Dear All,
Part of the JBC requirements for publishing structures is that “depending on the method used to solve the phase problem, the following data should be provided:
We solved our structure using molecular replacement, however I can’t find in the log files (please see below) the information relating to the second unrelated peak. I would be grateful if you could please provide assistance in this regard?
Kind regards,
Regards
Yogesh Khandokar
#CCP4I VERSION CCP4Interface 6.5.016
#CCP4I SCRIPT LOG phaser_MR
#CCP4I DATE 12 Sep 2015 13:33:49
#CCP4I USER 'UNKNOWN'
#CCP4I PROJECT JBC_Test
#CCP4I JOB_ID 1
#CCP4I SCRATCH C:/ccp4temp/
#CCP4I HOSTNAME YKHANDOKAR-DT
#CCP4I PID 5844
<pre>
<B><FONT COLOR="#FF0000">
<html><!-- CCP4 HTML LOGFILE -->
<!--SUMMARY_BEGIN-->
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### CCP4 PROGRAM SUITE: Phaser 2.5.7 ###
#####################################################################################
User: (unknown)
Run time: Sat Sep 12 13:33:49 2015
Version: 2.5.7
Release Date: Mon Jan 19 14:10:14 2015
If you use this software please cite:
$TEXT:Reference1: $$ $$
"Phaser Crystallographic Software"
A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni & R.J. Read
J. Appl. Cryst. (2007). 40, 658-674
<a href="http://journals.iucr.org/j/issues/2007/04/00/he5368/he5368.pdf">PDF</a>
$$
<!--SUMMARY_END-->
<!--END--></FONT></B>
<!--SUMMARY_BEGIN-->
*************************************************************************************
*** Phaser Module: PREPROCESSOR 2.5.7 ***
*************************************************************************************
<!--SUMMARY_END-->
ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT
<!--SUMMARY_BEGIN-->
$TEXT:Script: $$ Baubles Markup $$
#---PHASER COMMAND SCRIPT GENERATED BY CCP4I---
TITLE [No title given]
MODE MR_AUTO
ROOT "D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1"
#---DEFINE DATA---
HKLIN &
"D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/dL2_SP3_scaled2.mt &
z"
LABIN F=F_New SIGF=SIGF_New
SGALTERNATIVE SELECT HAND
#---DEFINE ENSEMBLES---
ENSEMBLE ensemble1 &
PDB &
"D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/MRmodel_singlechai &
n.pdb" IDENT 0.65
#---DEFINE COMPOSITION---
COMPOSITION BY AVERAGE
#---SEARCH PARAMETERS---
SEARCH ENSEMBLE ensemble1 NUMBER 2
#---EXPERT PARAMETERS---
#---OUTPUT CONTROL---
TOPFILES 2
#---DEVELOPER PARAMETERS---
## This script run with the command ##########
# phaser
################################################
$$
CPU Time: 0 days 0 hrs 0 mins 0.00 secs ( 0.00 secs)
Finished: Sat Sep 12 13:33:49 2015
*************************************************************************************
*** Phaser Module: READ DATA FROM MTZ FILE 2.5.7 ***
*************************************************************************************
Data read from mtz file:
D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/dL2_SP3_scaled2.mt
z
Space-Group Name (Hall Symbol): C 2 2 21 ( C 2c 2)
Space-Group Number: 20
Unit Cell: 46.18 118.44 86.64 90.00 90.00 90.00
Column Labels Selected: F_New SIGF_New
Resolution on Mtz file: 1.86 59.22
Resolution Selected: 1.86 24.67
Number of Reflections in Selected Resolution Range: 20208
CPU Time: 0 days 0 hrs 0 mins 0.02 secs ( 0.02 secs)
Finished: Sat Sep 12 13:33:49 2015
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.5.7 ***
*************************************************************************************
<!--SUMMARY_END-->
Steps:
Cell Content Analysis
Anisotropy correction
Translational NCS correction
Rotation Function
Translation Function
Packing
Refinement
Final Refinement (if data higher resolution than search resolution)
<!--SUMMARY_BEGIN-->
Number of search ensembles = 2
Search Method: FAST
Input Search Order:
#1: Ensemble ensemble1
#2: Ensemble ensemble1
Automatic (best predicted) search order WILL be used
One test spacegroup
C 2 2 21
CPU Time: 0 days 0 hrs 0 mins 0.04 secs ( 0.04 secs)
Finished: Sat Sep 12 13:33:49 2015
*************************************************************************************
*** Phaser Module: CELL CONTENT ANALYSIS 2.5.7 ***
*************************************************************************************
Space-Group Name (Hall Symbol): C 2 2 21 ( C 2c 2)
Space-Group Number: 20
Unit Cell: 46.18 118.44 86.64 90.00 90.00 90.00
MW of "average" protein to which Matthews applies: 25520
Resolution for Matthews calculation: 1.86
Z MW VM % solvent rel. freq.
1 25520 2.32 47.01 1.000 <== 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
<!--SUMMARY_END-->
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 -
$TABLE : Cell Content Analysis:
$SCATTER
:N*Composition vs Probability:0|2x0|1:1,2:
$$
N*Composition Probability
$$ loggraph $$
1 0.992785
$$
<!--SUMMARY_BEGIN-->
Most probable VM for resolution = 2.23805
Most probable MW of protein in asu for resolution = 26467.4
CPU Time: 0 days 0 hrs 0 mins 0.17 secs ( 0.17 secs)
Finished: Sat Sep 12 13:33:49 2015
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.5.7 ***
*************************************************************************************
Composition Table
-----------------
Total Scattering = 83214.2
Ensemble Fraction Scattering
ensemble1 51.69%
<B><FONT COLOR="#FF8800">
-------------------------------------------------------------------------------------
Warning: Search request requires more scattering than defined in composition.
Composition increased to accommodate search components.
-------------------------------------------------------------------------------------
</FONT></B>
Composition increased
from 83214
to 86884
Composition Table
-----------------
Total Scattering = 86884.2
Ensemble Fraction Scattering
ensemble1 49.50%
CPU Time: 0 days 0 hrs 0 mins 0.17 secs ( 0.17 secs)
Finished: Sat Sep 12 13:33:49 2015
*************************************************************************************
*** Phaser Module: CELL CONTENT ANALYSIS 2.5.7 ***
*************************************************************************************
Space-Group Name (Hall Symbol): C 2 2 21 ( C 2c 2)
Space-Group Number: 20
Unit Cell: 46.18 118.44 86.64 90.00 90.00 90.00
MW of "average" protein to which Matthews applies: 26646
Resolution for Matthews calculation: 1.86
Z MW VM % solvent rel. freq.
