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### PHENIX: Phaser 2.8.3 ###
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User: xbrazzolotto
Run time: Tue Jul 4 12:46:42 2023
Version: 2.8.3
Release Date: Thu Jan 20 22:18:48 2022 (git 7539, 219b54030... )
If you use this software please cite:
"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
PDF
******************************************************************************************
*** Phaser Module: PREPROCESSOR 2.8.3 ***
******************************************************************************************
CELL 154.808 154.808 128.517 90 90 90
ELLG HIRES ON
ENSEMBLE ense_1 PDB "/Users/xbrazzolotto/Desktop/Crystallography/20230701/RGUK1629/model.pdb" ID 1
HKLOUT ON
INFORMATION OFF
KEYWORDS OFF
LABIN I = I SIGI = SIGI
PEAKS ROT SELECT PERCENT CUTOFF 75
PEAKS TRA SELECT PERCENT CUTOFF 75
PURGE ROT PERCENT 75
PURGE TRA PERCENT 75
PURGE RNP PERCENT 75
RESHARPEN PERCENTAGE 100
ROOT "RGUK_20230701_phaser"
SEARCH ENSEMBLE ense_1
SGALT BASE I 4 2
SPACEGROUP I 4 2 2
TITLE Phaser test
TNCS RLIST ADD ON
XYZOUT ON
CPU Time: 0 days 0 hrs 0 mins 0.02 secs ( 0.02 secs)
Finished: Tue Jul 4 12:46:42 2023
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*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** 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 ense_1
** Automatic (best predicted) search order WILL be used
CPU Time: 0 days 0 hrs 0 mins 0.03 secs ( 0.03 secs)
Finished: Tue Jul 4 12:46:42 2023
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*** Phaser Module: CELL CONTENT ANALYSIS 2.8.3 ***
******************************************************************************************
Space-Group Name (Hall Symbol): I 4 2 2 ( I 4 2)
Space-Group Number: 97
Unit Cell: 154.81 154.81 128.52 90.00 90.00 90.00
--------------------
SPACE GROUP ANALYSIS
--------------------
Input Space Group: I 4 2 2
(a) Space groups derived by translation (screw) symmetry
--------------------------------------------------------
Z Space Group Hall Symbol
----
16 I 4 2 2 I 4 2
I 41 2 2 I 4bw 2bw
----
(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
----
2 I 1 * P 1 (-1/2*x+1/2*y+1/2*z,1/2*x-1/2*y+1/2*z,1/2*x+1/2*y-1/2*z)
---
4 C 1 2 1 * C 2y (x+y-1/2*z,-x+y+1/2*z,1/2*z)
I 1 1 2 * C 2y (-x+z,x,y)
C 1 2 1 * C 2y (x-y-1/2*z,x+y-1/2*z,1/2*z)
I 1 2 1 * C 2y (x,y,-x+z)
I 2 1 1 * C 2y (y,-x+z,x)
---
8 I 4 I 4
I 21 21 21 I 2b 2c
F 2 2 2 * F 2 2 (y-z,y+z,x)
I 2 2 2 I 2 2
I 41 I 4bw
---
16 I 41 2 2 I 4bw 2bw
I 4 2 2 I 4 2
----
Composition is of type: PROTEIN
MW to which Matthews applies: 85314
Resolution for Matthews calculation: 2.15
Z MW VM % solvent rel. freq.
