -0.560 0.057
There were 22 clashes between trace atoms for models 1:1
In total there were 22 clashes between trace atoms
--------------------------
PACKING FUNCTION #17 OF 22
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.042 0.973 0.597
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.042 -0.027 -0.403
In total there were no clashes between trace atoms
--------------------------
PACKING FUNCTION #18 OF 22
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.289 0.602 0.104
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC -0.211 0.102 -0.396
There were 18 clashes between trace atoms for models 1:1
In total there were 18 clashes between trace atoms
--------------------------
PACKING FUNCTION #19 OF 22
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.2
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.057 0.787 0.973
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 306.4 44.9 169.0 FRAC 0.037 0.193 -0.277
In total there were no clashes between trace atoms
--------------------------
PACKING FUNCTION #20 OF 22
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.2
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.907 0.285 0.723
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC -0.093 0.285 -0.277
There were 10 clashes between trace atoms for models 1:1
In total there were 10 clashes between trace atoms
--------------------------
PACKING FUNCTION #21 OF 22
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.2
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.077 0.265 0.574
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 51.3 114.8 106.6 FRAC -0.173 -0.176 -0.015
There were 24 clashes between trace atoms for models 1:1
In total there were 24 clashes between trace atoms
--------------------------
PACKING FUNCTION #22 OF 22
--------------------------
ANNOTATION: RFZ=2.1 TFZ=3.8
SOLU 6DIM ENSE dna EULER 45.5 47.2 108.3 FRAC 0.516 0.981 0.727
Solution #1 moved to closest CoM approach to Origin
After move:
SOLU 6DIM ENSE dna EULER 217.1 58.4 233.0 FRAC 0.273 -0.016 -0.019
There were 8 clashes between trace atoms for models 1:1
In total there were 8 clashes between trace atoms
-------------
PACKING TABLE
-------------
Solutions rejected if number of clashes > 0
# #CLASHES # ACCEPTED
1 3 NO
2 12 NO
3 13 NO
4 40 NO
5 0 1 YES
6 2 NO
7 4 NO
8 2 NO
9 4 NO
10 4 NO
11 3 NO
12 10 NO
13 7 NO
14 0 2 YES
15 36 NO
16 22 NO
17 0 3 YES
18 18 NO
19 0 4 YES
20 10 NO
21 24 NO
22 8 NO
4 accepted of 22 solutions
------------
OUTPUT FILES
------------
No script files output
No pdb files output
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 1 mins 56.73 secs (116.73 secs)
Finished: Wed Jul 19 11:35:47 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:35:47 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.0 ***
*************************************************************************************
-------------------------------
DATA FOR REFINEMENT AND PHASING
-------------------------------
Outliers with a probability less than 1e-06 will be rejected
No reflections are outliers
Space-Group Name (Number): I 41 3 2 (214)
Resolution of All Data (Number): 1.62 38.43 (5100)
Resolution of Selected Data (Number): 3.50 38.43 (581)
-------------------
WILSON DISTRIBUTION
-------------------
Parameters set for Wilson log-likelihood calculation
E = 0 and variance 1 for each reflection
Without correction for SigF to the variances,
Wilson log(likelihood) = - number of acentrics (358)
- half number of centrics (223/2)
= -469
With correction for SigF,
Wilson log(likelihood) = -462.199
------------
ENSEMBLE dna
------------
The RmsD of this model with respect to the real structure is 0.8
Unit Cell: 98.66 53.20 41.28 90.00 90.00 90.00
Calculating electron density...
Done
------------------
REFINEMENT #1 OF 4
------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 232.4 59.1 344.6 FRAC 0.230 0.358 0.037
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 16.372
#1 18.804 2.431 2.431
#2 18.973 2.601 0.169
#3 18.987 2.615 0.014
#4 18.987 2.615 0.000
#5 18.987 2.615 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna -3.1958 +0.6394 -3.2481 -0.0831 +0.0356 +0.1188
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
The log(likelihood) gain = 18.9868 (at start 16.3722)
The R-factor = 58.93 (at start 60.26)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
------------------
REFINEMENT #2 OF 4
------------------
ANNOTATION: RFZ=2.1 TFZ=4.0 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 307.6 120.9 164.6 FRAC 0.017 0.317 -0.107
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 13.821
#1 14.801 0.980 0.980
#2 14.859 1.038 0.058
#3 14.896 1.075 0.037
#4 14.896 1.075 0.000
#5 14.917 1.096 0.021
#6 15.019 1.198 0.102
#7 15.020 1.199 0.001
#8 15.020 1.199 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna -1.6750 -0.2515 -0.4375 +0.0464 -0.1412 +0.0574
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 307.3 120.4 162.8 FRAC 0.012 0.312 -0.114
The log(likelihood) gain = 15.0203 (at start 13.8211)
The R-factor = 59.59 (at start 59.82)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
------------------
REFINEMENT #3 OF 4
------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 36.4 44.9 169.0 FRAC 0.042 -0.027 -0.403
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 13.039
#1 17.040 4.001 4.001
#2 18.449 5.410 1.409
#3 18.482 5.443 0.033
#4 18.652 5.613 0.170
#5 18.742 5.703 0.090
#6 18.743 5.704 0.001
#7 18.747 5.708 0.004
#8 18.748 5.709 0.000
#9 18.779 5.740 0.031
#10 18.779 5.740 0.000
#11 18.781 5.742 0.002
#12 18.782 5.743 0.000
#13 18.782 5.743 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna -6.2489 -2.2788 +0.2145 +0.1826 +0.1186 -0.1736
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
The log(likelihood) gain = 18.7815 (at start 13.0390)
The R-factor = 60.69 (at start 61.48)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
------------------
REFINEMENT #4 OF 4
------------------
ANNOTATION: RFZ=1.9 TFZ=4.2 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 306.4 44.9 169.0 FRAC 0.037 0.193 -0.277
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start 12.823
#1 15.864 3.041 3.041
#2 16.240 3.417 0.376
#3 16.345 3.522 0.105
#4 16.388 3.565 0.042
#5 16.399 3.576 0.011
#6 16.399 3.576 0.000
#7 16.399 3.576 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna -2.3288 -2.5558 +1.7400 +0.0274 -0.1322 -0.0101
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 301.8 43.2 171.1 FRAC 0.060 0.180 -0.274
The log(likelihood) gain = 16.3987 (at start 12.8230)
The R-factor = 59.37 (at start 60.37)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
----------------
PRUNE DUPLICATES
----------------
Check for nearly equivalent solutions
No duplicate solutions pruned
Refinement Table: Space Group I 41 3 2
--------------------------------------
#+ = input number #* = output number
Unsorted (refinement order) Sorted in LL-gain order
Initial Refined Initial Refined
#+ LL-gain LL-gain Unique #* #+ LL-gain LL-gain Unique =#*
1 16.37 18.99 YES 1 1 16.37 18.99 YES
2 13.82 15.02 YES 2 3 13.04 18.78 YES
3 13.04 18.78 YES 3 4 12.82 16.40 YES
4 12.82 16.40 YES 4 2 13.82 15.02 YES
------------
OUTPUT FILES
------------
No script files output
No pdb files output
No mtz files output
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 2 mins 7.49 secs (127.49 secs)
Finished: Wed Jul 19 11:35:58 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:35:58 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.0 ***
*************************************************************************************
Purge solutions according to highest LLG
Top LLG value from Translation Function = 21.2564
Percent used for purge = 0.75
Top LLG value used for purge = 18.9868
Mean LLG used for purge = -14.0447
Number of solutions stored before purge = 4
Number of solutions stored (deleted) after purge = 4 (0)
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 2 mins 7.49 secs (127.49 secs)
Finished: Wed Jul 19 11:35:58 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:35:58 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.0 ***
*************************************************************************************
New Best Solution: TOP LL-GAIN 18.986830
Permutation #1
Search Ensemble dna
Space Group: I 41 3 2
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 2 mins 7.50 secs (127.50 secs)
Finished: Wed Jul 19 11:35:58 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:35:58 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT FAST ROTATION FUNCTION 2.0 ***
*************************************************************************************
-------------------------------
DATA FOR FAST ROTATION FUNCTION
-------------------------------
Outliers with a probability less than 1e-06 will be rejected
No reflections are outliers
Space-Group Name (Number): I 41 3 2 (214)
Resolution of All Data (Number): 1.62 38.43 (5100)
Resolution of Selected Data (Number): 3.50 38.43 (581)
--------------------------
ENSEMBLE FOR DECOMPOSITION
--------------------------
The RmsD of this model with respect to the real structure is 0.8
Unit Cell: 40.31 28.95 25.97 90.00 90.00 90.00
Calculating electron density...
Done
-------------------
WILSON DISTRIBUTION
-------------------
Parameters set for Wilson log-likelihood calculation
E = 0 and variance 1 for each reflection
Without correction for SigF to the variances,
Wilson log(likelihood) = - number of acentrics (358)
- half number of centrics (223/2)
= -469
With correction for SigF,
Wilson log(likelihood) = -462.199
------------
ENSEMBLE dna
------------
The RmsD of this model with respect to the real structure is 0.8
Unit Cell: 98.66 53.20 41.28 90.00 90.00 90.00
Calculating electron density...
Done
------------------------------
FAST ROTATION FUNCTION #1 OF 4
------------------------------
Search Ensemble: dna
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19
Fixed MR solutions
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
Spherical Harmonics
-------------------
Elmn for Data
0% 100%
|===========================================================================| DONE
Elmn for Search Ensemble
0% 100%
|==========================================================================| DONE
Scanning the Range of Beta Angles
---------------------------------
Performing a 13.298 degree search.
