Dear All,
I collected data of crystals at 6A resolution. The space group and the unit cell are similar to a very common contaminant (1iwg.pdb) so I did molecular replacement with the contaminant and Phaser found a solution with good statistics (below I attach the log file). Is it reliable at 6A resolution or shall I optimise the crystals hoping it is my protein?
Thanks for your suggestions
Li Wei
#CCP4I VERSION CCP4Interface 7.0.047
#CCP4I SCRIPT LOG phaser_MR
#CCP4I DATE 14 Aug 2018 22:53:56
#CCP4I USER liwei
#CCP4I PROJECT PROJECT2
#CCP4I JOB_ID 1
#CCP4I SCRATCH /tmp/liwei
#CCP4I HOSTNAME MacBook-Pro-of-Li-Wei.local
#CCP4I PID 52518
Phaser-2.7.17 (svn exported)
Enter keyword input:
<pre>
<B><FONT COLOR="#FF0000">
<html><!-- CCP4 HTML LOGFILE -->
<!--SUMMARY_BEGIN-->
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### CCP4 PROGRAM SUITE: Phaser 2.7.17 ###
##########################################################################################
User: liwei
Run time: Tue Aug 14 22:53:56 2018
Version: 2.7.17
Release Date: Wed Oct 11 14:49:55 2017 (svn exported)
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>
$$
<!--SUMMARY_END-->
<!--END--></FONT></B>
<!--SUMMARY_BEGIN-->
******************************************************************************************
*** Phaser Module: PREPROCESSOR 2.7.17 ***
******************************************************************************************
$TEXT:Script: $$ Baubles Markup $$
#---PHASER COMMAND SCRIPT GENERATED BY CCP4I---
TITLE data_26 model
MODE MR_AUTO
ROOT "/Users/liwei/Desktop/Files/PROJECT2_1"
#---DEFINE DATA---
HKLIN "/Users/liwei/Desktop/Files/5945972022_26baedata.mtz"
LABIN F=FP_ISOB SIGF=SIGFP_ISOB
SGALTERNATIVE SELECT HAND
#---DEFINE ENSEMBLES---
ENSEMBLE 1iwg &
PDB "/Users/liwei/Desktop/Files/1iwg.pdb" IDENT 90.0
#---DEFINE COMPOSITION---
COMPOSITION BY ASU
COMPOSITION PROTEIN NRES 1000 NUMBER 1
#---SEARCH PARAMETERS---
SEARCH ENSEMBLE 1iwg NUMBER 1
#---EXPERT PARAMETERS---
#---OUTPUT CONTROL---
#---DEVELOPER PARAMETERS---
## This script run with the command ##########
# /Applications/ccp4-7.0/bin/phaser
################################################
$$
CPU Time: 0 days 0 hrs 0 mins 0.00 secs ( 0.00 secs)
Finished: Tue Aug 14 22:53:56 2018
******************************************************************************************
*** Phaser Module: READ DATA FROM MTZ FILE 2.7.17 ***
******************************************************************************************
Read from Mtz File
------------------
Data read from mtz file: /Users/liwei/Desktop/Files/5945972022_26baedata.mtz
Space-Group Name (Hall Symbol): H 3 2 ( R 3 2")
Space-Group Number: 155
Unit Cell: 148.58 148.58 513.89 90.00 90.00 120.00
Column Labels Selected: FP_ISOB SIGFP_ISOB
Resolution on Mtz file: 6.39 80.31
Resolution Selected: 6.42 80.31
Number of Reflections in Selected Resolution Range: 4110
CPU Time: 0 days 0 hrs 0 mins 0.02 secs ( 0.02 secs)
Finished: Tue Aug 14 22:53:56 2018
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.7.17 ***
******************************************************************************************
** Steps:
** Cell Content Analysis
** Anisotropy correction
** Translational NCS correction
** Rotation Function
** Translation Function
** Packing
** Refinement
** Final Refinement (if data higher resolution than search resolution)
** Number of search ensembles = 1
** Search Method: FAST
** Input Search Order:
** #1 1iwg
** Automatic (best predicted) search order WILL be used
CPU Time: 0 days 0 hrs 0 mins 0.36 secs ( 0.36 secs)
Finished: Tue Aug 14 22:53:57 2018
******************************************************************************************
*** Phaser Module: CELL CONTENT ANALYSIS 2.7.17 ***
******************************************************************************************
Space-Group Name (Hall Symbol): H 3 2 ( R 3 2")
Space-Group Number: 155
Unit Cell: 148.58 148.58 513.89 90.00 90.00 120.00
<!--SUMMARY_END-->
--------------------
SPACE GROUP ANALYSIS
--------------------
Input Space Group: H 3 2
(a) Space groups derived by translation (screw) symmetry
--------------------------------------------------------
Z Space Group Hall Symbol
----
18 H 3 2 R 3 2"
----
(b) Subgroups of space group for perfect twinning expansions
------------------------------------------------------------
R: Reindexing operation required (*)
Only subgroups related by rotational symmetry are reported
Z Space Group R Hall Symbol
----
3 R 1 * P 1 (2/3*x-1/3*y-1/3*z,1/3*x+1/3*y-2/3*z,1/3*x+1/3*y+1/3*z)
---
6 C 1 2 1 * C 2y (2/3*x,1/3*x+y,-2/3*x+z)
C 1 2 1 * C 2y (x+y-1/3*z,-x+y+1/3*z,1/3*z)
C 1 2 1 * C 2y (1/3*x-y,2/3*x,2/3*x+z)
C 1 2 1 * C 2y (2/3*x,1/3*x+y,-2/3*x+z)
C 1 2 1 * C 2y (x+y-1/3*z,-x+y+1/3*z,1/3*z)
C 1 2 1 * C 2y (1/3*x-y,2/3*x,2/3*x+z)
---
9 H 3 R 3
H 3 R 3
H 3 R 3
H 3 R 3
H 3 R 3
---
18 H 3 2 R 3 2"
H 3 2 R 3 2"
H 3 2 R 3 2"
H 3 2 R 3 2"
H 3 2 R 3 2"
H 3 2 R 3 2"
H 3 2 R 3 2"
H 3 2 R 3 2"
H 3 2 R 3 2"
----
<!--SUMMARY_BEGIN-->
Composition is of type: PROTEIN
MW to which Matthews applies: 111000
Resolution for Matthews calculation: 6.42
Z MW VM % solvent rel. freq.