1 85314 2.26 45.49 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
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 -
Most probable VM for resolution = 2.2252
Most probable MW of protein in asu for resolution = 86508.4
CPU Time: 0 days 0 hrs 0 mins 0.15 secs ( 0.15 secs)
Finished: Tue Jul 4 12:46:42 2023
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*** Phaser Module: ANISOTROPY CORRECTION 2.8.3 ***
******************************************************************************************
------------------------------
DATA FOR ANISOTROPY CORRECTION
------------------------------
Resolution of All Data (Number): 2.15 48.95 (42463)
Resolution of Selected Data (Number): 2.15 48.95 (42463)
Outlier Rejection
-----------------
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
Outlier Rejection
-----------------
No reflections are outliers
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 4 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-283914.005 -283867.771 46.234
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
1.360 0.0000 -0.0000 1.0000
-0.680 0.0308 0.9995 0.0000
-0.680 0.9995 -0.0308 -0.0000
Anisotropic deltaB (i.e. range of principal components): 2.041
Outlier Rejection
-----------------
No reflections are outliers
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-283867.771 -283867.724 0.047
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
1.374 0.0000 -0.0000 1.0000
-0.687 0.0336 0.9994 0.0000
-0.687 0.9994 -0.0336 -0.0000
Anisotropic deltaB (i.e. range of principal components): 2.061
Outlier Rejection
-----------------
No reflections are outliers
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-283867.724 -283867.716 0.008
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
1.380 0.0000 -0.0000 1.0000
-0.690 1.0000 0.0070 -0.0000
-0.690 -0.0070 1.0000 0.0000
Anisotropic deltaB (i.e. range of principal components): 2.070
Outlier Rejection
-----------------
No reflections are outliers
Refined Anisotropy Parameters
-----------------------------
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
1.380 0.0000 -0.0000 1.0000
-0.690 1.0000 0.0070 -0.0000
-0.690 -0.0070 1.0000 0.0000
Anisotropic deltaB (i.e. range of principal components): 2.070
--------------
ABSOLUTE SCALE
--------------
Scale factor to put input Fs on absolute scale
Wilson Scale: 35.4502
Wilson B-factor: 43.6851
--------------------------------
DATA AFTER ANISOTROPY CORRECTION
--------------------------------
Resolution of All Data (Number): 2.15 48.95 (42463)
Resolution of Selected Data (Number): 2.15 48.95 (42463)
Outlier Rejection
-----------------
No reflections are outliers
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 4 mins 29.50 secs ( 269.50 secs)
Finished: Tue Jul 4 12:51:12 2023
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*** Phaser Module: TRANSLATIONAL NON-CRYSTALLOGRAPHIC SYMMETRY 2.8.3 ***
******************************************************************************************
Unit Cell: 154.81 154.81 128.52 90.00 90.00 90.00
---------------------
MAXIMUM NMOL ANALYSIS
---------------------
Stoichiometry of search components:
"ense_1"
Molecular weight of components: 59248.9
Volume of asymmetric unit: 192499
Packing to solvent content: 20%
Maximum automatic NMOL number: 2
-------------------------------------
DATA FOR TRANSLATIONAL NCS CORRECTION
-------------------------------------
Resolution of All Data (Number): 2.15 48.95 (42463)
Resolution of Selected Data (Number): 2.15 48.95 (42463)
Outlier Rejection
-----------------
No reflections are outliers
Weighted Intensity Moments for Data
-----------------------------------
Inverse variance-weighted 2nd Moment = /^2 == /^2
Untwinned Perfect Twin
2nd Moment Centric: 3.0 2.0
2nd Moment Acentric: 2.0 1.5
Measured
2nd Moment Centric: 2.83
2nd Moment Acentric: 2.17
Resolution for Twin Analysis (85% I/SIGI > 3): 3.17A (HiRes= 2.15A)
---------------------
ANISOTROPY CORRECTION
---------------------