0% 100%
|===============| DONE
Top 301 rotations before clustering will be rescored
0% 100%
|=============================================================| DONE
Scoring 500 randomly sampled rotations
0% 100%
|========================================================================| DONE
Mean Score (Sigma): 15.3999 (3.31752)
Highest Score (Z-score): 24.9735 (2.88576)
Top Peaks With Clustering From Rescoring of FRF #1
--------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 4 sites over 75% of top
The sites over 75% are:
# (#) Euler1 Euler2 Euler3 LLG Z-score Split #Group raw/top
1 28 35.1 29.8 44.6 +24.97 2.89 0.0 16 86.8/ 88.7
125.1 29.8 44.6
215.1 29.8 44.6
305.1 29.8 44.6
324.9 150.2 224.6
54.9 150.2 224.6
144.9 150.2 224.6
234.9 150.2 224.6
25.1 73.4 166.1
115.1 73.4 166.1
205.1 73.4 166.1
295.1 73.4 166.1
334.9 106.6 346.1
64.9 106.6 346.1
154.9 106.6 346.1
244.9 106.6 346.1
71.8 66.0 263.7
288.2 114.0 83.7
18.2 114.0 83.7
108.2 114.0 83.7
198.2 114.0 83.7
251.8 66.0 263.7
341.8 66.0 263.7
161.8 66.0 263.7
2 88 8.8 31.5 29.0 +23.31 2.38 40.6 8 79.5/ 79.5
98.8 31.5 29.0
188.8 31.5 29.0
278.8 31.5 29.0
351.2 148.5 209.0
81.2 148.5 209.0
171.2 148.5 209.0
261.2 148.5 209.0
31.2 85.4 126.6
121.2 85.4 126.6
211.2 85.4 126.6
301.2 85.4 126.6
328.8 94.6 306.6
58.8 94.6 306.6
148.8 94.6 306.6
238.8 94.6 306.6
84.6 58.9 219.3
275.4 121.1 39.3
5.4 121.1 39.3
95.4 121.1 39.3
185.4 121.1 39.3
264.6 58.9 219.3
354.6 58.9 219.3
174.6 58.9 219.3
3 72 80.0 30.8 159.0 +23.28 2.38 57.4 6 81.2/ 93.8
170.0 30.8 159.0
260.0 30.8 159.0
350.0 30.8 159.0
280.0 149.2 339.0
10.0 149.2 339.0
100.0 149.2 339.0
190.0 149.2 339.0
5.9 59.7 327.4
95.9 59.7 327.4
185.9 59.7 327.4
275.9 59.7 327.4
354.1 120.3 147.4
84.1 120.3 147.4
174.1 120.3 147.4
264.1 120.3 147.4
59.5 84.9 60.4
300.5 95.1 240.4
30.5 95.1 240.4
120.5 95.1 240.4
210.5 95.1 240.4
239.5 84.9 60.4
329.5 84.9 60.4
149.5 84.9 60.4
4 48 78.4 41.9 225.2 +23.16 2.34 42.2 5 83.5/ 89.2
168.4 41.9 225.2
258.4 41.9 225.2
348.4 41.9 225.2
281.6 138.1 45.2
11.6 138.1 45.2
101.6 138.1 45.2
191.6 138.1 45.2
10.2 49.2 29.8
100.2 49.2 29.8
190.2 49.2 29.8
280.2 49.2 29.8
349.8 130.8 209.8
79.8 130.8 209.8
169.8 130.8 209.8
259.8 130.8 209.8
48.7 82.3 126.5
311.3 97.7 306.5
41.3 97.7 306.5
131.3 97.7 306.5
221.3 97.7 306.5
228.7 82.3 126.5
318.7 82.3 126.5
138.7 82.3 126.5
Fast Rotation Function Table
----------------------------
Top (Z) Second (Z) Third (Z)
24.97 ( 2.89) 23.31 ( 2.38) 23.28 ( 2.38)
------------------------------
FAST ROTATION FUNCTION #2 OF 4
------------------------------
Search Ensemble: dna
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19
Fixed MR solutions
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
Spherical Harmonics
-------------------
Elmn for Data
0% 100%
|===========================================================================| DONE
Elmn for Search Ensemble
0% 100%
|==========================================================================| DONE
Scanning the Range of Beta Angles
---------------------------------
Performing a 13.298 degree search.
0% 100%
|===============| DONE
Top 190 rotations before clustering will be rescored
0% 100%
|================================================================| DONE
Scoring 500 randomly sampled rotations
0% 100%
|========================================================================| DONE
Mean Score (Sigma): 15.3908 (3.13901)
Highest Score (Z-score): 24.0055 (2.74442)
Top Peaks With Clustering From Rescoring of FRF #2
--------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 4 sites over 75% of top
The sites over 75% are:
# (#) Euler1 Euler2 Euler3 LLG Z-score Split #Group raw/top
1 86 69.2 35.2 229.8 +24.01 2.74 0.0 13 74.6/ 79.8
159.2 35.2 229.8
249.2 35.2 229.8
339.2 35.2 229.8
290.8 144.8 49.8
20.8 144.8 49.8
110.8 144.8 49.8
200.8 144.8 49.8
14.0 57.4 24.9
104.0 57.4 24.9
194.0 57.4 24.9
284.0 57.4 24.9
346.0 122.6 204.9
76.0 122.6 204.9
166.0 122.6 204.9
256.0 122.6 204.9
56.6 78.2 122.6
303.4 101.8 302.6
33.4 101.8 302.6
123.4 101.8 302.6
213.4 101.8 302.6
236.6 78.2 122.6
326.6 78.2 122.6
146.6 78.2 122.6
2 71 35.1 29.8 44.6 +23.74 2.66 46.8 7 76.5/ 80.8
125.1 29.8 44.6
215.1 29.8 44.6
305.1 29.8 44.6
324.9 150.2 224.6
54.9 150.2 224.6
144.9 150.2 224.6
234.9 150.2 224.6
25.1 73.4 166.1
115.1 73.4 166.1
205.1 73.4 166.1
295.1 73.4 166.1
334.9 106.6 346.1
64.9 106.6 346.1
154.9 106.6 346.1
244.9 106.6 346.1
71.8 66.0 263.7
288.2 114.0 83.7
18.2 114.0 83.7
108.2 114.0 83.7
198.2 114.0 83.7
251.8 66.0 263.7
341.8 66.0 263.7
161.8 66.0 263.7
3 20 0.3 37.5 296.6 +22.86 2.38 40.2 9 85.2/ 94.1
90.3 37.5 296.6
180.3 37.5 296.6
270.3 37.5 296.6
359.7 142.5 116.6
89.7 142.5 116.6
179.7 142.5 116.6
269.7 142.5 116.6
37.5 89.8 26.8
127.5 89.8 26.8
217.5 89.8 26.8
307.5 89.8 26.8
322.5 90.2 206.8
52.5 90.2 206.8
142.5 90.2 206.8
232.5 90.2 206.8
89.8 52.5 117.0
270.2 127.5 297.0
0.2 127.5 297.0
90.2 127.5 297.0
180.2 127.5 297.0
269.8 52.5 117.0
359.8 52.5 117.0
179.8 52.5 117.0
4 34 4.7 30.8 15.9 +22.62 2.30 31.6 1 81.2/ 81.2
94.7 30.8 15.9
184.7 30.8 15.9
274.7 30.8 15.9
355.3 149.2 195.9
85.3 149.2 195.9
175.3 149.2 195.9
265.3 149.2 195.9
30.7 87.6 110.0
120.7 87.6 110.0
210.7 87.6 110.0
300.7 87.6 110.0
329.3 92.4 290.0
59.3 92.4 290.0
149.3 92.4 290.0
239.3 92.4 290.0
87.2 59.4 201.4
272.8 120.6 21.4
2.8 120.6 21.4
92.8 120.6 21.4
182.8 120.6 21.4
267.2 59.4 201.4
357.2 59.4 201.4
177.2 59.4 201.4
Fast Rotation Function Table
----------------------------
Top (Z) Second (Z) Third (Z)
24.01 ( 2.74) 23.74 ( 2.66) 22.86 ( 2.38)
------------------------------
FAST ROTATION FUNCTION #3 OF 4
------------------------------
Search Ensemble: dna
ANNOTATION: RFZ=1.9 TFZ=4.2 PAK=0 LLG=16
Fixed MR solutions
SOLU 6DIM ENSE dna EULER 301.8 43.2 171.1 FRAC 0.060 0.180 -0.274
Spherical Harmonics
-------------------
Elmn for Data
0% 100%
|===========================================================================| DONE
Elmn for Search Ensemble
0% 100%
|==========================================================================| DONE
Scanning the Range of Beta Angles
---------------------------------
Performing a 13.298 degree search.