1 111000 4.92 74.99 0.014
2 222000 2.46 49.97 1.000 <== most probable
3 333000 1.64 24.96 0.008
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 ** (COMPOSITION*1)
4.17 --
3.85 ----
3.57 ------
3.33 ----------
3.12 ---------------
2.94 ---------------------
2.78 ----------------------------
2.63 -----------------------------------
2.50 -------------------------------------------
2.38 ************************************************ (COMPOSITION*2)
2.27 --------------------------------------------------
2.17 ------------------------------------------------
2.08 -----------------------------------------
2.00 ------------------------------
1.92 -------------------
1.85 ----------
1.79 -----
1.72 --
1.67 -
1.61 * (COMPOSITION*3)
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|4x0|1:1,2:
$$
N*Composition Probability
$$ loggraph $$
1 0.0205558
2 0.956573
3 0.00552532
$$
<!--SUMMARY_BEGIN-->
Most probable VM for resolution = 2.27337
Most probable MW of protein in asu for resolution = 240093
CPU Time: 0 days 0 hrs 0 mins 1.18 secs ( 1.18 secs)
Finished: Tue Aug 14 22:53:57 2018
******************************************************************************************
*** Phaser Module: ANISOTROPY CORRECTION 2.7.17 ***
******************************************************************************************
<!--SUMMARY_END-->
------------------------------
DATA FOR ANISOTROPY CORRECTION
------------------------------
Resolution of All Data (Number): 6.42 80.31 (4110)
Resolution of Selected Data (Number): 6.42 80.31 (4110)
Outliers with a probability less than 1e-06 will be rejected
Measurements with fewer bits of information than 0.01 will be rejected:
threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / 8.46225
There were 0 (0.0000%) reflections rejected
No reflections are outliers
---------------------
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
Outliers with a probability less than 1e-06 will be rejected
Measurements with fewer bits of information than 0.01 will be rejected:
threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / 8.46225
There were 0 (0.0000%) reflections rejected
No reflections are outliers
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-70849.741 -70849.741 -0.000
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
0.000 0.7082 -0.7039 -0.0550
0.000 -0.0389 0.0389 -0.9985
0.000 0.7050 0.7092 0.0002
Anisotropic deltaB (i.e. range of principal components): 0.000
Resharpening B (to restore strong direction of diffraction): 0.000
Wilson scale applied to get observed intensities: 4.4442e+00
Outliers with a probability less than 1e-06 will be rejected
Measurements with fewer bits of information than 0.01 will be rejected:
threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / 8.46225
There were 0 (0.0000%) reflections rejected
No reflections are outliers
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-70849.741 -70849.741 -0.000
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
0.000 0.7082 -0.7039 -0.0550
0.000 -0.0389 0.0389 -0.9985
0.000 0.7050 0.7092 0.0002
Anisotropic deltaB (i.e. range of principal components): 0.000
Resharpening B (to restore strong direction of diffraction): 0.000
Wilson scale applied to get observed intensities: 4.4442e+00
Outliers with a probability less than 1e-06 will be rejected
Measurements with fewer bits of information than 0.01 will be rejected:
threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / 8.46225
There were 0 (0.0000%) reflections rejected
No reflections are outliers
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-70849.741 -70849.741 -0.000
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
0.000 0.7082 -0.7039 -0.0550
0.000 -0.0389 0.0389 -0.9985
0.000 0.7050 0.7092 0.0002
Anisotropic deltaB (i.e. range of principal components): 0.000
Resharpening B (to restore strong direction of diffraction): 0.000
Wilson scale applied to get observed intensities: 4.4442e+00
<!--SUMMARY_BEGIN-->
Refined Anisotropy Parameters
-----------------------------
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
0.000 0.7082 -0.7039 -0.0550
0.000 -0.0389 0.0389 -0.9985
0.000 0.7050 0.7092 0.0002
Anisotropic deltaB (i.e. range of principal components): 0.000
Resharpening B (to restore strong direction of diffraction): 0.000
Wilson scale applied to get observed intensities: 4.4442e+00
<!--SUMMARY_END-->
--------------
ABSOLUTE SCALE
--------------
Scale factor to put input Fs on absolute scale
Wilson Scale: 0.474353
Wilson B-factor: 280.925
--------------------------------
DATA AFTER ANISOTROPY CORRECTION
--------------------------------
<!--SUMMARY_BEGIN-->
Resolution of All Data (Number): 6.42 80.31 (4110)
Resolution of Selected Data (Number): 6.42 80.31 (4110)
<!--SUMMARY_END-->
Outliers with a probability less than 1e-06 will be rejected
Measurements with fewer bits of information than 0.01 will be rejected:
threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / 8.46225
There were 0 (0.0000%) reflections rejected
No reflections are outliers
<!--SUMMARY_BEGIN-->
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 0 mins 1.45 secs ( 1.45 secs)
Finished: Tue Aug 14 22:53:57 2018
******************************************************************************************
*** Phaser Module: TRANSLATIONAL NON-CRYSTALLOGRAPHIC SYMMETRY 2.7.17 ***
******************************************************************************************
<!--SUMMARY_END-->
Unit Cell: 148.58 148.58 513.89 90.00 90.00 120.00
-------------------------------------
DATA FOR TRANSLATIONAL NCS CORRECTION
-------------------------------------
<!--SUMMARY_BEGIN-->
Resolution of All Data (Number): 6.42 80.31 (4110)
Resolution of Selected Data (Number): 6.42 80.31 (4110)
<!--SUMMARY_END-->
Outliers with a probability less than 1e-06 will be rejected
Measurements with fewer bits of information than 0.01 will be rejected:
threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / 8.46225
There were 0 (0.0000%) reflections rejected
No reflections are outliers