1 26646 2.22 44.67 1.000 <== 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
<!--SUMMARY_END-->
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 --------------------------------------------------
2.17 ************************************************* (COMPOSITION*1)
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 -
$TABLE : Cell Content Analysis after composition increased:
$SCATTER
:N*Composition vs Probability:0|2x0|1:1,2:
$$
N*Composition Probability
$$ loggraph $$
1 0.971695
$$
<!--SUMMARY_BEGIN-->
Most probable VM for resolution = 2.23805
Most probable MW of protein in asu for resolution = 26467.4
CPU Time: 0 days 0 hrs 0 mins 0.27 secs ( 0.27 secs)
Finished: Sat Sep 12 13:33:49 2015
*************************************************************************************
*** Phaser Module: ANISOTROPY CORRECTION 2.5.7 ***
*************************************************************************************
<!--SUMMARY_END-->
------------------------------
DATA FOR ANISOTROPY CORRECTION
------------------------------
<!--SUMMARY_BEGIN-->
Resolution of All Data (Number): 1.86 24.67 (20208)
Resolution of Selected Data (Number): 1.86 24.67 (20208)
<!--SUMMARY_END-->
---------------------
ANISOTROPY CORRECTION
---------------------
Protocol cycle #1 of 3
Refinement protocol for this macrocycle:
BIN SCALES: REFINE
ANISOTROPY: REFINE
SOLVENT K: FIX
SOLVENT B: FIX
Protocol cycle #2 of 3
Refinement protocol for this macrocycle:
BIN SCALES: REFINE
ANISOTROPY: REFINE
SOLVENT K: FIX
SOLVENT B: FIX
Protocol cycle #3 of 3
Refinement protocol for this macrocycle:
BIN SCALES: REFINE
ANISOTROPY: REFINE
SOLVENT K: FIX
SOLVENT B: FIX
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 6 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
3718.576 4969.707 1251.131
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
5.411 -0.0000 0.0000 1.0000
2.622 1.0000 -0.0000 0.0000
-8.033 0.0000 1.0000 -0.0000
Anisotropic deltaB (i.e. range of principal components): 13.444
Resharpening B (to restore strong direction of diffraction): -8.033
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
4969.707 4969.724 0.016
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
5.411 -0.0000 0.0000 1.0000
2.622 1.0000 -0.0000 0.0000
-8.033 0.0000 1.0000 -0.0000
Anisotropic deltaB (i.e. range of principal components): 13.444
Resharpening B (to restore strong direction of diffraction): -8.033
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
4969.724 4969.743 0.019
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
5.411 -0.0000 0.0000 1.0000
2.622 1.0000 -0.0000 0.0000
-8.033 0.0000 1.0000 -0.0000
Anisotropic deltaB (i.e. range of principal components): 13.445
Resharpening B (to restore strong direction of diffraction): -8.033
<!--SUMMARY_BEGIN-->
Refined Anisotropy Parameters
-----------------------------
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
5.411 -0.0000 0.0000 1.0000
2.622 1.0000 -0.0000 0.0000
-8.033 0.0000 1.0000 -0.0000
Anisotropic deltaB (i.e. range of principal components): 13.445
Resharpening B (to restore strong direction of diffraction): -8.033
<!--SUMMARY_END-->
--------------
ABSOLUTE SCALE
--------------
Scale factor to put input Fs on absolute scale
Wilson Scale: 0.938999
Wilson B-factor: 15.8446
<!--SUMMARY_BEGIN-->
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 0 mins 1.54 secs ( 1.54 secs)
Finished: Sat Sep 12 13:33:50 2015
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.5.7 ***
*************************************************************************************
eLLG Values Computed for All Data
---------------------------------
eLLG with all data for ensemble "ensemble1": 551.8
Automatic (Best Predicted) Search Order
---------------------------------------
Search Order determined by best expected LLG
#1: Ensemble ensemble1
#2: Ensemble ensemble1
CPU Time: 0 days 0 hrs 0 mins 1.55 secs ( 1.55 secs)
Finished: Sat Sep 12 13:33:50 2015
*************************************************************************************
*** Phaser Module: TRANSLATIONAL NON-CRYSTALLOGRAPHIC SYMMETRY 2.5.7 ***
*************************************************************************************
<!--SUMMARY_END-->
Unit Cell: 46.18 118.44 86.64 90.00 90.00 90.00
-------------------------------------
DATA FOR TRANSLATIONAL NCS CORRECTION
-------------------------------------
Intensity Moments for Data
--------------------------
2nd Moment = <E^4>/<E^2>^2 == <J^2>/<J>^2
Untwinned Perfect Twin
2nd Moment Centric: 3.0 2.0
2nd Moment Acentric: 2.0 1.5
Measured
2nd Moment Centric: 4.21
2nd Moment Acentric: 2.68
Resolution for Twin Analysis (85% I/SIGI > 3): 2.93A (HiRes=1.86A)
$TABLE : Intensity distribution for Data:
$GRAPHS
:Cumulative intensity distribution (acentric and centric):N:1,2,3,4,5,6:
$$
Z ACent_theor ACent_twin ACent_obser Cent_theor Cent_obser
$$ loggraph $$
0 0 0 0 0 0
0.04 0.0392106 0.0030343 0.0604703 0.158519 0.192157
0.08 0.0768837 0.0115132 0.131243 0.222703 0.270588
0.12 0.11308 0.0245815 0.19037 0.270966 0.326797
0.16 0.147856 0.0414833 0.239866 0.310843 0.368627
0.2 0.181269 0.0615519 0.281971 0.345279 0.40915
0.24 0.213372 0.0842006 0.324748 0.375794 0.440523
0.28 0.244216 0.108914 0.359462 0.403299 0.478431
0.32 0.273851 0.13524 0.388354 0.428392 0.508497
0.36 0.302324 0.162786 0.415677 0.451494 0.52549
0.4 0.32968 0.191208 0.442553 0.472911 0.541176
0.44 0.355964 0.220208 0.464502 0.492878 0.551634
0.48 0.381217 0.24953 0.48533 0.511578 0.577778
0.52 0.405479 0.278952 0.505487 0.529158 0.588235
0.56 0.428791 0.308287 0.522284 0.54574 0.597386
0.6 0.451188 0.337373 0.541097 0.561422 0.611765
0.64 0.472708 0.366075 0.557895 0.576289 0.624837
0.68 0.493383 0.394281 0.574468 0.590413 0.648366
0.72 0.513248 0.421896 0.589026 0.603856 0.658824
0.76 0.532334 0.448846 0.607167 0.616672 0.669281
0.8 0.550671 0.475069 0.622172 0.628907 0.677124
0.84 0.56829 0.500518 0.63673 0.640603 0.690196
0.88 0.585217 0.525156 0.646809 0.651798 0.701961
0.92 0.601481 0.548959 0.657335 0.662525 0.70719
0.96 0.617107 0.571908 0.666293 0.672813 0.712418
1 0.632121 0.593994 0.676372 0.682689 0.717647
1.04 0.646545 0.615215 0.68645 0.692179 0.728105
1.08 0.660404 0.635573 0.697872 0.701302 0.732026
1.12 0.67372 0.655074 0.707727 0.710082 0.738562
1.16 0.686514 0.673732 0.717133 0.718534 0.746405
1.2 0.698806 0.691559 0.723852 0.726678 0.74902
1.24 0.710616 0.708574 0.734155 0.734529 0.756863
1.28 0.721963 0.724795 0.743785 0.742101 0.763399
1.32 0.732865 0.740245 0.754311 0.749408 0.76732
1.36 0.743339 0.754946 0.759462 0.756463 0.772549
1.4 0.753403 0.768922 0.767525 0.763276 0.781699
1.44 0.763072 0.782197 0.775364 0.769861 0.786928
1.48 0.772362 0.794797 0.782307 0.776226 0.79085
1.52 0.781288 0.806747 0.790594 0.782381 0.794771
1.56 0.789864 0.818072 0.798208 0.788335 0.794771
1.6 0.798103 0.828799 0.804927 0.794097 0.797386
1.64 0.80602 0.838951 0.810974 0.799674 0.805229
1.68 0.813626 0.848554 0.816573 0.805076 0.814379
1.72 0.820934 0.857633 0.822172 0.810307 0.818301
1.76 0.827955 0.866211 0.826204 0.815376 0.819608
1.8 0.834701 0.874311 0.832251 0.820287 0.823529
1.84 0.841183 0.881957 0.837402 0.825049 0.827451
1.88 0.84741 0.889169 0.842329 0.829666 0.828758
1.92 0.853393 0.895971 0.847032 0.834143 0.83268
1.96 0.859142 0.902382 0.850616 0.838487 0.835294
2 0.864665 0.908422 0.854199 0.842701 0.837908
$$
---------------------
ANISOTROPY CORRECTION
---------------------
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
4969.743 4969.766 0.024
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
5.411 -0.0000 0.0000 1.0000
2.622 1.0000 -0.0000 0.0000
-8.034 0.0000 1.0000 -0.0000
Anisotropic deltaB (i.e. range of principal components): 13.445
Resharpening B (to restore strong direction of diffraction): -8.034
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 4 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
4969.766 4969.912 0.146
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
5.412 -0.0000 -0.0000 1.0000
2.622 1.0000 -0.0000 0.0000
-8.034 0.0000 1.0000 0.0000
Anisotropic deltaB (i.e. range of principal components): 13.446
Resharpening B (to restore strong direction of diffraction): -8.034
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
4969.912 4969.923 0.011
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
5.412 -0.0000 -0.0000 1.0000
2.622 1.0000 -0.0000 0.0000
-8.034 0.0000 1.0000 0.0000
Anisotropic deltaB (i.e. range of principal components): 13.446
Resharpening B (to restore strong direction of diffraction): -8.034
<!--SUMMARY_BEGIN-->
Refined Anisotropy Parameters
-----------------------------
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
5.412 -0.0000 -0.0000 1.0000