0% 100%
|===============| DONE
Top 251 rotations before clustering will be rescored
0% 100%
|===============================================================| DONE
Scoring 500 randomly sampled rotations
0% 100%
|========================================================================| DONE
Mean Score (Sigma): 13.0537 (3.44041)
Highest Score (Z-score): 21.9217 (2.5776)
Top Peaks With Clustering From Rescoring of FRF #3
--------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 4 sites over 75% of top
The sites over 75% are:
# (#) Euler1 Euler2 Euler3 LLG Z-score Split #Group raw/top
1 115 35.1 29.8 44.6 +21.92 2.58 0.0 12 76.2/ 80.5
125.1 29.8 44.6
215.1 29.8 44.6
305.1 29.8 44.6
324.9 150.2 224.6
54.9 150.2 224.6
144.9 150.2 224.6
234.9 150.2 224.6
25.1 73.4 166.1
115.1 73.4 166.1
205.1 73.4 166.1
295.1 73.4 166.1
334.9 106.6 346.1
64.9 106.6 346.1
154.9 106.6 346.1
244.9 106.6 346.1
71.8 66.0 263.7
288.2 114.0 83.7
18.2 114.0 83.7
108.2 114.0 83.7
198.2 114.0 83.7
251.8 66.0 263.7
341.8 66.0 263.7
161.8 66.0 263.7
2 216 4.7 30.8 15.9 +20.05 2.03 37.4 1 69.0/ 69.0
94.7 30.8 15.9
184.7 30.8 15.9
274.7 30.8 15.9
355.3 149.2 195.9
85.3 149.2 195.9
175.3 149.2 195.9
265.3 149.2 195.9
30.7 87.6 110.0
120.7 87.6 110.0
210.7 87.6 110.0
300.7 87.6 110.0
329.3 92.4 290.0
59.3 92.4 290.0
149.3 92.4 290.0
239.3 92.4 290.0
87.2 59.4 201.4
272.8 120.6 21.4
2.8 120.6 21.4
92.8 120.6 21.4
182.8 120.6 21.4
267.2 59.4 201.4
357.2 59.4 201.4
177.2 59.4 201.4
3 178 74.7 40.1 222.3 +19.88 1.98 47.1 1 71.2/ 71.2
164.7 40.1 222.3
254.7 40.1 222.3
344.7 40.1 222.3
285.3 139.9 42.3
15.3 139.9 42.3
105.3 139.9 42.3
195.3 139.9 42.3
12.6 51.6 22.6
102.6 51.6 22.6
192.6 51.6 22.6
282.6 51.6 22.6
347.4 128.4 202.6
77.4 128.4 202.6
167.4 128.4 202.6
257.4 128.4 202.6
50.9 80.2 120.5
309.1 99.8 300.5
39.1 99.8 300.5
129.1 99.8 300.5
219.1 99.8 300.5
230.9 80.2 120.5
320.9 80.2 120.5
140.9 80.2 120.5
4 248 8.4 36.9 290.9 +19.74 1.94 56.4 1 67.7/ 67.7
98.4 36.9 290.9
188.4 36.9 290.9
278.4 36.9 290.9
351.6 143.1 110.9
81.6 143.1 110.9
171.6 143.1 110.9
261.6 143.1 110.9
36.6 85.0 27.7
126.6 85.0 27.7
216.6 85.0 27.7
306.6 85.0 27.7
323.4 95.0 207.7
53.4 95.0 207.7
143.4 95.0 207.7
233.4 95.0 207.7
83.7 53.6 121.4
276.3 126.4 301.4
6.3 126.4 301.4
96.3 126.4 301.4
186.3 126.4 301.4
263.7 53.6 121.4
353.7 53.6 121.4
173.7 53.6 121.4
Fast Rotation Function Table
----------------------------
Top (Z) Second (Z) Third (Z)
21.92 ( 2.58) 20.05 ( 2.03) 19.88 ( 1.98)
------------------------------
FAST ROTATION FUNCTION #4 OF 4
------------------------------
Search Ensemble: dna
ANNOTATION: RFZ=2.1 TFZ=4.0 PAK=0 LLG=15
Fixed MR solutions
SOLU 6DIM ENSE dna EULER 307.3 120.4 162.8 FRAC 0.012 0.312 -0.114
Spherical Harmonics
-------------------
Elmn for Data
0% 100%
|===========================================================================| DONE
Elmn for Search Ensemble
0% 100%
|==========================================================================| DONE
Scanning the Range of Beta Angles
---------------------------------
Performing a 13.298 degree search.
0% 100%
|===============| DONE
Top 209 rotations before clustering will be rescored
0% 100%
|======================================================================| DONE
Scoring 500 randomly sampled rotations
0% 100%
|========================================================================| DONE
Mean Score (Sigma): 11.7086 (3.2091)
Highest Score (Z-score): 19.5093 (2.43084)
Top Peaks With Clustering From Rescoring of FRF #4
--------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 5 sites over 75% of top
The sites over 75% are:
# (#) Euler1 Euler2 Euler3 LLG Z-score Split #Group raw/top
1 113 74.7 40.1 222.3 +19.51 2.43 0.0 12 73.9/ 85.9
164.7 40.1 222.3
254.7 40.1 222.3
344.7 40.1 222.3
285.3 139.9 42.3
15.3 139.9 42.3
105.3 139.9 42.3
195.3 139.9 42.3
12.6 51.6 22.6
102.6 51.6 22.6
192.6 51.6 22.6
282.6 51.6 22.6
347.4 128.4 202.6
77.4 128.4 202.6
167.4 128.4 202.6
257.4 128.4 202.6
50.9 80.2 120.5
309.1 99.8 300.5
39.1 99.8 300.5
129.1 99.8 300.5
219.1 99.8 300.5
230.9 80.2 120.5
320.9 80.2 120.5
140.9 80.2 120.5
2 38 10.2 42.1 248.3 +19.43 2.40 47.8 13 82.5/ 84.0
100.2 42.1 248.3
190.2 42.1 248.3
280.2 42.1 248.3
349.8 137.9 68.3
79.8 137.9 68.3
169.8 137.9 68.3
259.8 137.9 68.3
41.7 83.2 345.9
131.7 83.2 345.9
221.7 83.2 345.9
311.7 83.2 345.9
318.3 96.8 165.9
48.3 96.8 165.9
138.3 96.8 165.9
228.3 96.8 165.9
80.9 48.7 81.9
279.1 131.3 261.9
9.1 131.3 261.9
99.1 131.3 261.9
189.1 131.3 261.9
260.9 48.7 81.9
350.9 48.7 81.9
170.9 48.7 81.9
3 123 35.1 29.8 44.6 +18.82 2.21 47.1 9 73.1/ 77.4
125.1 29.8 44.6
215.1 29.8 44.6
305.1 29.8 44.6
324.9 150.2 224.6
54.9 150.2 224.6
144.9 150.2 224.6
234.9 150.2 224.6
25.1 73.4 166.1
115.1 73.4 166.1
205.1 73.4 166.1
295.1 73.4 166.1
334.9 106.6 346.1
64.9 106.6 346.1
154.9 106.6 346.1
244.9 106.6 346.1
71.8 66.0 263.7
288.2 114.0 83.7
18.2 114.0 83.7
108.2 114.0 83.7
198.2 114.0 83.7
251.8 66.0 263.7
341.8 66.0 263.7
161.8 66.0 263.7
4 3 79.8 36.2 181.0 +18.26 2.04 37.6 13 95.8/100.0
169.8 36.2 181.0
259.8 36.2 181.0
349.8 36.2 181.0
280.2 143.8 1.0
10.2 143.8 1.0
100.2 143.8 1.0
190.2 143.8 1.0
7.4 54.5 348.5
97.4 54.5 348.5
187.4 54.5 348.5
277.4 54.5 348.5
352.6 125.5 168.5
82.6 125.5 168.5
172.6 125.5 168.5
262.6 125.5 168.5
54.2 84.0 82.8
305.8 96.0 262.8
35.8 96.0 262.8
125.8 96.0 262.8
215.8 96.0 262.8
234.2 84.0 82.8
324.2 84.0 82.8
144.2 84.0 82.8
5 180 8.8 31.5 29.0 +18.13 2.00 20.5 1 69.2/ 69.2
98.8 31.5 29.0
188.8 31.5 29.0
278.8 31.5 29.0
351.2 148.5 209.0
81.2 148.5 209.0
171.2 148.5 209.0
261.2 148.5 209.0
31.2 85.4 126.6
121.2 85.4 126.6
211.2 85.4 126.6
301.2 85.4 126.6
328.8 94.6 306.6
58.8 94.6 306.6
148.8 94.6 306.6
238.8 94.6 306.6
84.6 58.9 219.3
275.4 121.1 39.3
5.4 121.1 39.3
95.4 121.1 39.3
185.4 121.1 39.3
264.6 58.9 219.3
354.6 58.9 219.3
174.6 58.9 219.3
Fast Rotation Function Table
----------------------------
Top (Z) Second (Z) Third (Z)
19.51 ( 2.43) 19.43 ( 2.40) 18.82 ( 2.21)
---------------
FINAL SELECTION
---------------
Number of sets stored before final selection = 4
Number of solutions stored before final selection = 17
Number of sets stored (deleted) after final selection = 2 (2)
Number of solutions stored (deleted) after final selection = 8 (9)
$TABLE : Rotation Function Summary:
$GRAPHS :Graph1 RF Number vs LL-gain:AUTO:1,2:
:Graph2 RF Number vs Z-Score:AUTO:1,3:
$$
Number LL-gain Z-Score $$ loggraph $$
1 24.97 2.886
2 24.01 2.744
3 23.74 2.660
4 23.31 2.383
5 23.28 2.377
6 23.16 2.338
7 22.86 2.379
8 22.62 2.302
$$
------------
OUTPUT FILES
------------
No script files output
No pdb files output
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 2 mins 32.03 secs (152.03 secs)
Finished: Wed Jul 19 11:36:22 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:36:22 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.0 ***
*************************************************************************************
Loop over space groups
SpaceGroup #1 of 2
Best space group from search with first ensemble: I 41 3 2
Permutation #1 of 1
Search Ensemble dna
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 2 mins 32.04 secs (152.04 secs)
Finished: Wed Jul 19 11:36:22 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:36:22 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT FAST TRANSLATION FUNCTION 2.0 ***
*************************************************************************************
----------------------------------
DATA FOR FAST TRANSLATION FUNCTION
----------------------------------
Outliers with a probability less than 1e-06 will be rejected
No reflections are outliers
Space-Group Name (Number): I 41 3 2 (214)
Resolution of All Data (Number): 1.62 38.43 (5100)
Resolution of Selected Data (Number): 3.50 38.43 (581)
-------------------
WILSON DISTRIBUTION
-------------------
Parameters set for Wilson log-likelihood calculation
E = 0 and variance 1 for each reflection
Without correction for SigF to the variances,
Wilson log(likelihood) = - number of acentrics (358)
- half number of centrics (223/2)
= -469
With correction for SigF,
Wilson log(likelihood) = -462.199
--------------------
SPACE GROUP I 41 3 2
--------------------
Space Group Name (Number): I 41 3 2 (214)
---------------------------------
FAST TRANSLATION FUNCTION #1 OF 2
---------------------------------
Fixed MR solutions
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
This FTF set has 4 trial orientations
#TRIAL Euler1 Euler2 Euler3 Ensemble
1 35.1 29.8 44.6 dna
2 8.8 31.5 29.0 dna
3 80.0 30.8 159.0 dna
4 78.4 41.9 225.2 dna
SET #1 of 2 TRIAL #1 of 4
-------------------------
Search Euler = 35.1 29.8 44.6, Ensemble = dna
------------
ENSEMBLE dna
------------
The RmsD of this model with respect to the real structure is 0.8
Unit Cell: 98.66 53.20 41.28 90.00 90.00 90.00
Calculating electron density...