Weighted Intensity Moments for Data
-----------------------------------
Inverse variance-weighted 2nd Moment = <wE^4>/<wE^2>^2 == <wJ^2>/<wJ>^2
Untwinned Perfect Twin
2nd Moment Centric: 3.0 2.0
2nd Moment Acentric: 2.0 1.5
Measured
2nd Moment Centric: 3.98
2nd Moment Acentric: 2.02
Resolution for Twin Analysis (85% I/SIGI > 3): 6.42A (HiRes= 6.42A)
$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 0.0149701 0.158519 0.116883
0.08 0.0768837 0.0115132 0.0404192 0.222703 0.188312
0.12 0.11308 0.0245815 0.0721557 0.270966 0.244156
0.16 0.147856 0.0414833 0.110479 0.310843 0.3
0.2 0.181269 0.0615519 0.149401 0.345279 0.345455
0.24 0.213372 0.0842006 0.19012 0.375794 0.385714
0.28 0.244216 0.108914 0.227844 0.403299 0.420779
0.32 0.273851 0.13524 0.260479 0.428392 0.453247
0.36 0.302324 0.162786 0.295509 0.451494 0.480519
0.4 0.32968 0.191208 0.32485 0.472911 0.511688
0.44 0.355964 0.220208 0.356886 0.492878 0.528571
0.48 0.381217 0.24953 0.382335 0.511578 0.548052
0.52 0.405479 0.278952 0.407784 0.529158 0.567532
0.56 0.428791 0.308287 0.429042 0.54574 0.590909
0.6 0.451188 0.337373 0.453593 0.561422 0.606494
0.64 0.472708 0.366075 0.47515 0.576289 0.624675
0.68 0.493383 0.394281 0.489521 0.590413 0.638961
0.72 0.513248 0.421896 0.510479 0.603856 0.646753
0.76 0.532334 0.448846 0.533234 0.616672 0.657143
0.8 0.550671 0.475069 0.56018 0.628907 0.663636
0.84 0.56829 0.500518 0.579641 0.640603 0.672727
0.88 0.585217 0.525156 0.597904 0.651798 0.68961
0.92 0.601481 0.548959 0.613473 0.662525 0.703896
0.96 0.617107 0.571908 0.623353 0.672813 0.709091
1 0.632121 0.593994 0.637425 0.682689 0.718182
1.04 0.646545 0.615215 0.648802 0.692179 0.722078
1.08 0.660404 0.635573 0.663174 0.701302 0.731169
1.12 0.67372 0.655074 0.673353 0.710082 0.735065
1.16 0.686514 0.673732 0.684431 0.718534 0.737662
1.2 0.698806 0.691559 0.69521 0.726678 0.74026
1.24 0.710616 0.708574 0.707784 0.734529 0.745455
1.28 0.721963 0.724795 0.718263 0.742101 0.753247
1.32 0.732865 0.740245 0.730838 0.749408 0.757143
1.36 0.743339 0.754946 0.739521 0.756463 0.764935
1.4 0.753403 0.768922 0.750898 0.763276 0.772727
1.44 0.763072 0.782197 0.761377 0.769861 0.777922
1.48 0.772362 0.794797 0.771557 0.776226 0.787013
1.52 0.781288 0.806747 0.780838 0.782381 0.792208
1.56 0.789864 0.818072 0.788323 0.788335 0.797403
1.6 0.798103 0.828799 0.797904 0.794097 0.803896
1.64 0.80602 0.838951 0.80479 0.799674 0.806494
1.68 0.813626 0.848554 0.812874 0.805076 0.814286
1.72 0.820934 0.857633 0.820659 0.810307 0.819481
1.76 0.827955 0.866211 0.829341 0.815376 0.824675
1.8 0.834701 0.874311 0.838623 0.820287 0.833766
1.84 0.841183 0.881957 0.84491 0.825049 0.84026
1.88 0.84741 0.889169 0.848503 0.829666 0.844156
1.92 0.853393 0.895971 0.853593 0.834143 0.846753
1.96 0.859142 0.902382 0.861677 0.838487 0.848052
2 0.864665 0.908422 0.867665 0.842701 0.853247
$$
$TABLE : Weighted second moments for Data:
$GRAPHS
:Weighted second moments vs resolution (acentric only):AUTO:1,2,3,4:
$$
1/d^2 ACent_theor ACent_twin ACent_obser
$$ loggraph $$
0.0017 2.00042 1.50042 1.47967
0.0047 2.00085 1.50085 1.71942
0.0077 2.00147 1.50147 2.41165
0.0107 2.00238 1.50238 2.14267
0.0137 2.00971 1.50971 1.93186
0.0168 2.04138 1.54138 1.89608
0.0198 2.15688 1.65688 2.01701
0.0228 2.08427 1.58427 2.14555
$$
---------------------
ANISOTROPY CORRECTION
---------------------
Weighted Intensity Moments after Anisotropy Correction
------------------------------------------------------
Inverse variance-weighted 2nd Moment = <wE^4>/<wE^2>^2 == <wJ^2>/<wJ>^2
Untwinned Perfect Twin
2nd Moment Centric: 3.0 2.0
2nd Moment Acentric: 2.0 1.5
Measured
2nd Moment Centric: 3.98
2nd Moment Acentric: 2.02
Resolution for Twin Analysis (85% I/SIGI > 3): 6.42A (HiRes= 6.42A)
$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 0.0149701 0.158519 0.116883
0.08 0.0768837 0.0115132 0.0404192 0.222703 0.188312
0.12 0.11308 0.0245815 0.0721557 0.270966 0.244156
0.16 0.147856 0.0414833 0.110479 0.310843 0.3
0.2 0.181269 0.0615519 0.149401 0.345279 0.345455
0.24 0.213372 0.0842006 0.19012 0.375794 0.385714
0.28 0.244216 0.108914 0.227844 0.403299 0.420779
0.32 0.273851 0.13524 0.260479 0.428392 0.453247
0.36 0.302324 0.162786 0.295509 0.451494 0.480519
0.4 0.32968 0.191208 0.32485 0.472911 0.511688
0.44 0.355964 0.220208 0.356886 0.492878 0.528571
0.48 0.381217 0.24953 0.382335 0.511578 0.548052
0.52 0.405479 0.278952 0.407784 0.529158 0.567532
0.56 0.428791 0.308287 0.429042 0.54574 0.590909
0.6 0.451188 0.337373 0.453593 0.561422 0.606494
0.64 0.472708 0.366075 0.47515 0.576289 0.624675
0.68 0.493383 0.394281 0.489521 0.590413 0.638961
0.72 0.513248 0.421896 0.510479 0.603856 0.646753
0.76 0.532334 0.448846 0.533234 0.616672 0.657143
0.8 0.550671 0.475069 0.56018 0.628907 0.663636
0.84 0.56829 0.500518 0.579641 0.640603 0.672727
0.88 0.585217 0.525156 0.597904 0.651798 0.68961
0.92 0.601481 0.548959 0.613473 0.662525 0.703896
0.96 0.617107 0.571908 0.623353 0.672813 0.709091
1 0.632121 0.593994 0.637425 0.682689 0.718182
1.04 0.646545 0.615215 0.648802 0.692179 0.722078
1.08 0.660404 0.635573 0.663174 0.701302 0.731169
1.12 0.67372 0.655074 0.673353 0.710082 0.735065
1.16 0.686514 0.673732 0.684431 0.718534 0.737662
1.2 0.698806 0.691559 0.69521 0.726678 0.74026
1.24 0.710616 0.708574 0.707784 0.734529 0.745455
1.28 0.721963 0.724795 0.718263 0.742101 0.753247
1.32 0.732865 0.740245 0.730838 0.749408 0.757143
1.36 0.743339 0.754946 0.739521 0.756463 0.764935
1.4 0.753403 0.768922 0.750898 0.763276 0.772727
1.44 0.763072 0.782197 0.761377 0.769861 0.777922
1.48 0.772362 0.794797 0.771557 0.776226 0.787013
1.52 0.781288 0.806747 0.780838 0.782381 0.792208
1.56 0.789864 0.818072 0.788323 0.788335 0.797403
1.6 0.798103 0.828799 0.797904 0.794097 0.803896
1.64 0.80602 0.838951 0.80479 0.799674 0.806494
1.68 0.813626 0.848554 0.812874 0.805076 0.814286
1.72 0.820934 0.857633 0.820659 0.810307 0.819481
1.76 0.827955 0.866211 0.829341 0.815376 0.824675
1.8 0.834701 0.874311 0.838623 0.820287 0.833766
1.84 0.841183 0.881957 0.84491 0.825049 0.84026