2.622 1.0000 -0.0000 0.0000
-8.034 0.0000 1.0000 0.0000
Anisotropic deltaB (i.e. range of principal components): 13.446
Resharpening B (to restore strong direction of diffraction): -8.034
<!--SUMMARY_END-->
Intensity Moments after Anisotropy Correction
---------------------------------------------
2nd Moment = <E^4>/<E^2>^2 == <J^2>/<J>^2
Untwinned Perfect Twin
2nd Moment Centric: 3.0 2.0
2nd Moment Acentric: 2.0 1.5
Measured
2nd Moment Centric: 4.23
2nd Moment Acentric: 2.60
Resolution for Twin Analysis (85% I/SIGI > 3): 2.93A (HiRes=1.86A)
$TABLE : Intensity distribution after Anisotropy Correction:
$GRAPHS
:Cumulative intensity distribution (acentric and centric):N:1,2,3,4,5,6:
$$
Z ACent_theor ACent_twin ACent_obser Cent_theor Cent_obser
$$ loggraph $$
0 0 0 0 0 0
0.04 0.0392106 0.0030343 0.0568869 0.158519 0.183007
0.08 0.0768837 0.0115132 0.127212 0.222703 0.270588
0.12 0.11308 0.0245815 0.183427 0.270966 0.322876
0.16 0.147856 0.0414833 0.238522 0.310843 0.368627
0.2 0.181269 0.0615519 0.277044 0.345279 0.40915
0.24 0.213372 0.0842006 0.318477 0.375794 0.443137
0.28 0.244216 0.108914 0.349608 0.403299 0.473203
0.32 0.273851 0.13524 0.379843 0.428392 0.498039
0.36 0.302324 0.162786 0.408735 0.451494 0.529412
0.4 0.32968 0.191208 0.435162 0.472911 0.546405
0.44 0.355964 0.220208 0.457559 0.492878 0.559477
0.48 0.381217 0.24953 0.478835 0.511578 0.580392
0.52 0.405479 0.278952 0.497648 0.529158 0.6
0.56 0.428791 0.308287 0.51467 0.54574 0.616993
0.6 0.451188 0.337373 0.532811 0.561422 0.631373
0.64 0.472708 0.366075 0.550056 0.576289 0.645752
0.68 0.493383 0.394281 0.569093 0.590413 0.654902
0.72 0.513248 0.421896 0.58477 0.603856 0.667974
0.76 0.532334 0.448846 0.599328 0.616672 0.675817
0.8 0.550671 0.475069 0.613886 0.628907 0.686275
0.84 0.56829 0.500518 0.626204 0.640603 0.694118
0.88 0.585217 0.525156 0.638298 0.651798 0.703268
0.92 0.601481 0.548959 0.649944 0.662525 0.708497
0.96 0.617107 0.571908 0.662262 0.672813 0.715033
1 0.632121 0.593994 0.673012 0.682689 0.722876
1.04 0.646545 0.615215 0.684658 0.692179 0.732026
1.08 0.660404 0.635573 0.694961 0.701302 0.738562
1.12 0.67372 0.655074 0.703919 0.710082 0.743791
1.16 0.686514 0.673732 0.71243 0.718534 0.74902
1.2 0.698806 0.691559 0.721165 0.726678 0.756863
1.24 0.710616 0.708574 0.729003 0.734529 0.763399
1.28 0.721963 0.724795 0.738186 0.742101 0.768627
1.32 0.732865 0.740245 0.74692 0.749408 0.776471
1.36 0.743339 0.754946 0.754535 0.756463 0.784314
1.4 0.753403 0.768922 0.761926 0.763276 0.792157
1.44 0.763072 0.782197 0.771109 0.769861 0.798693
1.48 0.772362 0.794797 0.779619 0.776226 0.803922
1.52 0.781288 0.806747 0.788802 0.782381 0.806536
1.56 0.789864 0.818072 0.795969 0.788335 0.811765
1.6 0.798103 0.828799 0.801568 0.794097 0.814379
1.64 0.80602 0.838951 0.806271 0.799674 0.815686
1.68 0.813626 0.848554 0.812094 0.805076 0.819608
1.72 0.820934 0.857633 0.819485 0.810307 0.827451
1.76 0.827955 0.866211 0.824636 0.815376 0.831373
1.8 0.834701 0.874311 0.827548 0.820287 0.835294
1.84 0.841183 0.881957 0.831579 0.825049 0.837908
1.88 0.84741 0.889169 0.835162 0.829666 0.84183
1.92 0.853393 0.895971 0.841433 0.834143 0.843137
1.96 0.859142 0.902382 0.847256 0.838487 0.844444
2 0.864665 0.908422 0.851512 0.842701 0.845752
$$
------------------------
TRANSLATIONAL NCS VECTOR
------------------------
Space Group : C 2 2 21
Patterson Symmetry: C m m m
Resolution of All Data (Number): 1.86 24.67 (20208)
Resolution of Patterson (Number): 5.00 9.97 (934)
There was 1 non-origin distinct peak (i.e. over 20% of origin peak and more than
15 angstroms from the origin)
<!--SUMMARY_BEGIN-->
Peak Distance Vector
45.8% 45.3Å: FRAC +0.000 +0.111 -0.500 (ORTH -0.0 13.2 -43.3)
<!--SUMMARY_END-->
<!--SUMMARY_BEGIN-->
<B><FONT COLOR="#0077FF">
-------------------------------------------------------------------------------------
Advisory: Large non-origin Patterson peak indicates that translational NCS is present
-------------------------------------------------------------------------------------
</FONT></B>
<!--SUMMARY_END-->
---------------------------
TRANSLATIONAL NCS ROTATIONS
---------------------------
Special Position Perturbation
-----------------------------
NCS translation on special position with M = 4
NCS translation vector = 0 0.111111 -0.5
Starting point for refinement will be shifted from special position.
Resolution of All Data (Number): 1.86 24.67 (20208)
Resolution of Data (Number): 1.86 24.67 (20208)
NCS translation has been perturbed in X
NCS translation has been perturbed in Y
NCS translation has been perturbed in Z
NCS translation perturbed by (orthogonal angstroms): 0.310 0.310 0.310
NCS translation has been set to -0.00670946 0.108495 -0.503576
Molecular Radius for G-function = 15.2339 Angstroms
Use default sampling
Sampling = 1.74747
Use default range
Range = 1.92222
Num Angles = 5
Protocol cycle #1 of 3
Refinement protocol for this macrocycle:
ROTATION: REFINE
TRANSLATION: REFINE
VARIANCES: REFINE
Protocol cycle #2 of 3
Refinement protocol for this macrocycle:
ROTATION: REFINE
TRANSLATION: REFINE
VARIANCES: REFINE
Protocol cycle #3 of 3
Refinement protocol for this macrocycle:
ROTATION: REFINE
TRANSLATION: REFINE
VARIANCES: REFINE
There are 5 tncs perturbation angles to refine
Spreading calculation onto 2 threads.
Refining translational NCS parameters
0% 100%
|====| DONE
TRANSLATIONAL NCS REFINEMENT RESULTS
------------------------------------
Initial Rotation perturbations
------------------------------
Test rotation #1 = +0.0 +0.0 +0.0
Test rotation #2 = +0.3 -0.7 -0.5
Test rotation #3 = +0.3 +0.9 -0.5
Test rotation #4 = +1.1 -0.2 +0.9
Test rotation #5 = +0.3 +1.4 +0.9
<!--SUMMARY_BEGIN-->
Best Translational NCS Refinement Parameters
--------------------------------------------
Test rotation #4
with final rotation = -0.8558 -0.8577 0.1563
refined from initial rotation = 1.1359 -0.1566 0.9314
with final translation = -0.0058 0.1112 -0.5024
refined from initial translation = -0.0067 0.1085 -0.5036
with likelihood = -246084
<!--SUMMARY_END-->
Table of Results of Refinements from Perturbed Starting Rotations
-----------------------------------------------------------------
Trial Initial Rot'n Refined Rot'n (Angle) Refined Translation Likelihood
# 1 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 ( 0.0) -0.006 +0.111 -0.503 -246088.0
# 2 +0.3 -0.7 -0.5 +0.2 +0.3 -0.1 ( 0.4) -0.006 +0.111 -0.503 -246087.6
# 3 +0.3 +0.9 -0.5 +0.1 +0.2 -0.0 ( 0.2) -0.006 +0.111 -0.503 -246087.9
# 4 +1.1 -0.2 +0.9 -0.9 -0.9 +0.2 (-1.2) -0.006 +0.111 -0.502 -246084.1 *
# 5 +0.3 +1.4 +0.9 +0.0 +0.0 +0.1 ( 0.1) -0.006 +0.111 -0.503 -246088.0
Translational NCS rotation angle -0.855825 -0.857738 0.156295
for translational NCS translation vector -0.006 0.111 -0.502
D corresponding to RMS deviation of NCS related structure:
Range (low resolution - high resolution): 0.9677 - 0.9816
Intensity Moments after tNCS (best) refinement
----------------------------------------------
2nd Moment = <E^4>/<E^2>^2 == <J^2>/<J>^2
Untwinned Perfect Twin
2nd Moment Centric: 3.0 2.0
2nd Moment Acentric: 2.0 1.5
Measured
2nd Moment Centric: 2.81
2nd Moment Acentric: 1.84
Resolution for Twin Analysis (85% I/SIGI > 3): 2.93A (HiRes=1.86A)
$TABLE : Intensity distribution after tNCS (best) refinement:
$GRAPHS
:Cumulative intensity distribution (acentric and centric):N:1,2,3,4,5,6:
$$
Z ACent_theor ACent_twin ACent_obser Cent_theor Cent_obser
$$ loggraph $$
0 0 0 0 0 0
0.04 0.0392106 0.0030343 0.0228443 0.158519 0.104575
0.08 0.0768837 0.0115132 0.0539754 0.222703 0.155556
0.12 0.11308 0.0245815 0.0902576 0.270966 0.211765
0.16 0.147856 0.0414833 0.120717 0.310843 0.258824
0.2 0.181269 0.0615519 0.1514 0.345279 0.290196
0.24 0.213372 0.0842006 0.181411 0.375794 0.321569
0.28 0.244216 0.108914 0.210974 0.403299 0.356863
0.32 0.273851 0.13524 0.236954 0.428392 0.386928
0.36 0.302324 0.162786 0.266517 0.451494 0.415686
0.4 0.32968 0.191208 0.295857 0.472911 0.43268
0.44 0.355964 0.220208 0.327212 0.492878 0.458824
0.48 0.381217 0.24953 0.354759 0.511578 0.471895
0.52 0.405479 0.278952 0.378275 0.529158 0.48366
0.56 0.428791 0.308287 0.403583 0.54574 0.500654
0.6 0.451188 0.337373 0.428443 0.561422 0.517647
0.64 0.472708 0.366075 0.455543 0.576289 0.533333
0.68 0.493383 0.394281 0.478835 0.590413 0.551634
0.72 0.513248 0.421896 0.50056 0.603856 0.568627
0.76 0.532334 0.448846 0.521389 0.616672 0.579085
0.8 0.550671 0.475069 0.537962 0.628907 0.602614
0.84 0.56829 0.500518 0.556999 0.640603 0.618301
0.88 0.585217 0.525156 0.578275 0.651798 0.626144
0.92 0.601481 0.548959 0.597088 0.662525 0.643137
0.96 0.617107 0.571908 0.614334 0.672813 0.656209
1 0.632121 0.593994 0.629787 0.682689 0.670588