Weighted Intensity Moments after Anisotropy Correction
------------------------------------------------------
Inverse variance-weighted 2nd Moment = /^2 == /^2
Untwinned Perfect Twin
2nd Moment Centric: 3.0 2.0
2nd Moment Acentric: 2.0 1.5
Measured
2nd Moment Centric: 2.84
2nd Moment Acentric: 2.17
Resolution for Twin Analysis (85% I/SIGI > 3): 3.17A (HiRes= 2.15A)
-----------------
TRANSLATIONAL NCS
-----------------
tNCS vector not set
Space Group (without translational symmetry):I 4 2 2
Patterson Symmetry: I 4/m m m
Resolution of All Data (Number): 2.15 48.95 (42463)
Resolution of Patterson (Number): 5.00 10.00 (3095)
Raw Patterson Peaks Table
-------------------------
Sorted by Height
Height Vector
100.0%: FRAC +0.0000 +0.0000 +0.0000 (ORTH 0.0 0.0 0.0)
Patterson Top (All) = 5.96%
There were 334 peaks
Patterson Top (Non-origin) = 3.82%
Patterson Origin Vector Distance = 15
There were 328 non-origin peaks
Patterson Top (Cutoff) = 0.00%
Patterson cutoff = 20%
There were 0 non-origin peaks over cutoff
Patterson Top (Large Cell) = 0.00%
Unit Cell dimension was not smaller than origin Patterson vector distance
There were 0 non-origin and large cell peaks over cutoff
Patterson Top (Analysis) = 0.00%
Peaks within minimum Patterson vector distance of one another were deleted
There were 0 widely separated non-origin peaks over cutoff
There were no interesting non-origin Patterson peaks
No tNCS found in Patterson
--------
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 3.00 2.00
Theoretical for perfect twin 2.00 1.50
Initial (data as input) 2.83 2.17+/-0.041 1 1
After Anisotropy Correction 2.84 2.17+/-0.041 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): 3.17A (HiRes= 2.15A)
---------------------------------------
DATA AFTER TRANSLATIONAL NCS CORRECTION
---------------------------------------
Resolution of All Data (Number): 2.15 48.95 (42463)
Resolution of Selected Data (Number): 2.15 48.95 (42463)
Outlier Rejection
-----------------
No reflections are outliers
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 7 mins 46.93 secs ( 466.93 secs)
Finished: Tue Jul 4 12:54:29 2023
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*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** 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 7 mins 46.94 secs ( 466.94 secs)
Finished: Tue Jul 4 12:54:29 2023
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*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
Composition Table
-----------------
Total Scattering = 278189
Search occupancy factor = 1 (default)
Ensemble Frac.Scat. (Search Frac.Scat.)
ense_1 66.42% 66.42%
** Composition not increased
CPU Time: 0 days 0 hrs 7 mins 46.94 secs ( 466.94 secs)
Finished: Tue Jul 4 12:54:29 2023
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*** Phaser Module: EXPERIMENTAL ERROR CORRECTION PREPARATION 2.8.3 ***
******************************************************************************************
-----------------
TRANSLATIONAL NCS
-----------------
tNCS not present
-----------------------------
EXPERIMENTAL ERROR CORRECTION
-----------------------------
Calculate Luzzati D factors accounting for observational error...
Data have been provided as raw intensities
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 9 mins 37.31 secs ( 577.31 secs)
Finished: Tue Jul 4 12:56:19 2023
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*** Phaser Module: EXPECTED LLG OF ENSEMBLES 2.8.3 ***
******************************************************************************************
-----------------
TRANSLATIONAL NCS
-----------------
tNCS not present
Resolution of Data (Selected): 2.150 (2.15003)
Number of Reflections (Selected): 42463 (42463)
eLLG Target: 225
----------
ENSEMBLING
----------
Ensemble: ense_1
----------------
PDB file # 1: model.pdb
This file contains 1 model
The input RmsD of model #1 with respect to the real structure is 0.506
Guide to eLLG values
---------------------
eLLG Top solution correct?