1.88 0.84741 0.889169 0.848503 0.829666 0.844156
1.92 0.853393 0.895971 0.853593 0.834143 0.846753
1.96 0.859142 0.902382 0.861677 0.838487 0.848052
2 0.864665 0.908422 0.867665 0.842701 0.853247
$$
$TABLE : Weighted second moments after Anisotropy Correction:
$GRAPHS
:Weighted second moments vs resolution (acentric only):AUTO:1,2,3,4:
$$
1/d^2 ACent_theor ACent_twin ACent_obser
$$ loggraph $$
0.0017 2.00042 1.50042 1.47967
0.0047 2.00085 1.50085 1.71942
0.0077 2.00147 1.50147 2.41165
0.0107 2.00238 1.50238 2.14267
0.0137 2.00971 1.50971 1.93186
0.0168 2.04138 1.54138 1.89608
0.0198 2.15688 1.65688 2.01701
0.0228 2.08427 1.58427 2.14555
$$
-----------------
TRANSLATIONAL NCS
-----------------
tNCS vector not set
Space Group : H 3 2
Patterson Symmetry: R -3 m :H
Resolution of All Data (Number): 6.42 80.31 (4110)
Resolution of Patterson (Number): 6.42 12.80 (3481)
No large non-origin Patterson peaks
No tNCS found in Patterson
<!--SUMMARY_BEGIN-->
--------
TWINNING
--------
tNCS/Twin Detection Table
-------------------------
-Second Moments- --P-values--
Centric Acentric untwinned twin frac <5%
Theoretical for untwinned 3.00 2.00
including measurement error 3.05 2.04
Theoretical for perfect twin 2.00 1.50
Initial (data as input) 3.98 2.02+/-0.078 1 1
After Anisotropy Correction 3.98 2.02+/-0.078 1 1
After Anisotropy and tNCS ---n/a---
P-value < 0.01 for <5% twinned is considered worth investigating
Resolution for Twin Analysis (85% I/SIGI > 3): 6.42A (HiRes= 6.42A)
<!--SUMMARY_END-->
---------------------------------------
DATA AFTER TRANSLATIONAL NCS CORRECTION
---------------------------------------
<!--SUMMARY_BEGIN-->
Resolution of All Data (Number): 6.42 80.31 (4110)
Resolution of Selected Data (Number): 6.42 80.31 (4110)
<!--SUMMARY_END-->
Outliers with a probability less than 1e-06 will be rejected
Measurements with fewer bits of information than 0.01 will be rejected:
threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / 8.46225
There were 0 (0.0000%) reflections rejected
No reflections are outliers
------------
OUTPUT FILES
------------
No files output
<!--SUMMARY_BEGIN-->
CPU Time: 0 days 0 hrs 0 mins 1.95 secs ( 1.95 secs)
Finished: Tue Aug 14 22:53:58 2018
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.7.17 ***
******************************************************************************************
** Z-score test for definite solution is ON
** Z-score test for stopping search is OFF
** Deep search is ON
CPU Time: 0 days 0 hrs 0 mins 1.95 secs ( 1.95 secs)
Finished: Tue Aug 14 22:53:58 2018
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.7.17 ***
******************************************************************************************
Composition Table
-----------------
Total Scattering = 361947
Search occupancy factor = 1 (default)
Ensemble Frac.Scat. (Search Frac.Scat.)
1iwg 94.04% 94.04%
** Composition not increased
<!--SUMMARY_END-->
<!--SUMMARY_BEGIN-->
CPU Time: 0 days 0 hrs 0 mins 1.95 secs ( 1.95 secs)
Finished: Tue Aug 14 22:53:58 2018
******************************************************************************************
*** Phaser Module: EXPERIMENTAL ERROR CORRECTION PREPARATION 2.7.17 ***
******************************************************************************************
<!--SUMMARY_END-->
-----------------
TRANSLATIONAL NCS
-----------------
tNCS not present
-----------------------------
EXPERIMENTAL ERROR CORRECTION
-----------------------------
Calculate Luzzati D factors accounting for observational error...
<!--SUMMARY_BEGIN-->
Data have been provided as French-Wilson amplitudes
<!--SUMMARY_END-->
------------
OUTPUT FILES
------------
No files output
<!--SUMMARY_BEGIN-->
CPU Time: 0 days 0 hrs 0 mins 2.05 secs ( 2.05 secs)
Finished: Tue Aug 14 22:53:58 2018
******************************************************************************************
*** Phaser Module: EXPECTED LLG OF ENSEMBLES 2.7.17 ***
******************************************************************************************
<!--SUMMARY_END-->
-----------------
TRANSLATIONAL NCS
-----------------
tNCS not present
<!--SUMMARY_BEGIN-->
Resolution of Data: 6.416
Number of Reflections: 4110
eLLG Target: 225
<!--SUMMARY_END-->
----------
ENSEMBLING
----------
Ensemble: 1iwg
--------------
PDB file # 1: 1iwg.pdb
This file contains 1 model
The input RmsD of model #1 with respect to the real structure is 0.700
<!--SUMMARY_BEGIN-->
eLLG Values Computed for All Data
---------------------------------
Ensemble frac-scat rms reso eLLG
1iwg 0.94 0.700 6.42 537.0
Residues/Resolution for eLLG target
-----------------------------------
target-nres: Number of alanine residues to achieve target eLLG
target-reso: Resolution to achieve target eLLG
Ensemble eLLG-target target-nres/target-reso
1iwg 225.00 975 7.957
CPU Time: 0 days 0 hrs 0 mins 2.52 secs ( 2.52 secs)
Finished: Tue Aug 14 22:53:59 2018
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.7.17 ***
******************************************************************************************
** Search Order (next search *) (placed +):
** #1 1iwg *
CPU Time: 0 days 0 hrs 0 mins 2.52 secs ( 2.52 secs)
Finished: Tue Aug 14 22:53:59 2018
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT ROTATION FUNCTION 2.7.17 ***
******************************************************************************************
<!--SUMMARY_END-->
-----------------
TRANSLATIONAL NCS
-----------------
tNCS not present
--------------------------
DATA FOR ROTATION FUNCTION
--------------------------
<!--SUMMARY_BEGIN-->
High resolution limit unaltered by RMS of ensemble
High resolution limit lowered by expected LLG = 7.96
<!--SUMMARY_END-->
Outliers with a probability less than 1e-06 will be rejected
Measurements with fewer bits of information than 0.01 will be rejected:
threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / 8.46225
There were 0 (0.0000%) reflections rejected
No reflections are outliers
Resolution of All Data (Number): 6.42 80.31 (4110)
Resolution of Selected Data (Number): 7.96 80.31 (2540)
