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CCP4BB September 2015

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Subject:

Re: Second unrelated peak in Phaser

From:

Randy Read <[log in to unmask]>

Reply-To:

Randy Read <[log in to unmask]>

Date:

Sun, 13 Sep 2015 12:13:42 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (4364 lines)

Hi,

Those instructions are a bit out of date now, or at least not really appropriate for structures solved using Phaser.  I would probably just provide the final LLG and the TFZ score for the translation search for the last component (if more than one component), because those are good indicators of how unambiguous the solution is. In the unlikely event that an editor comes back and insists on satisfying these criteria, you could probably find the second highest peak by looking through the last translation search in the log file, but there won’t be one in the list if the second highest was less than 3/4 of the height of the top one.  You should also be able to find an R-factor (though not a correlation coefficient), but the R-factor is really one of the least sensitive scores in a translation search!

Best wishes,

Randy Read

-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research    Tel: +44 1223 336500
Wellcome Trust/MRC Building                         Fax: +44 1223 336827
Hills Road                                                            E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K.                               www-structmed.cimr.cam.ac.uk

> On 12 Sep 2015, at 04:49, yogesh khandokar <[log in to unmask]> wrote:
> 
> 
> 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:
> 
> 	• Molecular replacement: Program employed, search model (PDB code), resolution range of data, correlation coefficient and Rfactor of the correct solution and the second unrelated peak”
> 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-->
> 
>  
> #####################################################################################
> 
> #####################################################################################
> 
> #####################################################################################
> 
> ### 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
> 
>  
> <!--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 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-->
> 
>  
> --------------------
> 
> 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>
> 
> </html>
> 
>  
> #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
> 
> -- 
> 

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