Done
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19
Fixed MR solutions
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
Top 292 translations before clustering will be rescored
Highest Score (Z-score): -7.46728 (4.08212)
Top Peaks With Clustering From Rescoring of SET #1 of 2 TRIAL #1 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 21 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 47 0.732 0.082 0.270 -7.47 4.08 0 4 77.32/ 77.32
2 89 0.274 0.639 0.007 -9.42 3.97 9 2 74.40/ 74.40
3 210 0.128 0.031 0.912 -10.45 3.92 20 2 70.51/ 70.51
4 182 0.077 0.844 0.373 -11.31 3.87 28 2 71.37/ 71.37
5 223 0.605 0.232 0.656 -11.52 3.85 18 2 70.25/ 70.25
6 6 0.905 0.090 0.047 -14.14 3.71 21 2 84.03/ 84.03
7 147 0.605 0.125 0.474 -14.78 3.67 13 2 72.36/ 72.36
8 126 0.390 0.504 0.066 -16.28 3.59 6 6 73.20/ 73.20
9 42 0.852 0.265 0.943 -17.45 3.52 17 2 77.41/ 77.41
10 169 0.289 0.851 0.662 -17.90 3.50 20 4 71.65/ 74.60
11 87 0.861 0.327 0.006 -18.02 3.49 23 2 74.47/ 74.47
12 165 0.605 0.608 0.911 -18.71 3.45 18 2 71.86/ 71.86
13 73 0.510 0.869 0.011 -19.69 3.40 3 2 76.19/ 76.19
14 59 0.100 0.016 0.191 -20.30 3.36 23 4 76.75/ 77.07
15 12 0.827 0.957 0.232 -20.31 3.36 8 2 81.21/ 81.21
16 56 0.960 0.449 0.629 -20.56 3.35 18 2 77.00/ 77.00
17 228 0.617 0.746 0.463 -21.00 3.32 24 2 70.21/ 70.21
18 4 0.901 0.545 0.729 -23.43 3.19 18 2 86.87/ 86.87
19 199 0.406 0.585 0.209 -24.13 3.15 8 2 70.87/ 70.87
20 27 0.948 0.221 0.985 -24.52 3.13 20 4 78.78/ 78.78
21 81 0.293 0.193 0.422 -25.65 3.06 14 2 74.69/ 74.69
SET #1 of 2 TRIAL #2 of 4
-------------------------
Search Euler = 8.8 31.5 29.0, Ensemble = dna
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19
Fixed MR solutions
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
Top 194 translations before clustering will be rescored
Highest Score (Z-score): -3.40839 (4.73203)
Top Peaks With Clustering From Rescoring of SET #1 of 2 TRIAL #2 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 18 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 11 0.553 0.477 0.953 -3.41 4.73 0 2 75.21/ 75.21
2 25 0.050 0.624 0.707 -5.98 4.58 20 2 72.20/ 72.20
3 109 0.370 0.842 0.524 -11.77 4.22 10 2 66.28/ 66.28
4 33 0.661 0.098 0.450 -14.52 4.06 20 4 70.51/ 70.51
5 67 0.511 0.822 0.837 -15.11 4.02 18 2 67.99/ 67.99
6 44 0.987 0.757 0.780 -15.88 3.98 21 2 69.27/ 69.27
7 140 0.010 0.540 0.486 -16.39 3.94 5 2 65.15/ 65.15
8 17 0.766 0.884 0.503 -17.27 3.89 21 4 73.39/ 73.39
9 117 0.837 0.981 0.673 -17.48 3.88 24 2 66.02/ 66.02
10 92 0.254 0.711 0.404 -18.98 3.79 23 2 67.05/ 67.05
11 127 0.851 0.378 0.612 -19.34 3.77 18 2 65.65/ 65.65
12 85 0.341 0.806 0.228 -20.65 3.69 27 2 67.11/ 67.11
13 79 0.077 0.197 0.904 -21.62 3.63 15 2 67.31/ 67.31
14 36 0.300 0.176 0.073 -21.66 3.62 13 2 70.24/ 70.24
15 172 0.100 0.249 0.503 -21.95 3.61 24 2 64.07/ 64.07
16 108 0.248 0.850 0.256 -22.39 3.58 27 2 66.34/ 66.34
17 125 0.329 0.342 0.543 -22.46 3.58 21 2 65.66/ 65.66
18 142 0.914 0.077 0.942 -22.84 3.55 25 4 65.09/ 65.09
SET #1 of 2 TRIAL #3 of 4
-------------------------
Search Euler = 80.0 30.8 159.0, Ensemble = dna
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19
Fixed MR solutions
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
Top 52 translations before clustering will be rescored
Highest Score (Z-score): -7.66292 (4.27331)
Top Peaks With Clustering From Rescoring of SET #1 of 2 TRIAL #3 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 8 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 49 0.235 0.882 0.484 -7.66 4.27 0 2 69.45/ 69.45
2 5 0.018 0.804 0.540 -11.14 4.08 12 2 77.92/ 77.92
3 19 0.718 0.353 0.188 -13.30 3.96 14 4 74.43/ 74.43
4 41 0.272 0.612 0.527 -15.11 3.85 20 2 70.98/ 70.98
5 43 0.260 0.538 0.120 -18.74 3.65 30 4 70.81/ 71.34
6 4 0.213 0.790 0.684 -21.50 3.49 15 2 85.97/ 85.97
7 15 0.243 0.207 0.103 -22.92 3.41 10 2 75.41/ 75.41
8 47 0.649 0.038 0.902 -23.91 3.36 20 2 69.50/ 69.50
SET #1 of 2 TRIAL #4 of 4
-------------------------
Search Euler = 78.4 41.9 225.2, Ensemble = dna
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19
Fixed MR solutions
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
Top 394 translations before clustering will be rescored
Highest Score (Z-score): -1.00165 (4.86853)
Top Peaks With Clustering From Rescoring of SET #1 of 2 TRIAL #4 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 14 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 83 0.808 0.410 0.972 -1.00 4.87 0 4 68.59/ 74.34
2 30 0.864 0.401 0.019 -18.08 3.86 6 2 72.53/ 72.53
3 211 0.005 0.412 0.239 -18.69 3.82 13 2 63.85/ 63.85
4 11 0.865 0.031 0.047 -18.92 3.81 26 4 74.66/ 74.66
5 165 0.981 0.292 0.139 -18.92 3.81 19 4 65.38/ 72.59
6 222 0.968 0.680 0.678 -19.27 3.79 18 2 63.66/ 63.66
7 23 0.803 0.649 0.771 -19.31 3.79 13 2 72.76/ 72.76
8 41 0.264 0.302 0.175 -19.67 3.76 14 2 71.25/ 71.25
9 119 0.016 0.892 0.754 -19.70 3.76 27 2 66.77/ 66.77
10 382 0.395 0.861 0.278 -19.95 3.75 16 6 60.79/ 66.79
11 214 0.960 0.063 0.086 -20.09 3.74 24 2 63.78/ 63.78
12 177 0.838 0.552 0.061 -20.65 3.71 12 2 64.96/ 64.96
13 68 0.926 0.164 0.464 -20.99 3.69 27 2 69.53/ 69.53
14 167 0.241 0.839 0.840 -21.01 3.69 17 2 65.37/ 65.37
---------------------------------
FAST TRANSLATION FUNCTION #2 OF 2
---------------------------------
Fixed MR solutions
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
This FTF set has 4 trial orientations
#TRIAL Euler1 Euler2 Euler3 Ensemble
1 69.2 35.2 229.8 dna
2 35.1 29.8 44.6 dna
3 0.3 37.5 296.6 dna
4 4.7 30.8 15.9 dna
SET #2 of 2 TRIAL #1 of 4
-------------------------
Search Euler = 69.2 35.2 229.8, Ensemble = dna
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19
Fixed MR solutions
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
Top 80 translations before clustering will be rescored
Highest Score (Z-score): 3.7896 (4.79348)
Top Peaks With Clustering From Rescoring of SET #2 of 2 TRIAL #1 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 6 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 8 0.546 0.978 0.609 +3.79 4.79 0 2 77.50/ 77.50
2 30 0.082 0.098 0.970 -8.61 4.09 5 2 71.65/ 71.65
3 47 0.348 0.612 0.370 -12.49 3.87 12 4 69.36/ 69.36
4 55 0.343 0.238 0.307 -14.35 3.77 10 2 68.64/ 68.64
5 46 0.242 0.865 0.126 -14.44 3.76 12 2 69.80/ 69.80
6 36 0.186 0.819 0.684 -15.71 3.69 11 2 70.48/ 70.48
SET #2 of 2 TRIAL #2 of 4
-------------------------
Search Euler = 35.1 29.8 44.6, Ensemble = dna
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19
Fixed MR solutions
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
Top 280 translations before clustering will be rescored
Highest Score (Z-score): -5.74161 (4.65545)
Top Peaks With Clustering From Rescoring of SET #2 of 2 TRIAL #2 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 17 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 189 0.143 0.329 0.923 -5.74 4.66 0 4 68.44/ 74.51
2 66 0.639 0.914 0.899 -7.74 4.53 7 2 73.39/ 73.39
3 6 0.244 0.001 0.164 -12.99 4.21 9 2 87.24/ 87.24
4 126 0.607 0.689 0.411 -13.70 4.17 19 2 70.10/ 70.10
5 278 0.715 0.693 0.134 -14.41 4.12 10 2 67.30/ 67.30
6 9 0.208 0.230 0.775 -15.81 4.04 15 4 80.02/ 80.02
7 98 0.072 0.902 0.332 -16.06 4.02 17 2 71.67/ 71.67
8 53 0.330 0.960 0.070 -16.83 3.97 4 4 74.20/ 79.98
9 205 0.672 0.240 0.277 -18.82 3.85 15 2 68.18/ 68.18
10 42 0.779 0.214 0.733 -20.96 3.72 17 2 74.98/ 74.98
11 74 0.286 0.950 0.124 -21.40 3.69 4 2 73.16/ 73.16
12 30 0.408 0.388 0.437 -21.45 3.69 18 2 76.44/ 76.44
13 217 0.197 0.101 0.208 -21.93 3.66 15 2 67.98/ 67.98
14 89 0.647 0.468 0.887 -22.17 3.65 21 2 72.43/ 72.43
15 181 0.229 0.998 0.455 -23.89 3.54 11 2 68.80/ 68.80
16 257 0.796 0.495 0.726 -23.93 3.54 28 4 67.48/ 75.96
17 208 0.411 0.287 0.373 -24.50 3.50 17 2 68.18/ 68.18
SET #2 of 2 TRIAL #3 of 4
-------------------------
Search Euler = 0.3 37.5 296.6, Ensemble = dna
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19
Fixed MR solutions
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
Top 412 translations before clustering will be rescored
Highest Score (Z-score): -9.90158 (4.07135)
Top Peaks With Clustering From Rescoring of SET #2 of 2 TRIAL #3 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 43 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 315 0.157 0.022 0.938 -9.90 4.07 0 2 57.72/ 57.72
2 17 0.417 0.098 0.640 -14.60 3.81 12 4 71.05/ 74.11
3 109 0.981 0.043 0.445 -17.43 3.65 9 4 62.85/ 62.85
4 99 0.719 0.061 0.025 -17.59 3.64 18 2 63.30/ 63.30
5 44 0.001 0.957 0.429 -18.31 3.60 16 2 67.24/ 67.24
6 26 0.435 0.097 0.444 -18.39 3.59 12 2 69.29/ 69.29
7 2 0.894 0.391 0.583 -19.48 3.53 20 2 77.92/ 77.92
8 382 0.934 0.580 0.536 -19.66 3.52 19 6 57.02/ 62.28
9 254 0.850 0.348 0.454 -20.42 3.48 15 2 58.99/ 58.99
10 285 0.660 0.342 0.222 -20.48 3.47 22 2 58.17/ 58.17
11 103 0.215 0.508 0.010 -21.57 3.41 21 4 63.12/ 63.12
12 38 0.866 0.006 0.152 -21.76 3.40 13 2 67.89/ 67.89
13 61 0.348 0.093 0.822 -22.33 3.37 12 2 66.09/ 66.09
14 396 0.800 0.003 0.075 -22.34 3.37 16 2 56.81/ 56.81
15 237 0.724 0.872 0.561 -22.68 3.35 13 4 59.25/ 59.25
16 164 0.998 0.604 0.423 -23.02 3.33 14 2 60.78/ 60.78