-------------------
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 (2001)
- half number of centrics (539/2)
= -2270
With correction for SigF,
Wilson log(likelihood) = -2257.01
----------
ENSEMBLING
----------
Ensemble Generation: 1iwg
-------------------------
Ensemble configured for structure factor interpolation
Ensemble configured to resolution 7.96
Electron Density Calculation
0% 100%
|=======| DONE
Ensemble Generation Table
-------------------------
Resolution of Ensembles: 7.95683
Ensemble Scat% Radius Model# Rel-B Input-RMS Initial-Delta-VRMS Initial-RMS
1iwg 94.0 47.81 1 201.6 0.700 0.000 0.700
-----------------
ROTATION FUNCTION
-----------------
Ensemble configured to resolution 7.96
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: 1iwg
Sampling: 4.77 degrees
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 71 sites over 67.5% of top
71 peaks selected
The sites over 67.5% are:
# Euler1 Euler2 Euler3 FSS Z-score
1 72.8 0.4 169.6 100.000 6.61
2 81.3 1.2 283.6 96.355 6.37
3 96.9 1.0 27.3 94.975 6.28
#Sites = 71: output truncated to 3 sites
Top 71 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): 108.746 ( 6.87)
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 was 1 site over 75% of top
The sites over 75% are:
# Euler1 Euler2 Euler3 LLG Z-score Split #Group FSS-this-ang/FSS-top
1 72.8 0.4 169.6 108.75 6.87 0.0 37 100.000/ 100.000
192.8 0.4 169.6
312.8 0.4 169.6
47.2 179.6 349.6
167.2 179.6 349.6
287.2 179.6 349.6
<!--SUMMARY_BEGIN-->
Rotation Function Table: 1iwg
-----------------------------
(Z-scores from Fast Rotation Function)
#SET Top (Z) Second (Z) Third (Z)
1 108.75 6.87 --- --- --- ---
<!--SUMMARY_END-->
---------------
FINAL SELECTION
---------------
<!--SUMMARY_BEGIN-->
Select by Percentage of Top value: 75%
Top RF = 108.746
Purge RF mean = -42.583
Number of sets stored before final selection = 1
Number of solutions stored before final selection = 1
Number of sets stored (deleted) after final selection = 1 (0)
Number of solutions stored (deleted) after final selection = 1 (0)
Percent used for purge = 60.000%
Includes deep search down percent = 15%
Number of solutions stored above (below) deep threshold = 1 (0)
Rotation Function Final Selection Table
---------------------------------------
Rotation list length by SET
SET# Start Final Deleted Set (*) Deep: Start Final Deleted Set (*)
1 1 1 - 1 1 -
ALL 1 1 1 1
<!--SUMMARY_END-->
$TABLE : Rotation Function Component #1 (1iwg) :
$GRAPHS
:RF Number vs LL-gain:AUTO:1,2: :RF Number vs Z-Score:AUTO:1,3:
$$
Number LLG Z-Score
$$ loggraph $$
1 108.75 6.87
$$
<!--SUMMARY_BEGIN-->
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 0 mins 35.42 secs ( 35.42 secs)
Finished: Tue Aug 14 22:54:17 2018
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT TRANSLATION FUNCTION 2.7.17 ***
******************************************************************************************
<!--SUMMARY_END-->
-----------------
TRANSLATIONAL NCS
-----------------
tNCS not present
-----------------------------
DATA FOR TRANSLATION FUNCTION
-----------------------------
High Resolution Limit imposed by RF list = 7.96
Outliers with a probability less than 1e-06 will be rejected
Measurements with fewer bits of information than 0.01 will be rejected:
threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / 8.46225
There were 0 (0.0000%) reflections rejected
No reflections are outliers
<!--SUMMARY_BEGIN-->
Resolution of All Data (Number): 6.42 80.31 (4110)
Resolution of Selected Data (Number): 7.96 80.31 (2540)
<!--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 (2001)
- half number of centrics (539/2)
= -2270
With correction for SigF,
Wilson log(likelihood) = -2257.01
<!--SUMMARY_BEGIN-->
------------------------
ALTERNATIVE SPACE GROUPS
------------------------
Space Group(s) to be tested:
H 3 2
<!--SUMMARY_END-->
----------
ENSEMBLING
----------
Ensemble Generation Table
-------------------------
Resolution of Ensembles: 7.95683
Ensemble Scat% Radius Model# Rel-B Input-RMS Initial-Delta-VRMS Initial-RMS
1iwg 94.0 47.81 1 201.6 0.700 0.000 0.700
Trace Generation: 1iwg
----------------------
This trace is from coordinates
Calculate Hexagonal Grid...
Sampling #1: 5.73554 Angstroms
Sampling #2: 11.4711 Angstroms
Sampling #3: 8.60331 Angstroms
Sampling #4: 7.16942 Angstroms
Sampling #5: 6.45248 Angstroms
Sampling #6: 6.09401 Angstroms
Done
Trace Generation Table
----------------------
Ensemble Trace-type Length Sampling Close-contact
1iwg 933 6.09 3.52
---------------------
TRANSLATION FUNCTIONS
---------------------
Target Function: FAST LETF1
Translation Packing Function applied: top peak will pack
Translation Packing Cutoff: 50%
Sampling: 1.99 Angstroms
<!--SUMMARY_BEGIN-->
----------------------------
TRANSLATION FUNCTION #1 OF 1
----------------------------
<!--SUMMARY_END-->
SOLU SET
SOLU SPAC H 3 2
SOLU TRIAL ENSEMBLE 1iwg EULER 72.809 0.445 169.630 RFZ 6.87
<!--SUMMARY_BEGIN-->
This set has one trial orientation
<!--SUMMARY_END-->
# Euler Rot-LLG Ensemble
1 72.8 0.4 169.6 108.7 1iwg
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): -123.71 (25.49)
SET #1 of 1 TRIAL #1 of 1
-------------------------
Ensemble 1iwg Euler 72.81 0.44 169.63
Doing Fast Translation Function FFT...
Done
Packing Fast Search Translations...
15190 peaks
500 peaks over 166.913 checked for packing
Translation peak 1 first to be kept
Done
<!--SUMMARY_BEGIN-->
New Top Packing Fast Translation Function FSS = 566.01 (TFZ=18.3) at Trial #1
<!--SUMMARY_END-->
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
There were 30 sites over 67.5% of top
30 peaks selected
The sites over 67.5% are:
# Frac X Frac Y Frac Z FSS Z-score
1 0.286 0.631 0.658 566.01 18.30
2 0.285 0.631 0.875 342.97 9.74
3 0.286 0.631 0.649 339.29 9.60
#Sites = 30: output truncated to 3 sites
Top 30 translations before clustering will be rescored
Spreading calculation onto 2 threads.
Calculating Likelihood for TF SET #1 of 1 TRIAL #1 of 1
0% 100%
|================| DONE
Packing LLG Translations: pass 1 of 11...