<25 -no
25-36 -unlikely
36-49 -possibly
49-64 -probably
>64 -yes
-----------------
POLY-ALANINE ELLG
-----------------
Resolution = 2.15003
Default RMSD = 0.1 0.2 0.4 0.8 1.6 3.2
Minimum solvent = 20%
Maximum number of polyalanine residues = 984 (-full-)
Alanine residues for eLLG target = 139
Table of Alanine Residues for eLLG Target
-----------------------------------------
---RMSD---
eLLG-target | 0.10 0.20 0.40 0.80 1.60 3.20
225 | 139 146 175 320 -full--full-
196 | 130 136 164 299 -full--full-
169 | 120 126 152 278 936 -full-
144 | 111 117 140 256 864 -full-
121 | 102 107 129 235 792 -full-
100 | 92 97 117 213 720 -full-
81 | 83 87 105 192 648 -full-
64 | 74 78 93 171 576 -full-
49 | 65 68 82 149 504 -full-
36 | 55 58 70 128 432 -full-
25 | 46 48 58 106 360 -full-
16 | 37 39 46 85 288 -full-
9 | 27 29 35 64 216 -full-
4 | 18 19 23 42 144 931
1 | 9 9 11 21 72 465
--------------
MONOMERIC ELLG
--------------
Expected LLG (eLLG)
-------------------
eLLG: eLLG of ensemble alone
eLLG RMSD frac-scat Ensemble
3690.3 0.506 0.66421 ense_1
Resolution for eLLG target
--------------------------
eLLG-reso: Resolution to achieve target eLLG (225)
eLLG-reso Ensemble
5.915 ense_1
Resolution for eLLG target: data collection
-------------------------------------------
eLLG-reso: Resolution to achieve target eLLG (225) with perfect data
eLLG-reso Ensemble
5.918 ense_1
eLLG indicates that placement of a single copy of ensemble "ense_1" should be easy
Expected LLG (eLLG): Chains
---------------------------
eLLG: eLLG of chain alone
eLLG RMSD frac-scat chain Ensemble
3690.3 0.506 0.66421 " A" ense_1
Resolution for eLLG target: Chains
----------------------------------
eLLG-reso: Resolution to achieve target eLLG (225)
eLLG-reso chain Ensemble
5.915 " A" ense_1
--------------------
HOMO-OLIGOMERIC ELLG
--------------------
Number of copies for eLLG target
--------------------------------
eLLG-target RMSD frac-scat-known frac-scat num-copies Ensemble
225 0.506 0.00000 0.66421 1 ense_1
CPU Time: 0 days 0 hrs 11 mins 18.33 secs ( 678.33 secs)
Finished: Tue Jul 4 12:58:00 2023
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*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** Search Order (next search *) (placed +):
** #1 ense_1 *
CPU Time: 0 days 0 hrs 11 mins 18.33 secs ( 678.33 secs)
Finished: Tue Jul 4 12:58:00 2023
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT ROTATION FUNCTION 2.8.3 ***
******************************************************************************************
-----------------
TRANSLATIONAL NCS
-----------------
tNCS not present
--------------------------
DATA FOR ROTATION FUNCTION
--------------------------
High resolution limit unaltered by RMS of ensemble
High resolution limit lowered by expected LLG = 5.92
Outlier Rejection
-----------------
No reflections are outliers
Resolution of All Data (Number): 2.15 48.95 (42463)
Resolution of Selected Data (Number): 5.92 48.95 (2204)
-------------------
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 (1703)
- half number of centrics (501/2)
= -1953
With correction for SigF,
Wilson log(likelihood) = -1960.48
----------
ENSEMBLING
----------
Ensemble Generation: ense_1
---------------------------
Ensemble configured for structure factor interpolation
Ensemble configured to resolution 5.92
Electron Density Calculation
0% 100%
|=======| DONE
Ensemble Generation
-------------------
Resolution of Ensembles: 5.9155
Scat% Radius Model# Rel-B RMS DRMS VRMS Ensemble
66.4 33.1 1 1.7 0.506 0.000 0.506 ense_1
--------------
R-FACTOR CHECK
--------------
R-factor at 5.92A calculated
Space Group R-factor
I 4 2 2 38.37
Minimum R-factor of ensemble at origin in original orientation = 38.37
SOLU SET RF*0
SOLU SPAC I 4 2 2
SOLU TRIAL ENSEMBLE ense_1 EULER 0.000 0.000 0.000 RF 0.0 RFZ 0.00