1.04 0.646545 0.615215 0.645017 0.692179 0.675817
1.08 0.660404 0.635573 0.658903 0.701302 0.68366
1.12 0.67372 0.655074 0.672564 0.710082 0.696732
1.16 0.686514 0.673732 0.683987 0.718534 0.705882
1.2 0.698806 0.691559 0.698768 0.726678 0.715033
1.24 0.710616 0.708574 0.711534 0.734529 0.726797
1.28 0.721963 0.724795 0.723852 0.742101 0.732026
1.32 0.732865 0.740245 0.734826 0.749408 0.738562
1.36 0.743339 0.754946 0.745353 0.756463 0.74902
1.4 0.753403 0.768922 0.757223 0.763276 0.754248
1.44 0.763072 0.782197 0.76551 0.769861 0.75817
1.48 0.772362 0.794797 0.774692 0.776226 0.768627
1.52 0.781288 0.806747 0.783427 0.782381 0.775163
1.56 0.789864 0.818072 0.79037 0.788335 0.779085
1.6 0.798103 0.828799 0.798208 0.794097 0.788235
1.64 0.80602 0.838951 0.805375 0.799674 0.793464
1.68 0.813626 0.848554 0.811646 0.805076 0.801307
1.72 0.820934 0.857633 0.819485 0.810307 0.806536
1.76 0.827955 0.866211 0.8271 0.815376 0.80915
1.8 0.834701 0.874311 0.836058 0.820287 0.814379
1.84 0.841183 0.881957 0.842329 0.825049 0.819608
1.88 0.84741 0.889169 0.848152 0.829666 0.831373
1.92 0.853393 0.895971 0.854871 0.834143 0.835294
1.96 0.859142 0.902382 0.86159 0.838487 0.840523
2 0.864665 0.908422 0.866741 0.842701 0.840523
$$
Histogram of Epsilon Factors
----------------------------
Minimum EpsFac = 0.0261
Maximum EpsFac = 1.9722
Mean EpsFac = 1.0000 for 20208 reflections
Mid EpsFac Bin Value
| 0 343 686 1029 1372 1715
V | | | | | |
0.0 ** (46)
0.1 ********************** (727)
0.2 *************************************** (1339)
0.3 ************************************************** (1693)
0.4 ***************************************** (1398)
0.5 ************************* (850)
0.6 ******************************************** (1492)
0.7 *********** (368)
0.8 ******************** (656)
0.9 ********************************************* (1519)
1.0
1.1 ********************************************** (1557)
1.2 ********************* (687)
1.3 *********** (365)
1.4 ******************************************* (1444)
1.5 ************************* (833)
1.6 ****************************************** (1424)
1.7 ************************************************** (1717)
1.8 *************************************** (1339)
1.9 ********************* (704)
2.0 ** (50)
<!--SUMMARY_BEGIN-->
tNCS/Twin Detection Table
-------------------------
NCS translation vector = -0.006 0.111 -0.502
-Second Moments- --P-values--
Centric Acentric untwinned twin frac <5%
Theoretical for untwinned 3.00 2.00
Theoretical for perfect twin 2.00 1.50
Initial (data as input) 4.21 2.68+/-0.121 1 1
After Anisotropy Correction 4.23 2.60+/-0.111 1 1
After Anisotropy and tNCS 2.81 1.84+/-0.053 0.00096 0.0941
Resolution for Twin Analysis (85% I/SIGI > 3): 2.93A (HiRes=1.86A)
<!--SUMMARY_END-->
------------
OUTPUT FILES
------------
No files output
<!--SUMMARY_BEGIN-->
CPU Time: 0 days 0 hrs 0 mins 9.69 secs ( 9.69 secs)
Finished: Sat Sep 12 13:33:59 2015
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.5.7 ***
*************************************************************************************
Input Search Components
-----------------------
Ensemble ensemble1 : #copies = 2
Translational NCS Edited Sets of Search Components
--------------------------------------------------
Ensemble ensemble1 : #sets = 1
CPU Time: 0 days 0 hrs 0 mins 9.69 secs ( 9.69 secs)
Finished: Sat Sep 12 13:33:59 2015
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.5.7 ***
*************************************************************************************
Search Order (next search *):
#1: Ensemble ensemble1 *
CPU Time: 0 days 0 hrs 0 mins 9.69 secs ( 9.69 secs)
Finished: Sat Sep 12 13:33:59 2015
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT ROTATION FUNCTION 2.5.7 ***
*************************************************************************************
<!--SUMMARY_END-->
---------------------
ANISOTROPY CORRECTION
---------------------
No refinement of parameters
------------------------
TRANSLATIONAL NCS VECTOR
------------------------
NCS translation vector input = -0.00577836 0.111244 -0.502449
---------------------------
TRANSLATIONAL NCS ROTATIONS
---------------------------
NCS rotation input = -0.855825 -0.857738 0.156295
No refinement of parameters
Histogram of Epsilon Factors
----------------------------
Minimum EpsFac = 0.0261
Maximum EpsFac = 1.9722
Mean EpsFac = 1.0000 for 20208 reflections
Mid EpsFac Bin Value
| 0 343 686 1029 1372 1715
V | | | | | |
0.0 ** (46)
0.1 ********************** (727)
0.2 *************************************** (1339)
0.3 ************************************************** (1693)
0.4 ***************************************** (1398)
0.5 ************************* (850)
0.6 ******************************************** (1492)
0.7 *********** (368)
0.8 ******************** (656)
0.9 ********************************************* (1519)
1.0
1.1 ********************************************** (1557)
1.2 ********************* (687)
1.3 *********** (365)
1.4 ******************************************* (1444)
1.5 ************************* (833)
1.6 ****************************************** (1424)
1.7 ************************************************** (1717)
1.8 *************************************** (1339)
1.9 ********************* (704)
2.0 ** (50)
--------------------------
DATA FOR ROTATION FUNCTION
--------------------------
Expected LLG
------------
Target = 120.000
eLLG = 120.031 (at 4.23A)
eLLG indicates that placement of ensemble "ensemble1" will be straightforward
The data are sufficient to exceed the eLLG target
High resolution limit imposed by expected LLG = 4.23
Outliers with a probability less than 1e-006 will be rejected
There were 0 (0.0000%) reflections rejected
No reflections are outliers
<!--SUMMARY_BEGIN-->
Resolution of All Data (Number): 1.86 24.67 (20208)
Resolution of Selected Data (Number): 4.23 24.67 (1750)
Translational NCS:
Vector = -0.0058 0.1112 -0.5024
Rotation = -0.8558 -0.8577 0.1563
D values (lores-hires)= 0.9677-0.9816
<!--SUMMARY_END-->
-------------------
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 (1404)
- half number of centrics (346/2)
= -1577
With correction for SigF,
Wilson log(likelihood) = -943.642
----------
ENSEMBLING
----------
Ensemble Generation: ensemble1
------------------------------
Ensemble configured for structure factor interpolation
Ensemble configured to resolution 4.23
PDB file # 1: MRmodel_singlechain.pdb
This pdb file contains 1 model
The input RmsD of model #1 with respect to the real structure is 0.62
Allowed range (resolution and radius dependent) is 0.26 to 3.36
The initial RmsD of model #1 with respect to the real structure is 0.62
Input VRMS delta = 0.000000
VRMS delta lower/upper limit = -0.309493 / 10.788424
Final VRMS delta = 0.000000
Electron Density Calculation
0% 100%
|=======| DONE
Spreading calculation onto 2 threads.
Weighting Structure Factors
0% 100%
|================================================================| DONE
<!--SUMMARY_BEGIN-->
Ensembling Table
----------------
Resolution of Ensembles: 4.23184
Ensemble Scat% Radius Model# Rel-B RMS
ensemble1 49.5 20.15 620204659 0.0 0.618
<!--SUMMARY_END-->
Ensemble Generation for Spherical Harmonic Decomposition: ensemble1
-------------------------------------------------------------------
Ensemble configured for spherical harmonic decomposition
Ensemble configured to resolution 4.23
PDB file # 1: MRmodel_singlechain.pdb
This pdb file contains 1 model
The input RmsD of model #1 with respect to the real structure is 0.62
Allowed range (resolution and radius dependent) is 0.26 to 3.36
The initial RmsD of model #1 with respect to the real structure is 0.62
Input VRMS delta = 0.000000
VRMS delta lower/upper limit = -0.309493 / 10.788424
Final VRMS delta = 0.000000
Electron Density Calculation
0% 100%
|=======| DONE
Spreading calculation onto 2 threads.
Weighting Structure Factors
0% 100%
|=========| DONE
Elmn for Search Ensemble
Spreading calculation onto 2 threads.
Elmn Calculation for Search Ensemble
0% 100%
|===============================================================| DONE
Target Function: FAST LERF1
-------------------------
ROTATION FUNCTION #1 OF 1
-------------------------
Search Ensemble: ensemble1
Translational Ncs: Rotational spacegroup changed to P1
Sampling: 6.01 degrees
Known MR solutions
(empty solution set - no components)
Spherical Harmonics
-------------------
Elmn for Data
Spreading calculation onto 2 threads.
Elmn Calculation for Data
0% 100%
|====================================================================| DONE
Scanning the Range of Beta Angles
---------------------------------
Spreading calculation onto 2 threads.