17 302 0.265 0.939 0.031 -23.40 3.31 9 2 58.00/ 58.00
18 3 0.084 0.296 0.194 -23.62 3.30 3 2 76.22/ 76.22
19 182 0.464 0.626 0.778 -23.81 3.29 26 2 60.41/ 60.41
20 72 0.371 0.348 0.758 -23.85 3.28 18 2 64.95/ 64.95
21 278 0.976 0.177 0.326 -24.03 3.27 9 4 58.30/ 58.30
22 224 0.324 0.947 0.674 -24.47 3.25 12 2 59.40/ 59.40
23 85 0.992 0.543 0.522 -24.85 3.23 16 4 63.96/ 64.81
24 33 0.621 0.533 0.677 -25.00 3.22 26 2 68.09/ 68.09
25 115 0.465 0.065 0.852 -25.36 3.20 19 2 62.79/ 62.79
26 101 0.256 0.977 0.533 -25.40 3.20 8 2 63.30/ 63.30
27 345 0.534 0.260 0.039 -25.50 3.19 11 4 57.31/ 61.54
28 202 0.078 0.379 0.507 -25.53 3.19 15 2 59.90/ 59.90
29 13 0.659 0.380 0.527 -25.70 3.18 28 2 71.58/ 71.58
30 29 0.461 0.135 0.026 -25.70 3.18 13 2 68.68/ 68.68
31 393 0.785 0.349 0.265 -25.99 3.16 16 2 56.82/ 56.82
32 159 0.591 0.936 0.466 -26.03 3.16 9 2 61.11/ 61.11
33 225 0.023 0.636 0.832 -26.08 3.16 25 2 59.36/ 59.36
34 229 0.039 0.354 0.156 -26.38 3.14 8 2 59.35/ 59.35
35 42 0.101 0.860 0.436 -26.50 3.13 14 2 67.62/ 67.62
36 321 0.039 0.845 0.709 -26.52 3.13 16 2 57.68/ 57.68
37 39 0.474 0.125 0.740 -26.63 3.13 16 2 67.85/ 67.85
38 147 0.716 0.600 0.735 -26.77 3.12 27 2 61.75/ 61.75
39 195 0.309 0.985 0.302 -26.85 3.11 10 2 60.11/ 60.11
40 7 0.109 0.600 0.628 -27.24 3.09 13 2 73.56/ 73.56
41 106 0.000 0.276 0.267 -27.38 3.08 8 2 63.07/ 63.07
42 21 0.379 0.143 0.474 -27.81 3.06 13 2 70.17/ 70.17
43 294 0.711 0.812 0.680 -27.82 3.06 17 2 58.09/ 58.09
SET #2 of 2 TRIAL #4 of 4
-------------------------
Search Euler = 4.7 30.8 15.9, Ensemble = dna
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19
Fixed MR solutions
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
Top 462 translations before clustering will be rescored
Highest Score (Z-score): -8.18906 (4.34849)
Top Peaks With Clustering From Rescoring of SET #2 of 2 TRIAL #4 of 4
---------------------------------------------------------------------
# Rank of the peak after clustering search points
(#) Rank of the peak before clustering search points
FSS Fast Search Score
Z-Score Number of standard deviations of FFS above the mean
Split Distance (in degrees or Angstroms) to top peak
#Group Number of points clustered in peak
raw/top FSS of raw (unclustered) peak and top peak in cluster
You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 34 sites over 75% of top
The sites over 75% are:
# (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top
1 5 0.288 0.711 0.528 -8.19 4.35 0 4 75.66/ 77.08
2 102 0.902 0.372 0.067 -9.28 4.29 12 2 63.19/ 63.19
3 196 0.683 0.807 0.681 -9.82 4.25 17 2 59.74/ 59.74
4 10 0.898 0.630 0.515 -10.72 4.20 9 4 73.49/ 73.49
5 218 0.627 0.616 0.191 -11.27 4.17 12 2 59.33/ 59.33
6 60 0.061 0.215 0.425 -11.81 4.14 11 2 65.22/ 65.22
7 110 0.779 0.743 0.499 -14.37 3.99 15 2 62.91/ 62.91
8 140 0.845 0.054 0.206 -14.43 3.98 9 4 61.38/ 61.38
9 70 0.817 0.005 0.558 -14.92 3.96 24 2 64.65/ 64.65
10 324 0.364 0.532 0.093 -14.99 3.95 22 6 57.42/ 69.79
11 170 0.542 0.585 0.252 -19.49 3.69 14 2 60.39/ 60.39
12 48 0.963 0.310 0.629 -19.78 3.67 22 4 66.69/ 66.69
13 283 0.176 0.036 0.123 -19.85 3.67 11 2 58.01/ 58.01
14 461 0.709 0.250 0.610 -20.33 3.64 16 2 55.99/ 55.99
15 116 0.242 0.125 0.076 -20.62 3.62 13 2 62.39/ 62.39
16 61 0.093 0.273 0.244 -20.88 3.61 8 2 64.98/ 64.98
17 430 0.180 0.310 0.717 -21.05 3.60 21 2 56.26/ 56.26
18 105 0.555 0.472 0.826 -21.17 3.59 17 2 63.06/ 63.06
19 311 0.411 0.393 0.501 -22.65 3.51 20 2 57.65/ 57.65
20 200 0.676 0.298 0.858 -22.78 3.50 16 2 59.68/ 59.68
21 107 0.545 0.887 0.601 -23.31 3.47 11 2 62.92/ 62.92
22 41 0.948 0.355 0.702 -23.56 3.45 21 2 67.24/ 67.24
23 132 0.353 0.625 0.971 -23.63 3.45 21 4 61.64/ 64.47
24 379 0.476 0.331 0.074 -23.73 3.44 17 4 56.82/ 58.35
25 55 0.577 0.153 0.916 -24.02 3.43 14 2 65.93/ 65.93
26 231 0.592 0.053 0.786 -24.25 3.41 4 2 58.87/ 58.87
27 370 0.181 0.737 0.354 -24.44 3.40 10 2 56.92/ 56.92
28 454 0.022 0.121 0.644 -24.64 3.39 22 2 56.09/ 56.09
29 112 0.245 0.047 0.788 -24.89 3.38 19 4 62.59/ 62.59
30 43 0.410 0.140 0.805 -24.89 3.38 13 2 66.96/ 66.96
31 16 0.868 0.879 0.381 -25.31 3.35 12 2 70.98/ 70.98
32 154 0.807 0.870 0.659 -25.54 3.34 19 2 60.70/ 60.70
33 25 0.197 0.232 0.865 -26.70 3.27 12 2 68.71/ 68.71
34 330 0.165 0.258 0.308 -26.84 3.26 11 2 57.35/ 57.35
---------------
FINAL SELECTION
---------------
Mean used for final selection = -81.9868
Number of solutions stored before final selection = 161
Percentage of top value for final selection = 75
LLG value for final selection = -17.6545
Number of solutions stored (deleted) after final selection = 51 (110)
$TABLE : Translation Function Summary:
$GRAPHS :Graph1 TF Number vs LL-gain:AUTO:1,2:
:Graph2 TF Number vs Z-Score:AUTO:1,3:
$$
Number LL-gain Z-Score $$ loggraph $$
1 3.79 4.79
2 -1.00 4.87
3 -3.41 4.73
4 -5.74 4.66
5 -5.98 4.58
6 -7.47 4.08
7 -7.66 4.27
8 -7.74 4.53
9 -8.19 4.35
10 -8.61 4.09
11 -9.28 4.29
12 -9.42 3.97
13 -9.82 4.25
14 -9.90 4.07
15 -10.45 3.92
16 -10.72 4.20
17 -11.14 4.08
18 -11.27 4.17
19 -11.31 3.87
20 -11.52 3.85
21 -11.77 4.22
22 -11.81 4.14
23 -12.49 3.87
24 -12.99 4.21
25 -13.30 3.96
26 -13.70 4.17
27 -14.14 3.71
28 -14.35 3.77
29 -14.37 3.99
30 -14.41 4.12
31 -14.43 3.98
32 -14.44 3.76
33 -14.52 4.06
34 -14.60 3.81
35 -14.78 3.67
36 -14.92 3.96
37 -14.99 3.95
38 -15.11 4.02
39 -15.11 3.85
40 -15.71 3.69
41 -15.81 4.04
42 -15.88 3.98
43 -16.06 4.02
44 -16.28 3.59
45 -16.39 3.94
46 -16.83 3.97
47 -17.27 3.89
48 -17.43 3.65
49 -17.45 3.52
50 -17.48 3.88
51 -17.59 3.64
$$
-----------------
TABLES OF RESULTS
-----------------
Fast Translation Function Table: Space Group I 41 3 2
-----------------------------------------------------
#SET #TRIAL Top (Z) Second (Z) Third (Z) Ensemble
1 1 -7.47 ( 4.08) -9.42 ( 3.97) -10.45 ( 3.92) dna
1 2 -3.41 ( 4.73) -5.98 ( 4.58) -11.77 ( 4.22) dna
1 3 -7.66 ( 4.27) -11.14 ( 4.08) -13.30 ( 3.96) dna
1 4 -1.00 ( 4.87) -18.08 ( 3.86) -18.69 ( 3.82) dna
---- ------
2 1 3.79 ( 4.79) -8.61 ( 4.09) -12.49 ( 3.87) dna
2 2 -5.74 ( 4.66) -7.74 ( 4.53) -12.99 ( 4.21) dna
2 3 -9.90 ( 4.07) -14.60 ( 3.81) -17.43 ( 3.65) dna
2 4 -8.19 ( 4.35) -9.28 ( 4.29) -9.82 ( 4.25) dna
---- ------
------------
OUTPUT FILES
------------
No script files output
No pdb files output
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 4 mins 12.12 secs (252.12 secs)
Finished: Wed Jul 19 11:38:02 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:38:02 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT PACKING 2.0 ***
*************************************************************************************
Space Group Name (Number): I 41 3 2 (214)
Unit Cell: 76.86 76.86 76.86 90.00 90.00 90.00
----------------------
STRUCTURES FOR PACKING
----------------------
Packing will be performed with "trace" atoms (C-alphas for protein, P and selected
N for nucleic acid). When a protein molecule consists of more than one structure,
the structure with the highest homology is selected for packing. The structure is
then trimmed of loops that diverge more than 3A from other atoms in the molecule.
Ensemble: dna
-------------
Structure with lowest rms = 131d.pdb (0.8)
Trace length before selecting conserved = 41
Trace length after selecting conserved = 41
-------------------------
PACKING FUNCTION #1 OF 51
-------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.7 TFZ=4.8
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 69.2 35.2 229.8 FRAC 0.546 0.978 0.609
There were 6 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 56.6 78.2 122.6 FRAC -0.022 -0.391 -0.454
There was 1 clash between trace atoms for models 2:2
In total there were 7 clashes between trace atoms
-------------------------
PACKING FUNCTION #2 OF 51
-------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.3 TFZ=4.9
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 78.4 41.9 225.2 FRAC 0.808 0.410 0.972
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 349.8 130.8 209.8 FRAC -0.028 0.192 0.090
In total there were no clashes between trace atoms
-------------------------
PACKING FUNCTION #3 OF 51
-------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.4 TFZ=4.7
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 8.8 31.5 29.0 FRAC 0.553 0.477 0.953
There were 10 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 58.8 94.6 306.6 FRAC -0.197 -0.297 0.273
There were 15 clashes between trace atoms for models 2:2
In total there were 25 clashes between trace atoms
-------------------------
PACKING FUNCTION #4 OF 51
-------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.7 TFZ=4.7
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.143 0.329 0.923
There was 1 clash between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 115.1 73.4 166.1 FRAC 0.107 -0.327 -0.421
In total there was 1 clash between trace atoms
-------------------------
PACKING FUNCTION #5 OF 51
-------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.4 TFZ=4.6
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 8.8 31.5 29.0 FRAC 0.050 0.624 0.707
There were 15 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 8.8 31.5 29.0 FRAC 0.050 -0.376 -0.293
There were 7 clashes between trace atoms for models 2:2