30 peaks
1 peaks over 388.416 checked for packing
Translation peak 1 first to be kept
Done
Exit: found a peak that packs
<!--SUMMARY_BEGIN-->
New Top (ML) Translation Function LLG = 388.42 (TFZ=18.3) at Trial #1
<!--SUMMARY_END-->
Top Peaks With Clustering
Select peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 21 sites over 75% of top
The sites over 75% are:
# Frac X Frac Y Frac Z LLG Z-score Split #Group FSS-this-xyz/FSS-top
1 0.286 0.631 0.658 388.42 18.30 0.0 4 566.01/ 566.01
2 0.285 0.631 0.540 134.76 9.21 60.9 1 329.09/ 329.09
3 0.285 0.631 0.875 128.00 9.74 111.5 1 342.97/ 342.97
#SITES = 21: OUTPUT TRUNCATED TO 3 SITES
<!--SUMMARY_BEGIN-->
Translation Function Table
--------------------------
SET ROT*deep Top (Z) Second (Z) Third (Z) Ensemble SpaceGroup
1 1 388.4 18.30 134.8 9.21 128.0 9.74 1iwg H 3 2
--- ---
---------------
FINAL SELECTION
---------------
LLG will be used for purge, not FSS
Top TF = 388.42
Top TFZ = 18.30
Mean TF = -123.71
Percent used for purge = 75%
Cutoff for acceptance = 260.4
TFZ used for final selection = 9.15081
Number of solutions over TF final cutoff = 1
Number of solutions over TFZ final cutoff = 7
Number of solutions over TF & TFZ cutoff = 1
Number of solutions stored before final selection = 21
Number of solutions stored (deleted) after final selection = 7 (14)
<!--SUMMARY_END-->
$TABLE : Translation Function Component #1 (1iwg):
$GRAPHS
:TF Number vs LL-gain:AUTO:1,2: :TF Number vs Z-Score:AUTO:1,3:
$$
Number LLG Z-Score
$$ loggraph $$
1 388.42 18.30
2 134.76 9.21
3 128.00 9.74
4 119.63 9.40
5 116.37 9.37
6 116.15 9.46
7 116.13 9.16
$$
<!--SUMMARY_BEGIN-->
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 0 mins 42.29 secs ( 42.29 secs)
Finished: Tue Aug 14 22:54:22 2018
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT PACKING ANALYSIS 2.7.17 ***
******************************************************************************************
<!--SUMMARY_END-->
---------
ENSEMBLES
---------
Trace Generation Table
----------------------
Ensemble Trace-type Length Sampling Close-contact
1iwg 933 6.09 3.52
-----------------
ENSEMBLE SYMMETRY
-----------------
Ensemble "1iwg" Point Group: 1
Clash background has been packed at 10.00%
----------------
PACKING FUNCTION
----------------
There are 7 solutions to pack
Spreading calculation onto 2 threads.
Packing analysis
0% 100%
|=====| DONE
<!--SUMMARY_BEGIN-->
Packing Table
-------------
Solutions accepted if pairwise clashes less than 10 % of trace atoms
#in #out Clash-% Symm TF-SET ROT TFpk# TF TFZ SpaceGroup
1 Top1 8.039 -- 1 1 1 388.42 18.30 H 3 2
2 --- 17.04 -- 1 1 2 134.76 9.21 H 3 2
3 --- 97.43 -- 1 1 3 128.00 9.74 H 3 2
4 --- 34.08 -- 1 1 4 119.63 9.40 H 3 2
5 --- 45.34 -- 1 1 5 116.37 9.37 H 3 2
6 --- 20.69 -- 1 1 6 116.15 9.46 H 3 2
7 --- 83.17 -- 1 1 7 116.13 9.16 H 3 2
1 accepted of 7 solutions
1 packs of 1 accepted solution
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 0 mins 46.04 secs ( 46.04 secs)
Finished: Tue Aug 14 22:54:24 2018
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.7.17 ***
******************************************************************************************
<!--SUMMARY_END-->
-----------------
TRANSLATIONAL NCS
-----------------
tNCS not present
-------------------------------
DATA FOR REFINEMENT AND PHASING
-------------------------------
High resolution limit imposed by solution list = 7.96
Outliers with a probability less than 1e-06 will be rejected
Measurements with fewer bits of information than 0.01 will be rejected:
threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / 8.46225
There were 0 (0.0000%) reflections rejected
No reflections are outliers
<!--SUMMARY_BEGIN-->
Resolution of All Data (Number): 6.42 80.31 (4110)
Resolution of Selected Data (Number): 7.96 80.31 (2540)
<!--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 (2001)
- half number of centrics (539/2)
= -2270
With correction for SigF,
Wilson log(likelihood) = -2257.01
----------
ENSEMBLING
----------
Ensemble Generation Table
-------------------------
Resolution of Ensembles: 7.95683
Ensemble Scat% Radius Model# Rel-B Input-RMS Initial-Delta-VRMS Initial-RMS
1iwg 94.0 47.81 1 201.6 0.700 0.000 0.700
----------
REFINEMENT
----------
Protocol cycle #1 of 1
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION : REFINE
BFACTOR : REFINE
MODEL VRMS : FIX
MAP CELL SCALE: FIX
MAP OFACTOR : 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
--------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE 1iwg EULER 47.2 179.6 349.6 FRAC 0.30 -0.38 0.67 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 4 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
388.816 419.382 30.566
Final Parameters:
SOLU SET
SOLU 6DIM ENSE 1iwg EULER 175.4 179.4 117.6 FRAC 0.34 -0.37 0.67 BFAC -2.34
---------------
TFZ EQUIVALENTS
---------------
Refined TFZ equivalents calculated
1 top TFZ equivalents calculated
1 (Topfiles)
0 with TFZ > 6 (TFZ for Possibly Solved)
SOLUTION #1 OF 1
----------------
TOPFILE
TFZ equivalent calculation #1 of 1
Spreading calculation onto 2 threads.
Generating Statistics
0% 100%
|===============================================================| DONE
Mean Score (Sigma): -132.37 (26.75)
Refined TF/TFZ equivalent = 419.65/ 20.6 (Unrefined TF/TFZ=388.42/ 18.3)
Mean and Sigma after Refinement (for Purge)
-------------------------------------------
Scoring 500 randomly sampled orientations and translations
Spreading calculation onto 2 threads.
Generating Statistics
0% 100%
|==| DONE
Mean Score for Purge before Refinement: -123.71
Mean Score for Purge after Refinement : -132.37
$TABLE : Refinement After Placing Component #1 (1iwg 7.96A) :
$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 $$
1 419.65 388.42 51.35 52.34
$$
---------------
FIND DUPLICATES
---------------
Check for nearly equivalent solutions
Spreading calculation onto 2 threads.
