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### PHENIX: Phaser 2.8.3 ###
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User: xbrazzolotto
Run time: Tue Jul 4 12:44:34 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" RMS 1
HKLOUT ON
INFORMATION OFF
KEYWORDS OFF
LABIN F = F SIGF = SIGF
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
SEARCH ENSEMBLE ense_1
SGALT BASE I 4 2
SPACEGROUP I 4 2 2
TNCS RLIST ADD ON
XYZOUT ON
CPU Time: 0 days 0 hrs 0 mins 0.02 secs ( 0.02 secs)
Finished: Tue Jul 4 12:44:34 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 0.02 secs ( 0.02 secs)
Finished: Tue Jul 4 12:44:34 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 0.14 secs ( 0.14 secs)
Finished: Tue Jul 4 12:44:34 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 5 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-468678.629 -468623.554 55.075
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
1.078 0.0000 -0.0000 1.0000
-0.539 1.0000 0.0026 -0.0000
-0.539 -0.0026 1.0000 0.0000
Anisotropic deltaB (i.e. range of principal components): 1.617
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
-468623.554 -468623.344 0.210
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
1.099 0.0000 -0.0000 1.0000
-0.549 1.0000 0.0023 -0.0000
-0.549 -0.0023 1.0000 0.0000
Anisotropic deltaB (i.e. range of principal components): 1.648
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
-468623.344 -468623.259 0.085
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
1.113 0.0000 -0.0000 1.0000
-0.556 1.0000 0.0023 -0.0000
-0.556 -0.0023 1.0000 0.0000
Anisotropic deltaB (i.e. range of principal components): 1.669
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)
1.113 0.0000 -0.0000 1.0000
-0.556 1.0000 0.0023 -0.0000
-0.556 -0.0023 1.0000 0.0000
Anisotropic deltaB (i.e. range of principal components): 1.669
--------------
ABSOLUTE SCALE
--------------
Scale factor to put input Fs on absolute scale
Wilson Scale: 3.45752
Wilson B-factor: 44.8966
--------------------------------
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 0 mins 1.90 secs ( 1.90 secs)
Finished: Tue Jul 4 12:44:35 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: 2.92
2nd Moment Acentric: 2.12
Resolution for Twin Analysis (85% I/SIGI > 3): 3.39A (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: 2.92
2nd Moment Acentric: 2.12
Resolution for Twin Analysis (85% I/SIGI > 3): 3.39A (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) = 5.95%
There were 332 peaks
Patterson Top (Non-origin) = 3.80%
Patterson Origin Vector Distance = 15
There were 326 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) 2.92 2.12+/-0.046 1 1
After Anisotropy Correction 2.92 2.12+/-0.046 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): 3.39A (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 0 mins 2.05 secs ( 2.05 secs)
Finished: Tue Jul 4 12:44:36 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 0 mins 2.05 secs ( 2.05 secs)
Finished: Tue Jul 4 12:44:36 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 0 mins 2.05 secs ( 2.05 secs)
Finished: Tue Jul 4 12:44:36 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 French-Wilson amplitudes
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 0 mins 2.11 secs ( 2.11 secs)
Finished: Tue Jul 4 12:44:36 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 1.000
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 = 137
Table of Alanine Residues for eLLG Target
-----------------------------------------
---RMSD---
eLLG-target | 0.10 0.20 0.40 0.80 1.60 3.20
225 | 137 144 174 320 -full--full-
196 | 128 134 162 298 -full--full-
169 | 119 125 151 277 936 -full-
144 | 110 115 139 256 864 -full-