In total there were 22 clashes between trace atoms
-------------------------
PACKING FUNCTION #6 OF 51
-------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.9 TFZ=4.1
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.732 0.082 0.270
There were 9 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.232 -0.418 -0.230
There were 4 clashes between trace atoms for models 2:2
In total there were 13 clashes between trace atoms
-------------------------
PACKING FUNCTION #7 OF 51
-------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.4 TFZ=4.3
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 80.0 30.8 159.0 FRAC 0.235 0.882 0.484
There were 8 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 275.9 59.7 327.4 FRAC -0.015 0.266 0.132
In total there were 8 clashes between trace atoms
-------------------------
PACKING FUNCTION #8 OF 51
-------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.7 TFZ=4.5
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.639 0.914 0.899
There were 13 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 251.8 66.0 263.7 FRAC 0.586 0.101 0.139
There were 2 clashes between trace atoms for models 2:2
In total there were 15 clashes between trace atoms
-------------------------
PACKING FUNCTION #9 OF 51
-------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.3 TFZ=4.3
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 4.7 30.8 15.9 FRAC 0.288 0.711 0.528
There were 3 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 329.3 92.4 290.0 FRAC 0.028 0.212 0.289
There were 9 clashes between trace atoms for models 2:2
In total there were 12 clashes between trace atoms
--------------------------
PACKING FUNCTION #10 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.7 TFZ=4.1
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 69.2 35.2 229.8 FRAC 0.082 0.098 0.970
There were 15 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 303.4 101.8 302.6 FRAC 0.098 0.030 0.418
There were 2 clashes between trace atoms for models 2:2
In total there were 17 clashes between trace atoms
--------------------------
PACKING FUNCTION #11 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.3 TFZ=4.3
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 4.7 30.8 15.9 FRAC 0.902 0.372 0.067
There were 4 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 210.7 87.6 110.0 FRAC 0.433 0.098 -0.128
There was 1 clash between trace atoms for models 2:2
In total there were 5 clashes between trace atoms
--------------------------
PACKING FUNCTION #12 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.9 TFZ=4.0
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.274 0.639 0.007
There were 7 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 305.1 29.8 44.6 FRAC -0.111 -0.024 -0.243
There were 17 clashes between trace atoms for models 2:2
In total there were 24 clashes between trace atoms
--------------------------
PACKING FUNCTION #13 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.3 TFZ=4.3
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 4.7 30.8 15.9 FRAC 0.683 0.807 0.681
There were 2 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 87.2 59.4 201.4 FRAC -0.193 -0.319 -0.317
There were 10 clashes between trace atoms for models 2:2
In total there were 12 clashes between trace atoms
--------------------------
PACKING FUNCTION #14 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.4 TFZ=4.1
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 0.3 37.5 296.6 FRAC 0.157 0.022 0.938
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 217.5 89.8 26.8 FRAC 0.062 0.343 0.022
There were 26 clashes between trace atoms for models 2:2
In total there were 26 clashes between trace atoms
--------------------------
PACKING FUNCTION #15 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.9 TFZ=3.9
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.128 0.031 0.912
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 244.9 106.6 346.1 FRAC 0.122 0.338 0.219
There were 2 clashes between trace atoms for models 2:2
In total there were 2 clashes between trace atoms
--------------------------
PACKING FUNCTION #16 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.3 TFZ=4.2
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 4.7 30.8 15.9 FRAC 0.898 0.630 0.515
There were 11 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 85.3 149.2 195.9 FRAC -0.120 -0.352 0.235
In total there were 11 clashes between trace atoms
--------------------------
PACKING FUNCTION #17 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.4 TFZ=4.1
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 80.0 30.8 159.0 FRAC 0.018 0.804 0.540
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 95.9 59.7 327.4 FRAC 0.232 -0.710 0.054
There were 28 clashes between trace atoms for models 2:2
In total there were 28 clashes between trace atoms
--------------------------
PACKING FUNCTION #18 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.3 TFZ=4.2
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 4.7 30.8 15.9 FRAC 0.627 0.616 0.191
There were 9 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 149.3 92.4 290.0 FRAC 0.309 -0.373 0.384
There were 2 clashes between trace atoms for models 2:2
In total there were 11 clashes between trace atoms
--------------------------
PACKING FUNCTION #19 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.9 TFZ=3.9
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.077 0.844 0.373
There were 5 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 125.1 29.8 44.6 FRAC 0.406 -0.173 -0.377
There were 14 clashes between trace atoms for models 2:2
In total there were 19 clashes between trace atoms
--------------------------
PACKING FUNCTION #20 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.9 TFZ=3.9
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.605 0.232 0.656
There were 10 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 324.9 150.2 224.6 FRAC 0.105 0.268 0.344
There were 16 clashes between trace atoms for models 2:2
In total there were 26 clashes between trace atoms
--------------------------
PACKING FUNCTION #21 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.4 TFZ=4.2
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 8.8 31.5 29.0 FRAC 0.370 0.842 0.524
There were 11 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 121.2 85.4 126.6 FRAC 0.380 -0.226 -0.408
In total there were 11 clashes between trace atoms
--------------------------
PACKING FUNCTION #22 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.3 TFZ=4.1
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 4.7 30.8 15.9 FRAC 0.061 0.215 0.425
There were 15 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 30.7 87.6 110.0 FRAC -0.075 -0.439 -0.285
There were 14 clashes between trace atoms for models 2:2
In total there were 29 clashes between trace atoms
--------------------------
PACKING FUNCTION #23 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.7 TFZ=3.9
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 69.2 35.2 229.8 FRAC 0.348 0.612 0.370
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 213.4 101.8 302.6 FRAC 0.380 0.138 0.402
There were 22 clashes between trace atoms for models 2:2
In total there were 22 clashes between trace atoms
--------------------------
PACKING FUNCTION #24 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.7 TFZ=4.2
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.244 0.001 0.164
There were 8 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 244.9 106.6 346.1 FRAC 0.006 0.086 0.249
There were 30 clashes between trace atoms for models 2:2
In total there were 38 clashes between trace atoms
--------------------------
PACKING FUNCTION #25 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.4 TFZ=4.0
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 80.0 30.8 159.0 FRAC 0.718 0.353 0.188
There were 5 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 350.0 30.8 159.0 FRAC 0.103 0.032 -0.562
There were 11 clashes between trace atoms for models 2:2
In total there were 16 clashes between trace atoms
--------------------------
PACKING FUNCTION #26 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.7 TFZ=4.2
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.607 0.689 0.411
There were 4 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 334.9 106.6 346.1 FRAC -0.089 -0.107 0.311
In total there were 4 clashes between trace atoms
--------------------------
PACKING FUNCTION #27 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.9 TFZ=3.7
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.905 0.090 0.047
There were 6 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 54.9 150.2 224.6 FRAC -0.160 0.155 0.203
There were 7 clashes between trace atoms for models 2:2
In total there were 13 clashes between trace atoms
--------------------------
PACKING FUNCTION #28 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.7 TFZ=3.8
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 69.2 35.2 229.8 FRAC 0.343 0.238 0.307
There were 12 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 69.2 35.2 229.8 FRAC -0.157 -0.262 -0.193