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 12 mins 59.61 secs ( 779.61 secs)
Finished: Tue Jul 4 12:59:42 2023
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** R-factor = 38.37
** R-factor for PDB file at origin in original orientation is less than 40.00
** Molecular replacement is not necessary and is aborted
CPU Time: 0 days 0 hrs 12 mins 59.62 secs ( 779.62 secs)
Finished: Tue Jul 4 12:59:42 2023
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** Solutions will be refined to highest resolution
** Resolution for refinement: 2.15003
** Protocol for MR refinement is DEFAULT
** VRMS (variances) of ensemble(s) WILL be refined
CPU Time: 0 days 0 hrs 13 mins 50.13 secs ( 830.13 secs)
Finished: Tue Jul 4 13:00:32 2023
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.8.3 ***
******************************************************************************************
-----------------
TRANSLATIONAL NCS
-----------------
tNCS not present
-------------------------------
DATA FOR REFINEMENT AND PHASING
-------------------------------
Outlier Rejection
-----------------
No reflections are outliers
Resolution of All Data (Number): 2.15 48.95 (42463)
Resolution of Selected Data (Number): 2.15 48.95 (42463)
-------------------
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 (38608)
- half number of centrics (3855/2)
= -40535
With correction for SigF,
Wilson log(likelihood) = -39905.3
----------
ENSEMBLING
----------
Ensemble Generation: ense_1
---------------------------
Ensemble configured for structure factor interpolation
Ensemble configured to resolution 2.15
Electron Density Calculation
0% 100%
|=======| DONE
Ensemble Generation
-------------------
Resolution of Ensembles: 2.15003
Scat% Radius Model# Rel-B RMS DRMS VRMS Ensemble
66.4 33.1 1 11.7 0.506 0.000 0.506 ense_1
----------
REFINEMENT
----------
Protocol cycle #1 of 1
Refinement protocol for this macrocycle:
ROTATION: REFINE
TRANSLATION: REFINE
BFACTOR: REFINE
MODEL VRMS: REFINE
CELL SCALE: FIX
OCCUPANCY FACTOR: FIX
LAST ONLY: FALSE
ROTATION RESTRAINT: OFF
TRANSLATION RESTRAINT: OFF
There is 1 solution to refine
Refining solutions
0% 100%
|==| DONE
REFINING SET #1 OF 1
--------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE ense_1 EULER 0.0 0.0 0.0 FRAC 0.00 0.00 0.00 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 12 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
9672.839 15498.953 5826.114
Final Parameters:
SOLU SET
SOLU 6DIM ENSE ense_1 EULER 182.3 0.2 177.8 FRAC 0.00 -0.00 -0.00 BFAC -2.86
SOLU ENSEMBLE ense_1 VRMS DELTA -0.2444 #RMSD 0.51 #VRMS 0.11
Mean and Sigma after Refinement (for Purge)
-------------------------------------------
Scoring 500 randomly sampled orientations and translations
Generating Statistics
0% 100%
|==| DONE
No Mean Score for Purge before Refinement
Mean Score for Purge after Refinement : -23202.15
---------------
FIND DUPLICATES
---------------
Check for nearly equivalent solutions
Calculating Duplicates for 1 solutions
0% 100%
|==| DONE
No duplicate solutions found
---------------------
FIND TEMPLATE MATCHES
---------------------
No Template Solution(s) for comparison
---------------
PURGE SELECTION
---------------
Purge solutions according to highest LLG from Refinement
--------------------------------------------------------
Top LLG (all) = 15496.6
Top LLG (packs) = 15496.6
Mean LLG = -23202.1
Percent used for purge = 75%
Cutoff for acceptance = 5821.9
Number used for purge = 50
Cutoff for acceptance = 15496.6
Overall cutoff for acceptance (excluding high TFZ) = 15496.6
Number of solutions stored before purge = 1
Number of solutions stored (deleted) after purge = 1 (0)
---------------
TFZ EQUIVALENTS
---------------
Refined TFZ equivalents calculated
1 top TFZ equivalents calculated
SOLUTION #1 OF 1
----------------