Calculating Duplicates for 1 solutions
0% 100%
|==| DONE
No duplicate solutions found
---------------------
FIND TEMPLATE MATCHES
---------------------
No Template Solution(s) for comparison
<!--SUMMARY_BEGIN-->
---------------
PURGE SELECTION
---------------
Purge solutions according to highest LLG from Refinement
--------------------------------------------------------
Top LLG (all) = 419.645
Top LLG (packs) = 419.645
Mean LLG = -132.366
Percent used for purge = 75%
Cutoff for acceptance = 281.6
Overall cutoff for acceptance (excluding high TFZ) = 419.6
Number of solutions stored before purge = 1
Number of solutions stored (deleted) after purge = 1 (0)
-------
RESULTS
-------
Refinement Table (Sorted)
-------------------------
#out =#out #in =T (Start LLG Rval TFZ) (Refined LLG Rval TFZ==) SpaceGroup Cntrst
Top1 --- 1 388.4 52.3 18.3 419.6 51.3 20.6 H 3 2 n/a
Refinement Table (Variance Ranges)
----------------------------------
Range of delta-VRMS and VRMS given over current solution list (1 solution(s))
Ensemble Model# RMS Delta-VRMS min/max (VRMS min/max)
1iwg 1 0.700 +0.000/+0.000 ( 0.700/ 0.700 )
<!--SUMMARY_END-->
------------
OUTPUT FILES
------------
Calculation of Map Coefficients
-------------------------------
1 top map coefficients calculated
Map coefficient calculated for top solution #1
SOLU SPAC H 3 2
SOLU 6DIM ENSE 1iwg EULER 64.6 0.6 297.6 FRAC -0.00 -0.04 -0.01 BFAC -2.34 #TFZ==20.6
No files output
<!--SUMMARY_BEGIN-->
CPU Time: 0 days 0 hrs 0 mins 49.59 secs ( 49.59 secs)
Finished: Tue Aug 14 22:54:26 2018
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.7.17 ***
******************************************************************************************
** Current is Best Solution (first search)
** Current solution has 1 component
** New Best LLG = 419.6 (resolution = 7.96)
** Best Component so far = 1iwg
CPU Time: 0 days 0 hrs 0 mins 49.59 secs ( 49.59 secs)
Finished: Tue Aug 14 22:54:26 2018
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.7.17 ***
******************************************************************************************
** Solutions will be refined to highest resolution
** Protocol for MR refinement is DEFAULT
** VRMS (variances) of ensemble(s) WILL be refined
CPU Time: 0 days 0 hrs 0 mins 49.61 secs ( 49.61 secs)
Finished: Tue Aug 14 22:54:26 2018
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.7.17 ***
******************************************************************************************
<!--SUMMARY_END-->
-----------------
TRANSLATIONAL NCS
-----------------
tNCS not present
-------------------------------
DATA FOR REFINEMENT AND PHASING
-------------------------------
Outliers with a probability less than 1e-06 will be rejected
Measurements with fewer bits of information than 0.01 will be rejected:
threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / 8.46225
There were 0 (0.0000%) reflections rejected
No reflections are outliers
<!--SUMMARY_BEGIN-->
Resolution of All Data (Number): 6.42 80.31 (4110)
Resolution of Selected Data (Number): 6.42 80.31 (4110)
<!--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 (3340)
- half number of centrics (770/2)
= -3725
With correction for SigF,
Wilson log(likelihood) = -3732.99
----------
ENSEMBLING
----------
Ensemble Generation: 1iwg
-------------------------
Ensemble configured for structure factor interpolation
Ensemble configured to resolution 6.42
Electron Density Calculation
0% 100%
|=======| DONE
Ensemble Generation Table
-------------------------
Resolution of Ensembles: 6.41564
Ensemble Scat% Radius Model# Rel-B Input-RMS Initial-Delta-VRMS Initial-RMS
1iwg 94.0 47.81 1 87.5 0.700 0.000 0.700
----------
REFINEMENT
----------
Protocol cycle #1 of 1
Refinement protocol for this macrocycle:
ROTATION : REFINE
TRANSLATION : REFINE
BFACTOR : REFINE
MODEL VRMS : REFINE
MAP CELL SCALE: FIX
MAP OFACTOR : 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
--------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE 1iwg EULER 64.6 0.6 297.6 FRAC -0.00 -0.04 -0.01 BFAC -2.34 #TFZ==20.6
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 4 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
770.595 788.505 17.911
Final Parameters:
SOLU SET
SOLU 6DIM ENSE 1iwg EULER 61.1 0.3 301.3 FRAC 0.01 -0.03 -0.01 BFAC -2.06 #TFZ==20.6
SOLU ENSEMBLE 1iwg VRMS DELTA -0.0818 #RMSD 0.70 #VRMS 0.64
---------------
TFZ EQUIVALENTS
---------------
Refined TFZ equivalents calculated
1 top TFZ equivalents calculated
1 (Topfiles)
0 with TFZ > 6 (TFZ for Possibly Solved)
SOLUTION #1 OF 1
----------------
TOPFILE
TFZ equivalent calculation #1 of 1
Spreading calculation onto 2 threads.
Generating Statistics
0% 100%
|===============================================================| DONE
Mean Score (Sigma): -629.68 (55.06)
Refined TF/TFZ equivalent = 786.72/ 25.7 (Unrefined TF/TFZ=769.93/ 20.6)
Mean and Sigma after Refinement (for Purge)
-------------------------------------------
Scoring 500 randomly sampled orientations and translations
Spreading calculation onto 2 threads.
Generating Statistics
0% 100%
|==| DONE
Mean Score for Purge before Refinement: -132.37
Mean Score for Purge after Refinement : -629.68
$TABLE : Refinement After Placing Component #1 (1iwg 6.42A) :
$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 $$
1 786.72 769.93 50.27 50.69
$$
---------------
FIND DUPLICATES
---------------
Check for nearly equivalent solutions
Spreading calculation onto 2 threads.
Calculating Duplicates for 1 solutions
0% 100%
|==| DONE
No duplicate solutions found
---------------------
FIND TEMPLATE MATCHES
---------------------
No Template Solution(s) for comparison
<!--SUMMARY_BEGIN-->
---------------
PURGE SELECTION
---------------
Purge solutions according to highest LLG from Refinement
--------------------------------------------------------
Top LLG (all) = 786.716
Top LLG (packs) = 786.716
Mean LLG = -629.685
Percent used for purge = 75%
Cutoff for acceptance = 432.6
Overall cutoff for acceptance (excluding high TFZ) = 786.7
Number of solutions stored before purge = 1
Number of solutions stored (deleted) after purge = 1 (0)
-------
RESULTS
-------
Refinement Table (Sorted)
-------------------------
Refinement to full resolution
#out =#out #in =T (Start LLG Rval TFZ) (Refined LLG Rval TFZ==) SpaceGroup Cntrst
Top1 --- 1 769.9 50.7 20.6 786.7 50.3 25.7 H 3 2 n/a
Refinement Table (Variance Ranges)
----------------------------------
Range of delta-VRMS and VRMS given over current solution list (1 solution(s))
Ensemble Model# RMS Delta-VRMS min/max (VRMS min/max)
1iwg 1 0.700 -0.082/-0.082 ( 0.638/ 0.638 )
<!--SUMMARY_END-->
------------
OUTPUT FILES
------------
Calculation of Map Coefficients
-------------------------------
1 top map coefficients calculated
Map coefficient calculated for top solution #1
SOLU SPAC H 3 2
SOLU 6DIM ENSE 1iwg EULER 61.1 0.3 301.3 FRAC 0.01 -0.03 -0.01 BFAC -2.06 #TFZ==25.7
SOLU ENSEMBLE 1iwg VRMS DELTA -0.0818 #RMSD 0.70 #VRMS 0.64
No files output
<!--SUMMARY_BEGIN-->
CPU Time: 0 days 0 hrs 1 mins 1.09 secs ( 61.09 secs)
Finished: Tue Aug 14 22:54:34 2018
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.7.17 ***
******************************************************************************************
** Refinement may have introduced clashes
** Packing will be checked
CPU Time: 0 days 0 hrs 1 mins 1.09 secs ( 61.09 secs)
Finished: Tue Aug 14 22:54:34 2018
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT PACKING ANALYSIS 2.7.17 ***
******************************************************************************************
<!--SUMMARY_END-->
---------
ENSEMBLES
---------
Trace Generation Table
----------------------
Ensemble Trace-type Length Sampling Close-contact
1iwg 933 6.09 3.52
-----------------
ENSEMBLE SYMMETRY
-----------------
Ensemble "1iwg" Point Group: 1
Clash background has been packed at 10.00%
----------------
PACKING FUNCTION
----------------
There is 1 solution to pack
Spreading calculation onto 2 threads.