Clmn Calculation
0% 100%
|================| DONE
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
Also store peaks over 54% of top
There were 143 sites over 67.5% of top
143 peaks selected
The sites over 67.5% are:
# Euler1 Euler2 Euler3 FSS Z-score
1 358.3 86.0 270.1 100.000 5.86
2 357.9 88.8 93.8 98.472 5.77
3 177.9 88.8 93.8 96.193 5.64
#SITES = 143: OUTPUT TRUNCATED TO 3 SITES
Top 143 rotations before clustering will be rescored
Spreading calculation onto 2 threads
Calculating Likelihood for RF #1 of 1
0% 100%
|=========================================================================| DONE
Mean and Standard Deviation
---------------------------
Scoring 500 randomly sampled rotations
Spreading calculation onto 2 threads
Generating Statistics for RF #1 of 1
0% 100%
|===============================================================| DONE
Highest Score (Z-score): 16.9486 (5.69)
Top Peaks With Clustering
Select peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
Also store peaks over 60% of top
There were 25 sites over 75% of top
The sites over 75% are:
# Euler1 Euler2 Euler3 LLG Z-score Split #Group FSS-this-ang/FSS-top
1 177.9 88.8 93.8 16.949 5.69 0.0 4 96.193/ 96.193
2 182.7 89.8 268.1 14.455 5.60 174.4 3 94.582/ 94.582
3 357.9 88.8 93.8 14.335 5.59 180.0 4 98.472/ 98.472
#SITES = 25: OUTPUT TRUNCATED TO 3 SITES
<!--SUMMARY_BEGIN-->
Rotation Function Table: ensemble1
----------------------------------
(Z-scores from Fast Rotation Function)
#SET Top (Z) Second (Z) Third (Z)
1 16.95 5.69 14.45 5.60 14.33 5.59
---- ---------- ----- ---------- ----- ---------- -----
<!--SUMMARY_END-->
---------------
FINAL SELECTION
---------------
<!--SUMMARY_BEGIN-->
Select by Percentage of Top value: 75
Top RF = 16.9486
Purge RF mean = -143.56
Number of sets stored before final selection = 1
Number of solutions stored before final selection = 25
Number of sets stored (deleted) after final selection = 1 (0)
Number of solutions stored (deleted) after final selection = 25 (0)
Percent used for purge = 60%
Includes deep search down percent = 15%
Number of solutions stored above (below) deep threshold = 9 (16)
Rotation Function Final Selection Table
---------------------------------------
Rotation list length by SET
SET# Start Final Deleted Set (*) Deep: Start Final Deleted Set (*)
1 9 9 - 25 25 -
ALL 9 9 25 25
<!--SUMMARY_END-->
$TABLE : Rotation Function Component #1 (ensemble1) :
$GRAPHS
:RF Number vs LL-gain:AUTO:1,2: :RF Number vs Z-Score:AUTO:1,3:
$$
Number LLG Z-Score
$$ loggraph $$
1 16.95 5.69
2 14.45 5.60
3 14.33 5.59
4 -1.38 5.04
5 -6.75 4.85
6 -10.79 4.70
7 -11.62 4.67
8 -13.02 4.63
9 -13.63 4.60
10 -25.21 4.19
11 -31.65 3.97
12 -33.75 3.89
13 -35.75 3.82
14 -36.24 3.80
15 -38.20 3.73
16 -39.66 3.68
17 -40.06 3.67
18 -40.92 3.64
19 -40.99 3.63
20 -43.32 3.55
21 -44.14 3.52
22 -45.01 3.49
23 -45.45 3.48
24 -46.18 3.45
25 -46.65 3.43
$$
<!--SUMMARY_BEGIN-->
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 0 mins 11.35 secs ( 11.35 secs)
Finished: Sat Sep 12 13:34:00 2015
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT TRANSLATION FUNCTION 2.5.7 ***
*************************************************************************************
<!--SUMMARY_END-->
---------------------
ANISOTROPY CORRECTION
---------------------
No refinement of parameters
------------------------
TRANSLATIONAL NCS VECTOR
------------------------
NCS translation vector input = -0.00577836 0.111244 -0.502449
---------------------------
TRANSLATIONAL NCS ROTATIONS
---------------------------
NCS rotation input = -0.855825 -0.857738 0.156295
No refinement of parameters
Histogram of Epsilon Factors
----------------------------
Minimum EpsFac = 0.0261
Maximum EpsFac = 1.9722
Mean EpsFac = 1.0000 for 20208 reflections
Mid EpsFac Bin Value
| 0 343 686 1029 1372 1715
V | | | | | |
0.0 ** (46)
0.1 ********************** (727)
0.2 *************************************** (1339)
0.3 ************************************************** (1693)
0.4 ***************************************** (1398)
0.5 ************************* (850)
0.6 ******************************************** (1492)
0.7 *********** (368)
0.8 ******************** (656)
0.9 ********************************************* (1519)
1.0
1.1 ********************************************** (1557)
1.2 ********************* (687)
1.3 *********** (365)
1.4 ******************************************* (1444)
1.5 ************************* (833)
1.6 ****************************************** (1424)
1.7 ************************************************** (1717)
1.8 *************************************** (1339)
1.9 ********************* (704)
2.0 ** (50)
-----------------------------
DATA FOR TRANSLATION FUNCTION
-----------------------------
High Resolution Limit imposed by RF list = 4.23
Outliers with a probability less than 1e-006 will be rejected
There were 0 (0.0000%) reflections rejected
No reflections are outliers
<!--SUMMARY_BEGIN-->
Resolution of All Data (Number): 1.86 24.67 (20208)
Resolution of Selected Data (Number): 4.23 24.67 (1750)
Translational NCS:
Vector = -0.0058 0.1112 -0.5024
Rotation = -0.8558 -0.8577 0.1563
D values (lores-hires)= 0.9677-0.9816
<!--SUMMARY_END-->
-------------------
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 (1404)
- half number of centrics (346/2)
= -1577
With correction for SigF,
Wilson log(likelihood) = -943.642
<!--SUMMARY_BEGIN-->
------------------------
ALTERNATIVE SPACE GROUPS
------------------------
Space Group(s) to be tested:
C 2 2 21
<!--SUMMARY_END-->
----------
ENSEMBLING
----------
<!--SUMMARY_BEGIN-->
Ensembling Table
----------------
Resolution of Ensembles: 4.23184
Ensemble Scat% Radius Model# Rel-B RMS
ensemble1 49.5 20.15 620204659 0.0 0.618
<!--SUMMARY_END-->
---------------------
TRANSLATION FUNCTIONS
---------------------
Target Function: FAST LETF1
Sampling: 1.06 Angstroms
----------------------------
TRANSLATION FUNCTION #1 OF 1
----------------------------
<!--SUMMARY_BEGIN-->
Set #1: Known MR solutions
(empty solution set - no components)
This TF set has 25 trial orientations
<!--SUMMARY_END-->
#TRIAL Euler1 Euler2 Euler3 Ensemble
1 177.9 88.8 93.8 ensemble1
2 182.7 89.8 268.1 ensemble1
3 357.9 88.8 93.8 ensemble1
4 2.4 82.2 272.1 ensemble1
5 354.8 88.0 262.3 ensemble1
6 177.6 97.9 91.7 ensemble1
7 179.8 94.9 279.0 ensemble1
8 174.8 88.0 262.3 ensemble1
9 175.6 89.7 275.0 ensemble1
----- angles below here for deep search only -----
10 185.9 90.3 87.8 ensemble1
11 2.4 97.5 264.1 ensemble1
12 355.3 90.5 81.1 ensemble1
13 358.5 93.5 207.6 ensemble1
14 183.5 80.8 266.0 ensemble1
15 177.6 82.7 83.8 ensemble1
16 189.5 92.8 208.3 ensemble1
17 176.4 91.5 81.6 ensemble1
18 198.8 98.4 200.8 ensemble1
19 183.0 86.4 26.9 ensemble1
20 351.5 90.1 254.4 ensemble1
21 7.8 89.3 73.7 ensemble1
22 4.7 87.5 255.7 ensemble1
23 168.6 90.2 281.5 ensemble1
24 184.6 89.6 211.6 ensemble1
25 184.5 96.9 271.2 ensemble1
Scoring 500 randomly sampled orientations and translations
Spreading calculation onto 2 threads.
Generating Statistics for TF SET #1 of 1
0% 100%
|==============| DONE
Mean Score (Sigma): -810.51 (69.46)
SET #1 of 1 TRIAL #1 of 9
-------------------------
Search Euler = 177.9 88.8 93.8, Ensemble = ensemble1
Doing Fast Translation Function FFT...
Done
Fast Translation Function Score (FSS): Highest = 447.115
New Top Fast Translation Function Score (FSS) = 447.115
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
There was 1 site over 67.5% of top
1 peak selected
The sites over 67.5% are:
# Frac X Frac Y Frac Z FSS Z-score
1 0.450 0.701 0.216 447.12 11.70
Top 1 translations before clustering will be rescored
Spreading calculation onto 2 threads.
Calculating Likelihood for TF SET #1 of 1 TRIAL #1 of 25
0% 100%
|==| DONE
Top Peaks With Clustering
Select 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 FSS-this-xyz/FSS-top
1 0.450 0.701 0.216 -34.274 11.70 0.0 1 447.12/ 447.12
SET #1 of 1 TRIAL #2 of 9
-------------------------
Search Euler = 182.7 89.8 268.1, Ensemble = ensemble1
Doing Fast Translation Function FFT...