121 | 100 105 127 234 792 -full-
100 | 91 96 116 213 720 -full-
81 | 82 86 104 192 648 -full-
64 | 73 77 92 170 576 -full-
49 | 64 67 81 149 504 -full-
36 | 55 57 69 128 432 -full-
25 | 45 48 58 106 360 -full-
16 | 36 38 46 85 288 -full-
9 | 27 28 34 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
753.1 1.000 0.66421 ense_1
Resolution for eLLG target
--------------------------
eLLG-reso: Resolution to achieve target eLLG (225)
eLLG-reso Ensemble
5.278 ense_1
Resolution for eLLG target: data collection
-------------------------------------------
eLLG-reso: Resolution to achieve target eLLG (225) with perfect data
eLLG-reso Ensemble
5.285 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
753.1 1.000 0.66421 " A" ense_1
Resolution for eLLG target: Chains
----------------------------------
eLLG-reso: Resolution to achieve target eLLG (225)
eLLG-reso chain Ensemble
5.278 " A" ense_1
--------------------
HOMO-OLIGOMERIC ELLG
--------------------
Number of copies for eLLG target
--------------------------------
eLLG-target RMSD frac-scat-known frac-scat num-copies Ensemble
225 1.000 0.00000 0.66421 1 ense_1
CPU Time: 0 days 0 hrs 0 mins 2.25 secs ( 2.25 secs)
Finished: Tue Jul 4 12:44:36 2023
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** Search Order (next search *) (placed +):
** #1 ense_1 *
CPU Time: 0 days 0 hrs 0 mins 2.25 secs ( 2.25 secs)
Finished: Tue Jul 4 12:44:36 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 = 5.28
Outlier Rejection
-----------------
No reflections are outliers
Resolution of All Data (Number): 2.15 48.95 (42463)
Resolution of Selected Data (Number): 5.28 48.95 (3055)
-------------------
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 (2425)
- half number of centrics (630/2)
= -2740
With correction for SigF,
Wilson log(likelihood) = -2739.53
----------
ENSEMBLING
----------
Ensemble Generation: ense_1
---------------------------
Ensemble configured for structure factor interpolation
Ensemble configured to resolution 5.28
Electron Density Calculation
0% 100%
|=======| DONE
Ensemble Generation
-------------------
Resolution of Ensembles: 5.27819
Scat% Radius Model# Rel-B RMS DRMS VRMS Ensemble
66.4 33.1 1 -12.2 1.000 0.000 1.000 ense_1
--------------
R-FACTOR CHECK
--------------
R-factor at 5.28A calculated
Space Group R-factor
I 4 2 2 36.92
Minimum R-factor of ensemble at origin in original orientation = 36.92
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 0 mins 2.61 secs ( 2.61 secs)
Finished: Tue Jul 4 12:44:36 2023
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** R-factor = 36.92
** 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 0 mins 2.61 secs ( 2.61 secs)
Finished: Tue Jul 4 12:44:36 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 0 mins 2.63 secs ( 2.63 secs)
Finished: Tue Jul 4 12:44:36 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) = -40917.9
----------
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 12.8 1.000 0.000 1.000 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 15 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
3862.374 15141.443 11279.069
Final Parameters:
SOLU SET
SOLU 6DIM ENSE ense_1 EULER 182.1 0.2 178.0 FRAC 0.00 -0.00 -0.00 BFAC -3.77
SOLU ENSEMBLE ense_1 VRMS DELTA -0.9556 #RMSD 1.00 #VRMS 0.21
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 : -21882.35
---------------
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) = 15139
Top LLG (packs) = 15139
Mean LLG = -21882.4
Percent used for purge = 75%
Cutoff for acceptance = 5883.7
Number used for purge = 50
Cutoff for acceptance = 15139.0
Overall cutoff for acceptance (excluding high TFZ) = 15139.0
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): -21882.35 (341.70)