TFZ equivalent calculation #1 of 1
TOPFILE
Generating Statistics
0% 100%
|========================================================================| DONE
Mean Score (Sigma): -23202.15 (342.41)
Refined TF/TFZ equivalent = 15496.55/113.0 (Unrefined TF=9672.92)
-------
RESULTS
-------
Refinement Table (Sorted)
-------------------------
Refinement to full resolution
#out =#out #in =T (Start LLG Rval TFZ) (Refined LLG Rval TFZ==) SpaceGroup Cntrst
Top1 --- 1 9672.9 32.2 n/a 15496.6 31.7 113.0 I 4 2 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)
ense_1 1 0.506 -0.244/-0.244 ( 0.108/ 0.108 )
------------
OUTPUT FILES
------------
Calculation of Map Coefficients
-------------------------------
1 top map coefficients calculated
Map coefficient calculated for top solution #1
SOLU SPAC I 4 2 2
SOLU 6DIM ENSE ense_1 EULER 182.3 0.2 177.8 FRAC 0.00 -0.00 -0.00 BFAC -2.86 #TFZ==113.0
SOLU ENSEMBLE ense_1 VRMS DELTA -0.2444 #RMSD 0.51 #VRMS 0.11
No files output
CPU Time: 0 days 0 hrs 15 mins 54.95 secs ( 954.95 secs)
Finished: Tue Jul 4 13:02:37 2023
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** Refinement may have introduced clashes
** Packing will be checked
CPU Time: 0 days 0 hrs 15 mins 54.95 secs ( 954.95 secs)
Finished: Tue Jul 4 13:02:37 2023
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT PACKING ANALYSIS 2.8.3 ***
******************************************************************************************
---------
ENSEMBLES
---------
Trace Generation: ense_1
------------------------
This trace is from coordinates
Trace Generation
----------------
Ensemble Trace-type Length Sampling Close-contact
ense_1 C-alpha 532 3.00 2.00
-----------------
ENSEMBLE SYMMETRY
-----------------
Ensemble "ense_1" Point Group: 1
Clash background has been packed at 10.00%
----------------
PACKING FUNCTION
----------------
There is 1 solution to pack
Packing analysis
0% 100%
|==| DONE
Packing Table
-------------
Solutions accepted if pairwise clashes less than 10 % of trace atoms
#in #out Clash-% Symm SpaceGroup Annotation
1 Top1 0 -- I 4 2 2 RF*0 TF*0 LLG=15497 TFZ==113.0 PAK=0
1 accepted of 1 solutions
1 packs of 1 accepted solution
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 15 mins 55.00 secs ( 955.00 secs)
Finished: Tue Jul 4 13:02:37 2023
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.8.3 ***
******************************************************************************************
-----------------
TRANSLATIONAL NCS
-----------------
tNCS not present
-------------------------------
DATA FOR REFINEMENT AND PHASING
-------------------------------
Outlier Rejection
-----------------
No reflections are outliers
Resolution of All Data (Number): 2.15 48.95 (42463)
Resolution of Selected Data (Number): 2.15 48.95 (42463)
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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 (38608)
- half number of centrics (3855/2)
= -40535
With correction for SigF,
Wilson log(likelihood) = -39905.3
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ENSEMBLING
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Ensemble Generation: ense_1
---------------------------
Ensemble configured for structure factor interpolation
Ensemble configured to resolution 2.15
Electron Density Calculation
0% 100%
|=======| DONE
Ensemble Generation
-------------------
Resolution of Ensembles: 2.15003
Scat% Radius Model# Rel-B RMS DRMS VRMS Ensemble
66.4 33.1 1 11.7 0.506 0.000 0.506 ense_1
Trace Generation
----------------
Ensemble Trace-type Length Sampling Close-contact
ense_1 C-alpha 532 3.00 2.00
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REFINEMENT
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Protocol cycle #1 of 1
Refinement protocol for this macrocycle:
ROTATION: REFINE
TRANSLATION: REFINE
BFACTOR: REFINE