Done
Fast Translation Function Score (FSS): Highest/Top = 257.029/447.115
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
There was 1 site over 67.5% of top
1 peak selected
The sites over 67.5% are:
# Frac X Frac Y Frac Z FSS Z-score
1 0.470 0.686 0.224 257.03 8.15
Top 1 translations before clustering will be rescored
Spreading calculation onto 2 threads.
Calculating Likelihood for TF SET #1 of 1 TRIAL #2 of 25
0% 100%
|==| DONE
Top Peaks With Clustering
Select 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 FSS-this-xyz/FSS-top
1 0.470 0.686 0.224 -239.01 8.15 0.0 1 257.03/ 257.03
SET #1 of 1 TRIAL #3 of 9
-------------------------
Search Euler = 357.9 88.8 93.8, Ensemble = ensemble1
Doing Fast Translation Function FFT...
Done
Fast Translation Function Score (FSS): Highest/Top = 450.058/447.115
New Top Fast Translation Function Score (FSS) = 450.058
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
There was 1 site over 67.5% of top
1 peak selected
The sites over 67.5% are:
# Frac X Frac Y Frac Z FSS Z-score
1 0.054 0.688 0.216 450.06 11.74
Top 1 translations before clustering will be rescored
Spreading calculation onto 2 threads.
Calculating Likelihood for TF SET #1 of 1 TRIAL #3 of 25
0% 100%
|==| DONE
Top Peaks With Clustering
Select 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 FSS-this-xyz/FSS-top
1 0.054 0.688 0.216 -28.271 11.74 0.0 1 450.06/ 450.06
SET #1 of 1 TRIAL #4 of 9
-------------------------
Search Euler = 2.4 82.2 272.1, Ensemble = ensemble1
Doing Fast Translation Function FFT...
Done
Fast Translation Function Score (FSS): Highest/Top = 22.2801/450.058
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
No peaks within selection criteria
No translations within selection criteria for rescoring
SET #1 of 1 TRIAL #5 of 9
-------------------------
Search Euler = 354.8 88.0 262.3, Ensemble = ensemble1
Doing Fast Translation Function FFT...
Done
Fast Translation Function Score (FSS): Highest/Top = 8.01813/450.058
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
No peaks within selection criteria
No translations within selection criteria for rescoring
SET #1 of 1 TRIAL #6 of 9
-------------------------
Search Euler = 177.6 97.9 91.7, Ensemble = ensemble1
Doing Fast Translation Function FFT...
Done
Fast Translation Function Score (FSS): Highest/Top = -4.87406/450.058
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
No peaks within selection criteria
No translations within selection criteria for rescoring
SET #1 of 1 TRIAL #7 of 9
-------------------------
Search Euler = 179.8 94.9 279.0, Ensemble = ensemble1
Doing Fast Translation Function FFT...
Done
Fast Translation Function Score (FSS): Highest/Top = 157.801/450.058
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
No peaks within selection criteria
No translations within selection criteria for rescoring
SET #1 of 1 TRIAL #8 of 9
-------------------------
Search Euler = 174.8 88.0 262.3, Ensemble = ensemble1
Doing Fast Translation Function FFT...
Done
Fast Translation Function Score (FSS): Highest/Top = 18.4305/450.058
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
No peaks within selection criteria
No translations within selection criteria for rescoring
SET #1 of 1 TRIAL #9 of 9
-------------------------
Search Euler = 175.6 89.7 275.0, Ensemble = ensemble1
Doing Fast Translation Function FFT...
Done
Fast Translation Function Score (FSS): Highest/Top = 275.492/450.058
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
There was 1 site over 67.5% of top
1 peak selected
The sites over 67.5% are:
# Frac X Frac Y Frac Z FSS Z-score
1 0.340 0.648 0.288 275.49 9.29
Top 1 translations before clustering will be rescored
Spreading calculation onto 2 threads.
Calculating Likelihood for TF SET #1 of 1 TRIAL #9 of 25
0% 100%
|==| DONE
Top Peaks With Clustering
Select 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 FSS-this-xyz/FSS-top
1 0.340 0.648 0.288 -262.87 9.29 0.0 1 275.49/ 275.49
-------------------------
DEEP TRANSLATION FUNCTION
-------------------------
<!--SUMMARY_BEGIN-->
Best TFZ is over Zscore cutoff
Do not search deep in RF list
Translation Function Table
--------------------------
SET ROT*deep Top (Z) Second (Z) Third (Z) Ensemble SpaceGroup
1 1 -34.3 11.70 - - - - ensemble C 2 2 21
1 2 -239.0 8.15 - - - - ensemble C 2 2 21
1 3 -28.3 11.74 - - - - ensemble C 2 2 21
1 4 - - - - - - ensemble C 2 2 21
1 5 - - - - - - ensemble C 2 2 21
1 6 - - - - - - ensemble C 2 2 21
1 7 - - - - - - ensemble C 2 2 21
1 8 - - - - - - ensemble C 2 2 21
1 9 -262.9 9.29 - - - - ensemble C 2 2 21
--- ---
---------------
FINAL SELECTION
---------------
LLG will be used for purge, not FSS
Top TF = -28.27
Top TFZ = 11.74
Mean TF = -810.51
Percent used for purge = 75%
Cutoff for acceptance = -223.8
TFZ used for final selection = 8
Number of solutions over TF final cutoff = 2
Number of solutions over TFZ final cutoff = 4
Number of solutions over TF & TFZ cutoff = 2
Number of solutions stored before final selection = 4
Number of solutions stored (deleted) after final selection = 4 (0)
<!--SUMMARY_END-->
$TABLE : Translation Function Component #1 (ensemble1):
$GRAPHS
:TF Number vs LL-gain:AUTO:1,2: :TF Number vs Z-Score:AUTO:1,3:
$$
Number LLG Z-Score
$$ loggraph $$
1 -28.27 11.74
2 -34.27 11.70
3 -239.01 8.15
4 -262.87 9.29
$$
<!--SUMMARY_BEGIN-->
----------------
EXPAND WITH TNCS
----------------
Solutions expanded by TNCS
<!--SUMMARY_END-->
Top solution before expansion:
SOLU SET RFZ=5.6 TFZ=11.7
SOLU SPAC C 2 2 21
SOLU 6DIM ENSE ensemble1 EULER 357.9 88.8 93.8 FRAC 0.05 0.69 0.22 BFAC 0.00
Top solution after expansion:
SOLU SET RFZ=5.6 TFZ=11.7 +TNCS
SOLU SPAC C 2 2 21
SOLU 6DIM ENSE ensemble1 EULER 357.9 88.8 93.8 FRAC 0.05 0.69 0.22 BFAC 0.00
SOLU 6DIM ENSE ensemble1 EULER 357.9 88.8 93.8 FRAC 0.05 0.80 -0.29 BFAC 0.00
<!--SUMMARY_BEGIN-->
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 0 mins 12.50 secs ( 12.50 secs)
Finished: Sat Sep 12 13:34:01 2015
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT PACKING ANALYSIS 2.5.7 ***
*************************************************************************************
<!--SUMMARY_END-->
---------
ENSEMBLES
---------
Packing Ensemble: ensemble1
-----------------
ENSEMBLE SYMMETRY
-----------------
Ensemble "ensemble1" Point Group: 1
----------------------
STRUCTURES FOR PACKING
----------------------
Packing will be performed with "trace" atoms. which are C-alphas for protein, P
and selected N for nucleic acid
If there are no trace atoms in the molecule(s) all atoms will be used in the
packing test
If the trace length exceeds 1000 atoms then the molecule(s) will be sampled on a
hexagonal grid and the clash distance increased in proportion to the size of the
hexagonal grid sampling
When an ensemble consists of more than one structure, the structure with the
highest homology is selected for packing and the structure trimmed of loops that
diverge more than 3A from other atoms in the ensemble
<!--SUMMARY_BEGIN-->
Ensemble: ensemble1
-------------------
All atoms = 968
Structure with lowest rms = MRmodel_singlechain.pdb (0.618239)
Trace length = 124
Trace atoms clash if they are closer than 3.00 Angstroms
<!--SUMMARY_END-->
----------------
PACKING FUNCTION
----------------
There are 4 solutions to pack
Spreading calculation onto 2 threads.