Refined TF/TFZ equivalent = 15139.01/108.3 (Unrefined TF=3862.33)
-------
RESULTS
-------
Refinement Table (Sorted)
-------------------------
Refinement to full resolution
#out =#out #in =T (Start LLG Rval TFZ) (Refined LLG Rval TFZ==) SpaceGroup Cntrst
Top1 --- 1 3862.3 29.9 n/a 15139.0 29.5 108.3 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 1.000 -0.956/-0.956 ( 0.211/ 0.211 )
------------
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 182.1 0.2 178.0 FRAC 0.00 -0.00 -0.00 BFAC -3.77 #TFZ==108.3
SOLU ENSEMBLE ense_1 VRMS DELTA -0.9556 #RMSD 1.00 #VRMS 0.21
No files output
CPU Time: 0 days 0 hrs 0 mins 26.86 secs ( 26.86 secs)
Finished: Tue Jul 4 12:45:00 2023
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** Refinement may have introduced clashes
** Packing will be checked
CPU Time: 0 days 0 hrs 0 mins 26.86 secs ( 26.86 secs)
Finished: Tue Jul 4 12:45:00 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=15139 TFZ==108.3 PAK=0
1 accepted of 1 solutions
1 packs of 1 accepted solution
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 0 mins 26.90 secs ( 26.90 secs)
Finished: Tue Jul 4 12:45:00 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) = -40917.9
----------
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 12.8 1.000 0.000 1.000 ense_1
Trace Generation
----------------
Ensemble Trace-type Length Sampling Close-contact
ense_1 C-alpha 532 3.00 2.00
----------
REFINEMENT
----------
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 182.1 0.2 178.0 FRAC 0.00 -0.00 -0.00 BFAC -3.77 #TFZ==108.3
SOLU ENSEMBLE ense_1 VRMS DELTA -0.9556 #RMSD 1.00 #VRMS 0.21
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
15141.443 15141.443 0.000
Final Parameters:
SOLU SET
SOLU 6DIM ENSE ense_1 EULER 182.1 0.2 178.0 FRAC 0.00 -0.00 -0.00 BFAC -3.77 #TFZ==108.3
SOLU ENSEMBLE ense_1 VRMS DELTA -0.9556 #RMSD 1.00 #VRMS 0.21
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: -21882.35
Mean Score for Purge after Refinement : -21882.36
---------------
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) = 15139
Top LLG (packs) = 15139
Mean LLG = -21882.4
Percent used for purge = 75%
Cutoff for acceptance = 5883.7
Number used for purge = 50
Cutoff for acceptance = 15139.0
Overall cutoff for acceptance (excluding high TFZ) = 15139.0
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): -21882.36 (341.70)
Refined TF/TFZ equivalent = 15139.02/108.3 (Unrefined TF/TFZ=15139.01/108.3)
-------
RESULTS
-------
Refinement Table (Sorted)
-------------------------
Refinement to full resolution
#out =#out #in =T (Start LLG Rval TFZ) (Refined LLG Rval TFZ==) SpaceGroup Cntrst
Top1 --- 1 15139.0 29.5 n/a 15139.0 29.5 108.3 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 1.000 -0.956/-0.956 ( 0.211/ 0.211 )
------------
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 182.1 0.2 178.0 FRAC 0.00 -0.00 -0.00 BFAC -3.77 #TFZ==108.3
SOLU ENSEMBLE ense_1 VRMS DELTA -0.9556 #RMSD 1.00 #VRMS 0.21
No files output
CPU Time: 0 days 0 hrs 0 mins 47.96 secs ( 47.96 secs)
Finished: Tue Jul 4 12:45:21 2023
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** SINGLE solution
** Solution written to PDB file: PHASER.1.pdb
** Solution written to MTZ file: PHASER.1.mtz
Solution annotation (history):
SOLU SET RF*0 TF*0 LLG=15139 TFZ==108.3 PAK=0 LLG=15139 TFZ==108.3
SOLU SPAC I 4 2 2
SOLU 6DIM ENSE ense_1 EULER 182.1 0.2 178.0 FRAC 0.00 -0.00 -0.00 BFAC -3.77 #TFZ==108.3
SOLU ENSEMBLE ense_1 VRMS DELTA -0.9556 #RMSD 1.00 #VRMS 0.21
CPU Time: 0 days 0 hrs 0 mins 47.98 secs ( 47.98 secs)
Finished: Tue Jul 4 12:45:22 2023
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 0 mins 47.98 secs ( 47.98 secs)
Finished: Tue Jul 4 12:45:22 2023