MODEL VRMS: FIX
CELL SCALE: FIX
OCCUPANCY FACTOR: FIX
LAST ONLY: FALSE
ROTATION RESTRAINT: OFF
TRANSLATION RESTRAINT: OFF
There is 1 solution to refine
Refining solutions
0% 100%
|==| DONE
REFINING SET #1 OF 1
--------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE ense_1 EULER 182.3 0.2 177.8 FRAC 0.00 -0.00 -0.00 BFAC -2.86 #TFZ==113.0
SOLU ENSEMBLE ense_1 VRMS DELTA -0.2444 #RMSD 0.51 #VRMS 0.11
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
15498.953 15498.953 0.000
Final Parameters:
SOLU SET
SOLU 6DIM ENSE ense_1 EULER 182.3 0.2 177.8 FRAC 0.00 -0.00 -0.00 BFAC -2.86 #TFZ==113.0
SOLU ENSEMBLE ense_1 VRMS DELTA -0.2444 #RMSD 0.51 #VRMS 0.11
Mean and Sigma after Refinement (for Purge)
-------------------------------------------
Scoring 500 randomly sampled orientations and translations
Generating Statistics
0% 100%
|==| DONE
Mean Score for Purge before Refinement: -23202.15
Mean Score for Purge after Refinement : -23202.11
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FIND DUPLICATES
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Check for nearly equivalent solutions
Calculating Duplicates for 1 solutions
0% 100%
|==| DONE
No duplicate solutions found
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FIND TEMPLATE MATCHES
---------------------
No Template Solution(s) for comparison
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PURGE SELECTION
---------------
Purge solutions according to highest LLG from Refinement
--------------------------------------------------------
Top LLG (all) = 15496.6
Top LLG (packs) = 15496.6
Mean LLG = -23202.1
Percent used for purge = 75%
Cutoff for acceptance = 5821.9
Number used for purge = 50
Cutoff for acceptance = 15496.6
Overall cutoff for acceptance (excluding high TFZ) = 15496.6
Number of solutions stored before purge = 1
Number of solutions stored (deleted) after purge = 1 (0)
---------------
TFZ EQUIVALENTS
---------------
Refined TFZ equivalents calculated
1 top TFZ equivalents calculated
SOLUTION #1 OF 1
----------------
TFZ equivalent calculation #1 of 1
TOPFILE
Generating Statistics
0% 100%
|========================================================================| DONE
Mean Score (Sigma): -23202.11 (342.40)
Refined TF/TFZ equivalent = 15496.62/113.0 (Unrefined TF/TFZ=15496.55/113.0)
-------
RESULTS
-------
Refinement Table (Sorted)
-------------------------
Refinement to full resolution
#out =#out #in =T (Start LLG Rval TFZ) (Refined LLG Rval TFZ==) SpaceGroup Cntrst
Top1 --- 1 15496.6 31.7 n/a 15496.6 31.7 113.0 I 4 2 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)
ense_1 1 0.506 -0.244/-0.244 ( 0.108/ 0.108 )
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OUTPUT FILES
------------
Calculation of Map Coefficients
-------------------------------
1 top map coefficients calculated
Map coefficient calculated for top solution #1
SOLU SPAC I 4 2 2
SOLU 6DIM ENSE ense_1 EULER 182.3 0.2 177.8 FRAC 0.00 -0.00 -0.00 BFAC -2.86 #TFZ==113.0
SOLU ENSEMBLE ense_1 VRMS DELTA -0.2444 #RMSD 0.51 #VRMS 0.11
No files output
CPU Time: 0 days 0 hrs 17 mins 57.44 secs ( 1077.44 secs)
Finished: Tue Jul 4 13:04:40 2023
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** SINGLE solution
** Solution written to PDB file: RGUK_20230701_phaser.1.pdb
** Solution written to MTZ file: RGUK_20230701_phaser.1.mtz
Solution annotation (history):
SOLU SET RF*0 TF*0 LLG=15497 TFZ==113.0 PAK=0 LLG=15497 TFZ==113.0
SOLU SPAC I 4 2 2
SOLU 6DIM ENSE ense_1 EULER 182.3 0.2 177.8 FRAC 0.00 -0.00 -0.00 BFAC -2.86 #TFZ==113.0
SOLU ENSEMBLE ense_1 VRMS DELTA -0.2444 #RMSD 0.51 #VRMS 0.11
CPU Time: 0 days 0 hrs 17 mins 57.47 secs ( 1077.47 secs)
Finished: Tue Jul 4 13:04:40 2023
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 17 mins 57.47 secs ( 1077.47 secs)
Finished: Tue Jul 4 13:04:40 2023