Packing analysis
0% 100%
|==| DONE
<!--SUMMARY_BEGIN-->
Packing Table
-------------
Solutions accepted if pairwise clashes less than 10 % of trace atoms
#in #out Clash-% Symm SpaceGroup Annotation
1 Top1 8.467 -- H 3 2 ... TFZ=18.3 PAK=8 LLG=420 TFZ==20.6 LLG=787 TFZ==25.7 PAK=8
1 accepted of 1 solutions
1 packs of 1 accepted solution
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 1 mins 2.18 secs ( 62.18 secs)
Finished: Tue Aug 14 22:54:35 2018
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.7.17 ***
******************************************************************************************
<!--SUMMARY_END-->
-----------------
TRANSLATIONAL NCS
-----------------
tNCS not present
-------------------------------
DATA FOR REFINEMENT AND PHASING
-------------------------------
Outliers with a probability less than 1e-06 will be rejected
Measurements with fewer bits of information than 0.01 will be rejected:
threshold sigma(Eobs^2) for centrics/acentrics is 11.9664 / 8.46225
There were 0 (0.0000%) reflections rejected
No reflections are outliers
<!--SUMMARY_BEGIN-->
Resolution of All Data (Number): 6.42 80.31 (4110)
Resolution of Selected Data (Number): 6.42 80.31 (4110)
<!--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 (3340)
- half number of centrics (770/2)
= -3725
With correction for SigF,
Wilson log(likelihood) = -3732.99
----------
ENSEMBLING
----------
Ensemble Generation Table
-------------------------
Resolution of Ensembles: 6.41564
Ensemble Scat% Radius Model# Rel-B Input-RMS Initial-Delta-VRMS Initial-RMS
1iwg 94.0 47.81 1 87.5 0.700 0.000 0.700
-------
SCORING
-------
There is 1 solution to score
Spreading calculation onto 2 threads.
Scoring solutions
0% 100%
|==| DONE
---------------
TFZ EQUIVALENTS
---------------
Refined TFZ equivalents calculated
1 top TFZ equivalents calculated
1 (Topfiles)
0 with TFZ > 6 (TFZ for Possibly Solved)
SOLUTION #1 OF 1
----------------
TOPFILE
TFZ equivalent calculation #1 of 1
Spreading calculation onto 2 threads.
Generating Statistics
0% 100%
|===============================================================| DONE
Mean Score (Sigma): -629.68 (55.06)
Refined TF/TFZ equivalent = 786.72/ 25.7 (Unrefined TF/TFZ=786.72/ 25.7)
Mean and Sigma after Refinement (for Purge)
-------------------------------------------
Scoring 500 randomly sampled orientations and translations
Spreading calculation onto 2 threads.
Generating Statistics
0% 100%
|==| DONE
Mean Score for Purge before Refinement: -629.68
Mean Score for Purge after Refinement : -629.68
$TABLE : Refinement After Placing Component #1 (1iwg 6.42A) :
$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 $$
1 786.72 786.72 50.27 50.27
$$
---------------
FIND DUPLICATES
---------------
Check for nearly equivalent solutions
Spreading calculation onto 2 threads.
Calculating Duplicates for 1 solutions
0% 100%
|==| DONE
No duplicate solutions found
---------------------
FIND TEMPLATE MATCHES
---------------------
No Template Solution(s) for comparison
<!--SUMMARY_BEGIN-->
-------
RESULTS
-------
Refinement Table (Sorted)
-------------------------
Refinement to full resolution
#out =#out #in =T (Start LLG Rval TFZ) (Refined LLG Rval TFZ==) SpaceGroup Cntrst
Top1 --- 1 786.7 50.3 n/a 786.7 50.3 25.7 H 3 2 n/a
Refinement Table (Variance Ranges)
----------------------------------
Range of delta-VRMS and VRMS given over current solution list (1 solution(s))
Ensemble Model# RMS Delta-VRMS min/max (VRMS min/max)
1iwg 1 0.700 -0.082/-0.082 ( 0.638/ 0.638 )
<!--SUMMARY_END-->
------------
OUTPUT FILES
------------
Calculation of Map Coefficients
-------------------------------
1 top map coefficients calculated
Map coefficient calculated for top solution #1
SOLU SPAC H 3 2
SOLU 6DIM ENSE 1iwg EULER 61.1 0.3 301.3 FRAC 0.01 -0.03 -0.01 BFAC -2.06 #TFZ==25.7
SOLU ENSEMBLE 1iwg VRMS DELTA -0.0818 #RMSD 0.70 #VRMS 0.64
No files output
<!--SUMMARY_BEGIN-->
CPU Time: 0 days 0 hrs 1 mins 6.24 secs ( 66.24 secs)
Finished: Tue Aug 14 22:54:38 2018
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.7.17 ***
******************************************************************************************
$TEXT:MR Result: $$ Baubles Markup $$
** SINGLE solution
** Solution written to SOL file: /Users/liwei/Desktop/Files/PROJECT2_1.sol
** Solution written to PDB file: /Users/liwei/Desktop/Files/PROJECT2_1.1.pdb
** Solution written to MTZ file: /Users/liwei/Desktop/Files/PROJECT2_1.1.mtz
Solution annotation (history):
SOLU SET RFZ=6.9 TFZ=18.3 PAK=8 LLG=420 TFZ==20.6 LLG=787 TFZ==25.7 PAK=8 LLG=787 TFZ==25.7
SOLU SPAC H 3 2
SOLU 6DIM ENSE 1iwg EULER 61.1 0.3 301.3 FRAC 0.01 -0.03 -0.01 BFAC -2.06 #TFZ==25.7
SOLU ENSEMBLE 1iwg VRMS DELTA -0.0818 #RMSD 0.70 #VRMS 0.64
$$
CPU Time: 0 days 0 hrs 1 mins 6.46 secs ( 66.46 secs)
Finished: Tue Aug 14 22:54:38 2018
<!--SUMMARY_END-->
--------------------
EXIT STATUS: SUCCESS
--------------------
<!--SUMMARY_BEGIN-->
CPU Time: 0 days 0 hrs 1 mins 6.47 secs ( 66.47 secs)
Finished: Tue Aug 14 22:54:38 2018
<!--SUMMARY_END-->
</pre>
</html>
#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 14 Aug 2018 22:54:39
#CCP4I TERMINATION OUTPUT_FILES /Users/liwei/Desktop/Files/PROJECT2_1.1.mtz PROJECT2 /Users/liwei/Desktop/Files/PROJECT2_1.1.pdb PROJECT2 /Users/liwei/Desktop/Files/PROJECT2_1.sol PROJECT2
#CCP4I MESSAGE Task completed successfully