There were 9 clashes between trace atoms for models 2:2
In total there were 21 clashes between trace atoms
--------------------------
PACKING FUNCTION #29 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.3 TFZ=4.0
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 4.7 30.8 15.9 FRAC 0.779 0.743 0.499
There were 15 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 94.7 30.8 15.9 FRAC 0.507 -0.471 -0.251
There were 11 clashes between trace atoms for models 2:2
In total there were 26 clashes between trace atoms
--------------------------
PACKING FUNCTION #30 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.7 TFZ=4.1
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.715 0.693 0.134
There was 1 clash between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 341.8 66.0 263.7 FRAC -0.116 0.057 -0.035
There were 3 clashes between trace atoms for models 2:2
In total there were 4 clashes between trace atoms
--------------------------
PACKING FUNCTION #31 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.3 TFZ=4.0
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 4.7 30.8 15.9 FRAC 0.845 0.054 0.206
There was 1 clash between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 239.3 92.4 290.0 FRAC 0.405 0.044 0.196
There were 11 clashes between trace atoms for models 2:2
In total there were 12 clashes between trace atoms
--------------------------
PACKING FUNCTION #32 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.7 TFZ=3.8
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 69.2 35.2 229.8 FRAC 0.242 0.865 0.126
There were 4 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 326.6 78.2 122.6 FRAC -0.124 -0.115 -0.508
There were 16 clashes between trace atoms for models 2:2
In total there were 20 clashes between trace atoms
--------------------------
PACKING FUNCTION #33 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.4 TFZ=4.1
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 8.8 31.5 29.0 FRAC 0.661 0.098 0.450
There were 7 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 278.8 31.5 29.0 FRAC -0.152 0.089 -0.300
There were 8 clashes between trace atoms for models 2:2
In total there were 15 clashes between trace atoms
--------------------------
PACKING FUNCTION #34 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.4 TFZ=3.8
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 0.3 37.5 296.6 FRAC 0.417 0.098 0.640
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 322.5 90.2 206.8 FRAC 0.140 0.083 -0.098
There were 58 clashes between trace atoms for models 2:2
In total there were 58 clashes between trace atoms
--------------------------
PACKING FUNCTION #35 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.9 TFZ=3.7
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.605 0.125 0.474
There were 9 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 25.1 73.4 166.1 FRAC -0.026 0.105 -0.375
There were 25 clashes between trace atoms for models 2:2
In total there were 34 clashes between trace atoms
--------------------------
PACKING FUNCTION #36 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.3 TFZ=4.0
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 4.7 30.8 15.9 FRAC 0.817 0.005 0.558
There were 7 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 92.8 120.6 21.4 FRAC 0.495 -0.442 0.183
There was 1 clash between trace atoms for models 2:2
In total there were 8 clashes between trace atoms
--------------------------
PACKING FUNCTION #37 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.3 TFZ=4.0
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 4.7 30.8 15.9 FRAC 0.364 0.532 0.093
There were 5 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 92.8 120.6 21.4 FRAC 0.468 -0.407 0.136
There were 5 clashes between trace atoms for models 2:2
In total there were 10 clashes between trace atoms
--------------------------
PACKING FUNCTION #38 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.4 TFZ=4.0
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 8.8 31.5 29.0 FRAC 0.511 0.822 0.837
There were 12 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 174.6 58.9 219.3 FRAC 0.413 -0.428 -0.239
There were 6 clashes between trace atoms for models 2:2
In total there were 18 clashes between trace atoms
--------------------------
PACKING FUNCTION #39 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.4 TFZ=3.9
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 80.0 30.8 159.0 FRAC 0.272 0.612 0.527
There were 9 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 174.1 120.3 147.4 FRAC 0.473 -0.228 -0.112
In total there were 9 clashes between trace atoms
--------------------------
PACKING FUNCTION #40 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.7 TFZ=3.7
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 69.2 35.2 229.8 FRAC 0.186 0.819 0.684
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 256.0 122.6 204.9 FRAC 0.564 0.066 -0.069
There were 13 clashes between trace atoms for models 2:2
In total there were 13 clashes between trace atoms
--------------------------
PACKING FUNCTION #41 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.7 TFZ=4.0
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.208 0.230 0.775
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 334.9 106.6 346.1 FRAC -0.225 -0.208 0.270
There were 12 clashes between trace atoms for models 2:2
In total there were 12 clashes between trace atoms
--------------------------
PACKING FUNCTION #42 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.4 TFZ=4.0
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 8.8 31.5 29.0 FRAC 0.987 0.757 0.780
There was 1 clash between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 8.8 31.5 29.0 FRAC -0.013 -0.243 -0.220
There were 4 clashes between trace atoms for models 2:2
In total there were 5 clashes between trace atoms
--------------------------
PACKING FUNCTION #43 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.7 TFZ=4.0
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.072 0.902 0.332
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 244.9 106.6 346.1 FRAC 0.178 -0.082 0.348
There were 37 clashes between trace atoms for models 2:2
In total there were 37 clashes between trace atoms
--------------------------
PACKING FUNCTION #44 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.9 TFZ=3.6
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.390 0.504 0.066
There were 2 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 305.1 29.8 44.6 FRAC -0.246 -0.140 -0.184
There were 32 clashes between trace atoms for models 2:2
In total there were 34 clashes between trace atoms
--------------------------
PACKING FUNCTION #45 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.4 TFZ=3.9
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 8.8 31.5 29.0 FRAC 0.010 0.540 0.486
There were 2 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 81.2 148.5 209.0 FRAC -0.210 -0.240 0.264
There were 8 clashes between trace atoms for models 2:2
In total there were 10 clashes between trace atoms
--------------------------
PACKING FUNCTION #46 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.7 TFZ=4.0
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.330 0.960 0.070
There was 1 clash between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 215.1 29.8 44.6 FRAC 0.170 0.040 -0.430
There were 11 clashes between trace atoms for models 2:2
In total there were 12 clashes between trace atoms
--------------------------
PACKING FUNCTION #47 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.4 TFZ=3.9
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 8.8 31.5 29.0 FRAC 0.766 0.884 0.503
There were 2 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 278.8 31.5 29.0 FRAC -0.366 -0.016 -0.247
There were 5 clashes between trace atoms for models 2:2
In total there were 7 clashes between trace atoms
--------------------------
PACKING FUNCTION #48 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.4 TFZ=3.6
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 0.3 37.5 296.6 FRAC 0.981 0.043 0.445
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 180.3 37.5 296.6 FRAC 0.519 -0.043 -0.055
There were 22 clashes between trace atoms for models 2:2
In total there were 22 clashes between trace atoms
--------------------------
PACKING FUNCTION #49 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.9 TFZ=3.5
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 35.1 29.8 44.6 FRAC 0.852 0.265 0.943
There were 9 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 125.1 29.8 44.6 FRAC 0.485 0.102 -0.307
In total there were 9 clashes between trace atoms
--------------------------
PACKING FUNCTION #50 OF 51
--------------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.4 TFZ=3.9
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 8.8 31.5 29.0 FRAC 0.837 0.981 0.673
There were 9 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 95.4 121.1 39.3 FRAC 0.519 -0.327 0.163
There were 7 clashes between trace atoms for models 2:2
In total there were 16 clashes between trace atoms