Packing analysis
0% 100%
|===| DONE
<!--SUMMARY_BEGIN-->
Packing Table
-------------
Solutions accepted if total number of clashes <= 5% of trace atoms
i.e. total number of clashes <= 12
AND if number of clashes <= 5% of trace atoms for each ensemble
i.e. ensemble1: number of clashes <= 6
# # #Clash Packs SpaceGroup Annotation
1 1 0 YES C 2 2 21 RFZ=5.6 TFZ=11.7 +TNCS
2 2 0 YES C 2 2 21 RFZ=5.7 TFZ=11.7 +TNCS
3 3 3 YES C 2 2 21 RFZ=5.6 TFZ=8.1 +TNCS
4 4 0 YES C 2 2 21 RFZ=4.6 TFZ=9.3 +TNCS
4 accepted of 4 solutions
------------
OUTPUT FILES
------------
D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.1.pdb
D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.2.pdb
D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.sol
CPU Time: 0 days 0 hrs 0 mins 12.62 secs ( 12.62 secs)
Finished: Sat Sep 12 13:34:01 2015
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.5.7 ***
*************************************************************************************
Composition Table
-----------------
Total Scattering = 86884.2
Ensemble Fraction Scattering
ensemble1 49.50%
<!--SUMMARY_END-->
---------------------
ANISOTROPY CORRECTION
---------------------
No refinement of parameters
------------------------
TRANSLATIONAL NCS VECTOR
------------------------
NCS translation vector input = -0.00577836 0.111244 -0.502449
---------------------------
TRANSLATIONAL NCS ROTATIONS
---------------------------
NCS rotation input = -0.855825 -0.857738 0.156295
No refinement of parameters
Histogram of Epsilon Factors
----------------------------
Minimum EpsFac = 0.0261
Maximum EpsFac = 1.9722
Mean EpsFac = 1.0000 for 20208 reflections
Mid EpsFac Bin Value
| 0 343 686 1029 1372 1715
V | | | | | |
0.0 ** (46)
0.1 ********************** (727)
0.2 *************************************** (1339)
0.3 ************************************************** (1693)
0.4 ***************************************** (1398)
0.5 ************************* (850)
0.6 ******************************************** (1492)
0.7 *********** (368)
0.8 ******************** (656)
0.9 ********************************************* (1519)
1.0
1.1 ********************************************** (1557)
1.2 ********************* (687)
1.3 *********** (365)
1.4 ******************************************* (1444)
1.5 ************************* (833)
1.6 ****************************************** (1424)
1.7 ************************************************** (1717)
1.8 *************************************** (1339)
1.9 ********************* (704)
2.0 ** (50)
-------------------------------
DATA FOR REFINEMENT AND PHASING
-------------------------------
High resolution limit imposed by solution list = 4.23
Outliers with a probability less than 1e-006 will be rejected
There were 0 (0.0000%) reflections rejected
No reflections are outliers
<!--SUMMARY_BEGIN-->
Resolution of All Data (Number): 1.86 24.67 (20208)
Resolution of Selected Data (Number): 4.23 24.67 (1750)
Translational NCS:
Vector = -0.0058 0.1112 -0.5024
Rotation = -0.8558 -0.8577 0.1563
D values (lores-hires)= 0.9677-0.9816
<!--SUMMARY_END-->
-------------------
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 (1404)
- half number of centrics (346/2)
= -1577
With correction for SigF,
Wilson log(likelihood) = -943.642
----------
ENSEMBLING
----------
<!--SUMMARY_BEGIN-->
Ensembling Table
----------------
Resolution of Ensembles: 4.23184
Ensemble Scat% Radius Model# Rel-B RMS
ensemble1 49.5 20.15 620204659 0.0 0.618
<!--SUMMARY_END-->
----------
REFINEMENT
----------
Protocol cycle #1 of 1
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION : REFINE
BFACTOR : REFINE
MODEL VRMS : FIX
MAP CELL SCALE: FIX
LAST ONLY : FALSE
There are 4 solutions to refine
Spreading calculation onto 2 threads.
Refining solutions
0% 100%
|===| DONE
REFINING SET # 1 OF 4
---------------------
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 13 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-50.153 232.031 282.184
Final Parameters:
SOLU SET
SOLU 6DIM ENSE ensemble1 EULER 0.1 88.9 92.6 FRAC 0.09 0.67 0.23 BFAC 7.08
SOLU 6DIM ENSE ensemble1 EULER 0.2 90.1 92.5 FRAC 0.09 0.78 -0.26 BFAC 7.08
SOLU ENSEMBLE ensemble1 VRMS DELTA +0.0000 RMSD 0.62 #VRMS
REFINING SET # 2 OF 4
---------------------
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 12 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-59.158 232.029 291.187
Final Parameters:
SOLU SET
SOLU 6DIM ENSE ensemble1 EULER 180.2 90.1 92.5 FRAC 0.41 0.72 0.24 BFAC 7.04
SOLU 6DIM ENSE ensemble1 EULER 180.1 88.9 92.6 FRAC 0.41 0.83 -0.27 BFAC 7.04
SOLU ENSEMBLE ensemble1 VRMS DELTA +0.0000 RMSD 0.62 #VRMS
REFINING SET # 3 OF 4
---------------------
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 13 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-267.714 232.028 499.741
Final Parameters:
SOLU SET
SOLU 6DIM ENSE ensemble1 EULER 179.9 91.1 272.6 FRAC 0.41 0.67 0.27 BFAC 7.05
SOLU 6DIM ENSE ensemble1 EULER 179.8 89.9 272.6 FRAC 0.41 0.78 -0.24 BFAC 7.05
SOLU ENSEMBLE ensemble1 VRMS DELTA +0.0000 RMSD 0.62 #VRMS
REFINING SET # 4 OF 4
---------------------
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 12 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-288.966 232.025 520.991
Final Parameters:
SOLU SET
SOLU 6DIM ENSE ensemble1 EULER 179.9 91.1 272.6 FRAC 0.41 0.67 0.27 BFAC 7.06
SOLU 6DIM ENSE ensemble1 EULER 179.8 89.8 272.6 FRAC 0.41 0.78 -0.24 BFAC 7.06
SOLU ENSEMBLE ensemble1 VRMS DELTA +0.0000 RMSD 0.62 #VRMS
$TABLE : Refinement After Placing Component #2 (ensemble1 4.23A) :
$GRAPHS
:Solution Number vs LL-gain:AUTO:1,2,3: :Solution Number vs R-value:AUTO:1,4,5:
$$
Number final-LLG initial-LLG final-R initial-R
$$ loggraph $$
1 233.28 -50.29 46.12 49.07
2 233.27 -266.08 46.21 52.36
3 233.27 -287.20 45.97 54.45
4 233.27 -58.54 46.17 49.65
$$
---------------
FIND DUPLICATES
---------------
Check for nearly equivalent solutions
Spreading calculation onto 2 threads.
Calculating Duplicates for 4 solutions
0% 100%
|===| DONE
No Template Solution for comparison
3 duplicate solutions pruned
No solutions moved to match template
<!--SUMMARY_BEGIN-->
Refinement Table (Unsorted)
---------------------------
Refinement to full resolution
#+ = input number #* = results number
#+ #* (Start LLG Rval TFZ) (Refined LLG Rval) Unique =# Tmplt SpaceGroup
1 1 -50.3 49.1 n/a 233.3 46.1 YES C 2 2 21
2 --- -58.5 49.7 n/a 233.3 46.2 NO 1 C 2 2 21
3 --- -266.1 52.4 n/a 233.3 46.2 NO 1 C 2 2 21
4 --- -287.2 54.5 n/a 233.3 46.0 NO 1 C 2 2 21
Refinement Table (Sorted)
-------------------------
Refinement to full resolution
#+ = input number #* = results number
#+ #* (Start LLG Rval TFZ) (Refined LLG Rval) Unique =# Tmplt SpaceGroup
1 1 -50.3 49.1 n/a 233.3 46.1 YES C 2 2 21
3 --- -266.1 52.4 n/a 233.3 46.2 NO 1 C 2 2 21
4 --- -287.2 54.5 n/a 233.3 46.0 NO 1 C 2 2 21
2 --- -58.5 49.7 n/a 233.3 46.2 NO 1 C 2 2 21
Ensembling Table
----------------
Resolution of Ensembles: 4.23184
Range of delta-VRMS and VRMS given over current solution list (4 solution(s))
Ensemble Scat% Radius Model# Rel-B RMS Delta-VRMS min/max (VRMS min/max)
ensemble1 49.5 20.15 620204659 0.0 0.618 +0.000/+0.000 (0.618/0.618)
<!--SUMMARY_END-->
---------------
TFZ EQUIVALENTS
---------------
Calculation of TFZ Equivalents
Translational NCS present
Refined TFZ equivalent not accurate and therefore not calculated
<!--SUMMARY_BEGIN-->
------------
OUTPUT FILES
------------
A sharpening B-factor of 100% of the isotropic B-factor in the direction of
smallest falloff (i.e. highest resolution) has been added to the anisotropically
corrected structure factors (FWT,DELFWT)
<!--SUMMARY_END-->
Calculation of Map Coefficients
-------------------------------
1 top map coefficients calculated
Map coefficient calculated for top solution #1
SOLU SPAC C 2 2 21
SOLU 6DIM ENSE ensemble1 EULER 0.1 88.9 92.6 FRAC 0.09 0.67 0.23 BFAC 7.08
SOLU 6DIM ENSE ensemble1 EULER 0.2 90.1 92.5 FRAC 0.09 0.78 -0.26 BFAC 7.08
SOLU ENSEMBLE ensemble1 VRMS DELTA +0.0000 RMSD 0.62 #VRMS 0.62
<!--SUMMARY_BEGIN-->
D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.1.pdb
D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.1.mtz
D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.sol
CPU Time: 0 days 0 hrs 0 mins 13.87 secs ( 13.87 secs)
Finished: Sat Sep 12 13:34:03 2015
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.5.7 ***
*************************************************************************************
Current is Best Solution (first search)
New Best LLG : 233.3 (4.23)
Best Search Component so far: ensemble1
CPU Time: 0 days 0 hrs 0 mins 13.87 secs ( 13.87 secs)
Finished: Sat Sep 12 13:34:03 2015
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.5.7 ***
*************************************************************************************
Composition Table
-----------------
Total Scattering = 86884.2
Ensemble Fraction Scattering
ensemble1 49.50%
<!--SUMMARY_END-->
---------------------
ANISOTROPY CORRECTION
---------------------
No refinement of parameters
------------------------
TRANSLATIONAL NCS VECTOR
------------------------
NCS translation vector input = -0.00577836 0.111244 -0.502449
---------------------------
TRANSLATIONAL NCS ROTATIONS
---------------------------
NCS rotation input = -0.855825 -0.857738 0.156295
No refinement of parameters
Histogram of Epsilon Factors
----------------------------
Minimum EpsFac = 0.0261
Maximum EpsFac = 1.9722
Mean EpsFac = 1.0000 for 20208 reflections
Mid EpsFac Bin Value
| 0 343 686 1029 1372 1715
V | | | | | |
0.0 ** (46)
0.1 ********************** (727)
0.2 *************************************** (1339)
0.3 ************************************************** (1693)
0.4 ***************************************** (1398)
0.5 ************************* (850)
0.6 ******************************************** (1492)
0.7 *********** (368)
0.8 ******************** (656)
0.9 ********************************************* (1519)
1.0
1.1 ********************************************** (1557)
1.2 ********************* (687)
1.3 *********** (365)
1.4 ******************************************* (1444)
1.5 ************************* (833)
1.6 ****************************************** (1424)
1.7 ************************************************** (1717)
1.8 *************************************** (1339)
1.9 ********************* (704)
2.0 ** (50)
-------------------------------
DATA FOR REFINEMENT AND PHASING
-------------------------------
Outliers with a probability less than 1e-006 will be rejected
There were 0 (0.0000%) reflections rejected
No reflections are outliers
<!--SUMMARY_BEGIN-->
Resolution of All Data (Number): 1.86 24.67 (20208)
Resolution of Selected Data (Number): 1.86 24.67 (20208)
Translational NCS:
Vector = -0.0058 0.1112 -0.5024
Rotation = -0.8558 -0.8577 0.1563
D values (lores-hires)= 0.9677-0.9816
<!--SUMMARY_END-->
-------------------
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 (18155)
- half number of centrics (2053/2)
= -19181
With correction for SigF,
Wilson log(likelihood) = -14694.2
----------
ENSEMBLING
----------
Ensemble Generation: ensemble1
------------------------------
Ensemble configured for structure factor interpolation
Ensemble configured to resolution 1.86
PDB file # 1: MRmodel_singlechain.pdb
This pdb file contains 1 model
The input RmsD of model #1 with respect to the real structure is 0.62
Allowed range (resolution and radius dependent) is 0.26 to 3.36
The initial RmsD of model #1 with respect to the real structure is 0.62
Input VRMS delta = 0.000000
VRMS delta lower/upper limit = -0.309493 / 10.788424
Final VRMS delta = 0.000000
Electron Density Calculation
0% 100%
|=======| DONE
Spreading calculation onto 2 threads.