--------------------------
PACKING FUNCTION #51 OF 51
--------------------------
ANNOTATION: RFZ=1.9 TFZ=4.3 PAK=0 LLG=19 RFZ=2.4 TFZ=3.6
SOLU 6DIM ENSE dna EULER 32.4 42.2 166.6 FRAC 0.080 -0.012 -0.412
SOLU 6DIM ENSE dna EULER 0.3 37.5 296.6 FRAC 0.719 0.061 0.025
There were 4 clashes between trace atoms for models 2:1
Solution #2 moved to closest CoM approach to current centre of complex
After move:
SOLU 6DIM ENSE dna EULER 0.3 37.5 296.6 FRAC -0.281 0.061 0.025
There were 9 clashes between trace atoms for models 2:2
In total there were 13 clashes between trace atoms
-------------
PACKING TABLE
-------------
Solutions rejected if number of clashes > 0
# #CLASHES # ACCEPTED
1 7 NO
2 0 1 YES
3 25 NO
4 1 NO
5 22 NO
6 13 NO
7 8 NO
8 15 NO
9 12 NO
10 17 NO
11 5 NO
12 24 NO
13 12 NO
14 26 NO
15 2 NO
16 11 NO
17 28 NO
18 11 NO
19 19 NO
20 26 NO
21 11 NO
22 29 NO
23 22 NO
24 38 NO
25 16 NO
26 4 NO
27 13 NO
28 21 NO
29 26 NO
30 4 NO
31 12 NO
32 20 NO
33 15 NO
34 58 NO
35 34 NO
36 8 NO
37 10 NO
38 18 NO
39 9 NO
40 13 NO
41 12 NO
42 5 NO
43 37 NO
44 34 NO
45 10 NO
46 12 NO
47 7 NO
48 22 NO
49 9 NO
50 16 NO
51 13 NO
1 accepted of 51 solutions
------------
OUTPUT FILES
------------
No script files output
No pdb files output
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 4 mins 17.68 secs (257.68 secs)
Finished: Wed Jul 19 11:38:08 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:38:08 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.0 ***
*************************************************************************************
-------------------------------
DATA FOR REFINEMENT AND PHASING
-------------------------------
Outliers with a probability less than 1e-06 will be rejected
No reflections are outliers
Space-Group Name (Number): I 41 3 2 (214)
Resolution of All Data (Number): 1.62 38.43 (5100)
Resolution of Selected Data (Number): 3.50 38.43 (581)
-------------------
WILSON DISTRIBUTION
-------------------
Parameters set for Wilson log-likelihood calculation
E = 0 and variance 1 for each reflection
Without correction for SigF to the variances,
Wilson log(likelihood) = - number of acentrics (358)
- half number of centrics (223/2)
= -469
With correction for SigF,
Wilson log(likelihood) = -462.199
------------
ENSEMBLE dna
------------
The RmsD of this model with respect to the real structure is 0.8
Unit Cell: 98.66 53.20 41.28 90.00 90.00 90.00
Calculating electron density...
Done
------------------
REFINEMENT #1 OF 1
------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.3 TFZ=4.9 PAK=0
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 231.0 58.2 341.0 FRAC 0.257 0.349 0.041
SOLU 6DIM ENSE dna EULER 349.8 130.8 209.8 FRAC -0.028 0.192 0.090
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start -0.637
#1 5.514 6.151 6.151
#2 5.615 6.252 0.101
#3 5.634 6.271 0.019
#4 5.634 6.272 0.001
#5 5.706 6.343 0.072
#6 5.724 6.361 0.018
#7 5.724 6.362 0.000
#8 5.724 6.362 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna +1.2186 -0.7386 +0.4576 +0.0054 -0.0637 +0.1732
#2 dna +1.3395 +0.0316 +1.3537 +0.0094 -0.0902 -0.0516
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 231.9 57.9 341.8 FRAC 0.247 0.352 0.039
SOLU 6DIM ENSE dna EULER 349.2 130.7 211.3 FRAC -0.019 0.193 0.095
The log(likelihood) gain = 5.7244 (at start -0.6372)
The R-factor = 55.69 (at start 58.45)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
----------------
PRUNE DUPLICATES
----------------
Check for nearly equivalent solutions
No duplicate solutions pruned
Refinement Table: Space Group I 41 3 2
--------------------------------------
#+ = input number #* = output number
Unsorted (refinement order) Sorted in LL-gain order
Initial Refined Initial Refined
#+ LL-gain LL-gain Unique #* #+ LL-gain LL-gain Unique =#*
1 -0.64 5.72 YES 1 1 -0.64 5.72 YES
------------
OUTPUT FILES
------------
No script files output
No pdb files output
No mtz files output
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 4 mins 25.11 secs (265.11 secs)
Finished: Wed Jul 19 11:38:15 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:38:15 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.0 ***
*************************************************************************************
Purge solutions according to highest LLG
Top LLG value from Translation Function = 3.7896
Percent used for purge = 0.75
Top LLG value used for purge = 5.72435
Mean LLG used for purge = -81.9868
Number of solutions stored before purge = 1
Number of solutions stored (deleted) after purge = 1 (0)
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 4 mins 25.12 secs (265.12 secs)
Finished: Wed Jul 19 11:38:15 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:38:15 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.0 ***
*************************************************************************************
New Best Solution: TOP LL-GAIN 5.724355
Permutation #1
Search Ensemble dna
Space Group: I 41 3 2
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 4 mins 25.13 secs (265.13 secs)
Finished: Wed Jul 19 11:38:15 2006
#####################################################################################
#####################################################################################
#####################################################################################
### CCP4 PROGRAM SUITE: Phaser 2.0 ###
#####################################################################################
User: phzwart
Run time: Wed Jul 19 11:38:15 2006
Version: 2.0
OS type: linux
Release Date: Wed Jun 21 12:23:03 2006
For Molecular Replacement please reference: Acta Cryst. (2005). D61, 458-464.
Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve,
L. C. Storoni and R. J. Read.
For Experimental Phasing please reference: Acta Cryst. (2004). D60, 1220-1228.
Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni and
R. J. Read.
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.0 ***
*************************************************************************************
-------------------------------
DATA FOR REFINEMENT AND PHASING
-------------------------------
Outliers with a probability less than 1e-06 will be rejected
No reflections are outliers
Space-Group Name (Number): I 41 3 2 (214)
Resolution of All Data (Number): 1.62 38.43 (5100)
Resolution of Selected Data (Number): 1.62 38.43 (5100)
-------------------
WILSON DISTRIBUTION
-------------------
Parameters set for Wilson log-likelihood calculation
E = 0 and variance 1 for each reflection
Without correction for SigF to the variances,
Wilson log(likelihood) = - number of acentrics (4085)
- half number of centrics (1015/2)
= -4592
With correction for SigF,
Wilson log(likelihood) = -4691.65
------------
ENSEMBLE dna
------------
The RmsD of this model with respect to the real structure is 0.8
Unit Cell: 98.66 53.20 41.28 90.00 90.00 90.00
Calculating electron density...
Done
------------------
REFINEMENT #1 OF 1
------------------
ANNOTATION: RFZ=2.1 TFZ=4.4 PAK=0 LLG=19 RFZ=2.3 TFZ=4.9 PAK=0 LLG=6
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 231.9 57.9 341.8 FRAC 0.247 0.352 0.039
SOLU 6DIM ENSE dna EULER 349.2 130.7 211.3 FRAC -0.019 0.193 0.095
MACROCYCLE #1
-------------
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION: REFINE
Optimization statistics macrocycle #1
Cycle end-this-cycle change-from-start change-from-last
start -64.865
#1 -53.096 11.768 11.768
#2 -49.039 15.826 4.058
#3 -48.618 16.247 0.421
#4 -48.479 16.386 0.139
#5 -48.470 16.395 0.009
#6 -48.469 16.395 0.000
---CONVERGENCE OF MACROCYCLE---
Perturbation of MR solutions (Degrees and Angstroms)
#1 dna +1.5652 -0.9822 +0.9230 +0.0064 +0.2867 -0.0020
#2 dna -1.8342 -0.2223 +0.3174 -0.0061 +0.2656 -0.2229
Reset perturbations to zero, update solutions
Fixed MR solutions
(No solutions of this type)
Moving MR solutions
SOLU 6DIM ENSE dna EULER 233.1 57.6 342.9 FRAC 0.233 0.361 0.035
SOLU 6DIM ENSE dna EULER 347.8 130.1 208.9 FRAC -0.020 0.202 0.079
The log(likelihood) gain = -48.4695 (at start -64.8648)
The R-factor = 59.94 (at start 60.17)
*** R-factor is a poor scoring function when data and/or models are poor ***
*** R-factor does not include a correction for bulk solvent ***
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PRUNE DUPLICATES
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Check for nearly equivalent solutions
No duplicate solutions pruned
Refinement Table: Space Group I 41 3 2
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#+ = input number #* = output number
Unsorted (refinement order) Sorted in LL-gain order
Initial Refined Initial Refined
#+ LL-gain LL-gain Unique #* #+ LL-gain LL-gain Unique =#*
1 -64.86 -48.47 YES 1 1 -64.86 -48.47 YES
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OUTPUT FILES
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Betty.1.pdb
Betty.1.mtz
Betty.sol
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EXIT STATUS: SUCCESS
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CPU Time: 0 days 0 hrs 5 mins 24.28 secs (324.28 secs)
Finished: Wed Jul 19 11:39:15 2006