Weighting Structure Factors
0% 100%
|========================================================================| DONE
<!--SUMMARY_BEGIN-->
Ensembling Table
----------------
Resolution of Ensembles: 1.85906
Range of delta-VRMS and VRMS given over current solution list (1 solution(s))
Ensemble Scat% Radius Model# Rel-B RMS Delta-VRMS min/max (VRMS min/max)
ensemble1 49.5 20.15 857072816 0.0 0.618 +0.000/+0.000 (0.618/0.618)
<!--SUMMARY_END-->
----------
REFINEMENT
----------
Protocol cycle #1 of 1
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION : REFINE
BFACTOR : REFINE
MODEL VRMS : REFINE
MAP CELL SCALE: FIX
LAST ONLY : FALSE
There is 1 solution to refine
Spreading calculation onto 2 threads.
Refining solutions
0% 100%
|==| DONE
REFINING SET # 1 OF 1
---------------------
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 8 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-2198.836 1714.273 3913.109
Final Parameters:
SOLU SET
SOLU 6DIM ENSE ensemble1 EULER 0.3 88.9 92.4 FRAC 0.09 0.67 0.23 BFAC -0.24
SOLU 6DIM ENSE ensemble1 EULER 0.5 90.4 92.3 FRAC 0.09 0.78 -0.26 BFAC -0.24
SOLU ENSEMBLE ensemble1 VRMS DELTA +0.0374 RMSD 0.62 #VRMS
$TABLE : Refinement After Placing Component #2 (ensemble1 1.86A) :
$GRAPHS
:Solution Number vs LL-gain:AUTO:1,2,3: :Solution Number vs R-value:AUTO:1,4,5:
$$
Number final-LLG initial-LLG final-R initial-R
$$ loggraph $$
1 1714.27 -2200.67 49.64 51.01
$$
---------------
FIND DUPLICATES
---------------
Check for nearly equivalent solutions
Spreading calculation onto 2 threads.
Calculating Duplicates for 1 solutions
0% 100%
|==| DONE
No Template Solution for comparison
No duplicate solutions pruned
No solutions moved to match template
<!--SUMMARY_BEGIN-->
Refinement Table (Unsorted)
---------------------------
Refinement to full resolution
#+ = input number #* = results number
#+ #* (Start LLG Rval TFZ) (Refined LLG Rval) Unique =# Tmplt SpaceGroup
1 1 -2200.7 51.0 n/a 1714.3 49.6 YES C 2 2 21
Refinement Table (Sorted)
-------------------------
Refinement to full resolution
#+ = input number #* = results number
#+ #* (Start LLG Rval TFZ) (Refined LLG Rval) Unique =# Tmplt SpaceGroup
1 1 -2200.7 51.0 n/a 1714.3 49.6 YES C 2 2 21
Ensembling Table
----------------
Resolution of Ensembles: 1.85906
Range of delta-VRMS and VRMS given over current solution list (1 solution(s))
Ensemble Scat% Radius Model# Rel-B RMS Delta-VRMS min/max (VRMS min/max)
ensemble1 49.5 20.15 857072816 0.0 0.618 +0.037/+0.037 (0.618/0.618)
<!--SUMMARY_END-->
---------------
TFZ EQUIVALENTS
---------------
Calculation of TFZ Equivalents
Translational NCS present
Refined TFZ equivalent not accurate and therefore not calculated
<!--SUMMARY_BEGIN-->
------------
OUTPUT FILES
------------
A sharpening B-factor of 100% of the isotropic B-factor in the direction of
smallest falloff (i.e. highest resolution) has been added to the anisotropically
corrected structure factors (FWT,DELFWT)
<!--SUMMARY_END-->
Calculation of Map Coefficients
-------------------------------
1 top map coefficients calculated
Map coefficient calculated for top solution #1
SOLU SPAC C 2 2 21
SOLU 6DIM ENSE ensemble1 EULER 0.3 88.9 92.4 FRAC 0.09 0.67 0.23 BFAC -0.24
SOLU 6DIM ENSE ensemble1 EULER 0.5 90.4 92.3 FRAC 0.09 0.78 -0.26 BFAC -0.24
SOLU ENSEMBLE ensemble1 VRMS DELTA +0.0374 RMSD 0.62 #VRMS 0.65
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D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.1.pdb
D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.1.mtz
D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.sol
CPU Time: 0 days 0 hrs 0 mins 21.67 secs ( 21.67 secs)
Finished: Sat Sep 12 13:34:10 2015
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.5.7 ***
*************************************************************************************
$TEXT:MR Result: $$ Baubles Markup $$
SINGLE solution
Solution written to SOL file:
D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.sol
Solution written to PDB file:
D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.1.pdb
Solution written to MTZ file:
D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.1.mtz
Solution annotation (history):
SOLU SET RFZ=5.6 TFZ=11.7 +TNCS PAK=0 LLG=233 LLG=1714
SOLU SPAC C 2 2 21
SOLU 6DIM ENSE ensemble1 EULER 0.3 88.9 92.4 FRAC 0.09 0.67 0.23 BFAC -0.24
SOLU 6DIM ENSE ensemble1 EULER 0.5 90.4 92.3 FRAC 0.09 0.78 -0.26 BFAC -0.24
SOLU ENSEMBLE ensemble1 VRMS DELTA +0.0374 RMSD 0.62 #VRMS 0.65
$$
CPU Time: 0 days 0 hrs 0 mins 21.75 secs ( 21.75 secs)
Finished: Sat Sep 12 13:34:11 2015
<B><FONT COLOR="##0077FF">
--------
ADVISORY
--------
$TEXT:Advisory: $$ Baubles Markup $$
Large non-origin Patterson peak indicates that translational NCS is present
$$
</FONT></B>
<B><FONT COLOR="#FF8800">
--------
WARNINGS
--------
$TEXT:Warning: $$ Baubles Markup $$
-------------------------------------------------------------------------------------
Search request requires more scattering than defined in composition. Composition
increased to accommodate search components.
-------------------------------------------------------------------------------------
$$
</FONT></B>
<!--SUMMARY_END-->
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EXIT STATUS: SUCCESS
--------------------
<!--SUMMARY_BEGIN-->
CPU Time: 0 days 0 hrs 0 mins 21.75 secs ( 21.75 secs)
Finished: Sat Sep 12 13:34:11 2015
<!--SUMMARY_END-->
</pre>
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#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 12 Sep 2015 13:34:11
#CCP4I TERMINATION OUTPUT_FILES D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.1.mtz JBC_Test D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.1.pdb JBC_Test D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.2.pdb JBC_Test D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.sol JBC_Test D:/Users/ykhand01/Documents/PHD/2015/Structure_solving/JBC_Test/JBC_Test_1.sum JBC_Test
#CCP4I MESSAGE Task completed successfully